diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 0000000000..beba468ea0 --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,112 @@ +# Contributing to LAMMPS via GitHub + +Thank your for considering to contribute to the LAMMPS software project. + +The following is a set of guidelines as well as explanations of policies and workflows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project. + +Thus please also have a look at: +* [The Section on submitting new features for inclusion in LAMMPS of the Manual](http://lammps.sandia.gov/doc/Section_modify.html#mod-15) +* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html) + +## Table of Contents + +[I don't want to read this whole thing, I just have a question!](#i-dont-want-to-read-this-whole-thing-i-just-have-a-question) + +[How Can I Contribute?](#how-can-i-contribute) +* [Discussing How To Use LAMMPS](#discussing-how-to-use-lammps) +* [Reporting Bugs](#reporting-bugs) +* [Suggesting Enhancements](#suggesting-enhancements) +* [Contributing Code](#contributing-code) + +[GitHub Workflows](#github-workflows) +* [Issues](#issues) +* [Pull Requests](#pull-requests) + +__ + +## I don't want to read this whole thing I just have a question! + +> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](http://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. + +## How Can I Contribute? + +There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code +to one of the [LAMMPS core developers](http://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers. + +### Discussing How To Use LAMMPS + +The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours. +You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](http://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response. + +Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better. + +If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive. + +### Reporting Bugs + +While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](http://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version. + +When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions. +You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly). + +To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative and in decreasing preference - either send an e-mail to the lammps-users mailing list, the original authors of the feature that you suspect to be affected, or one or more of the core LAMMPS developers. + +### Suggesting Enhancements + +The LAMMPS developers welcome suggestions for enhancements or new features. These should be submitted using the [GitHub Issue Tracker](https://github.com/lammps/lammps/issues) of the LAMMPS project. This is particularly recommended, when you plan to implement the feature or enhancement yourself, as this allows to coordinate in case there are other similar or conflicting ongoing developments. +The LAMMPS developers will review your submission and consider implementing it. Whether this will actually happen depends on many factors: how difficult it would be, how much effort it would take, how many users would benefit from it, how well the individual developer would understand the underlying physics of the feature, and whether this is a feature that would fit into a software like LAMMPS, or would be better implemented as a separate tool. Because of these factors, it matters how well the suggested enhancement is formulated and the overall benefit is argued convincingly. + +To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations against submitting an issue there, you can - as an alternative - send an e-mail to the lammps-users mailing list. + +### Contributing Code + +We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others. + +How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) + for instructions on how to submit your changes or new files through a GitHub pull request + +Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list. + +* All source files you provide must compile with the most current version of LAMMPS with multiple configurations. In particular you need to test compiling LAMMPS from scratch with `-DLAMMPS_BIGBIG` set in addition to the default `-DLAMMPS_SMALLBIG` setting. Your code will need to work correctly in serial and in parallel using MPI. +* For consistency with the rest of LAMMPS and especially, if you want your contribution(s) to be added to main LAMMPS code or one of its standard packages, it needs to be written in a style compatible with other LAMMPS source files. This means: 2-character indentation per level, no tabs, no lines over 80 characters. I/O is done via the C-style stdio library, class header files should not import any system headers outside , STL containers should be avoided in headers, and forward declarations used where possible or needed. All added code should be placed into the LAMMPS_NS namespace or a sub-namespace; global or static variables should be avoided, as they conflict with the modular nature of LAMMPS and the C++ class structure. Header files must not import namespaces with using. This all is so the developers can more easily understand, integrate, and maintain your contribution and reduce conflicts with other parts of LAMMPS. This basically means that the code accesses data structures, performs its operations, and is formatted similar to other LAMMPS source files, including the use of the error class for error and warning messages. +* If you want your contribution to be added as a user-contributed feature, and it is a single file (actually a `.cpp` and `.h` file) it can be rapidly added to the USER-MISC directory. Include the one-line entry to add to the USER-MISC/README file in that directory, along with the 2 source files. You can do this multiple times if you wish to contribute several individual features. +* If you want your contribution to be added as a user-contribution and it is several related features, it is probably best to make it a user package directory with a name like USER-FOO. In addition to your new files, the directory should contain a README text file. The README should contain your name and contact information and a brief description of what your new package does. If your files depend on other LAMMPS style files also being installed (e.g. because your file is a derived class from the other LAMMPS class), then an Install.sh file is also needed to check for those dependencies. See other README and Install.sh files in other USER directories as examples. Send us a tarball of this USER-FOO directory. +* Your new source files need to have the LAMMPS copyright, GPL notice, and your name and email address at the top, like other user-contributed LAMMPS source files. They need to create a class that is inside the LAMMPS namespace. If the file is for one of the USER packages, including USER-MISC, then we are not as picky about the coding style (see above). I.e. the files do not need to be in the same stylistic format and syntax as other LAMMPS files, though that would be nice for developers as well as users who try to read your code. +* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code. +* For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind +* If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide. + +Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature. + +If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory. + +Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details. + +With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event). + +To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request. + +If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms. + +## GitHub Workflows + +This section briefly summarizes the steps that will happen **after** you have submitted either an issue or a pull request on the LAMMPS GitHub project page. + +### Issues + +After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action. + +For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below. + +For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed. + +### Pull Requests + +For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. +Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub. +Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. +You may also receive comments and suggestions on the overall submission or specific details. If permitted, additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes. +The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer. +If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork. +Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone. + diff --git a/.github/ISSUE_TEMPLATE.md b/.github/ISSUE_TEMPLATE.md new file mode 100644 index 0000000000..53a17a1476 --- /dev/null +++ b/.github/ISSUE_TEMPLATE.md @@ -0,0 +1,31 @@ +## Summary + +_Please provide a brief description of the issue_ + +## Type of Issue + +_Is this a 'Bug Report' or a 'Suggestion for an Enhancement'?_ + +## Detailed Description (Enhancement Suggestion) + +_Explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, provide references to relevant background information, and whether you are willing to implement the enhancement yourself or would like to participate in the implementation_ + +## LAMMPS Version (Bug Report) + +_Please specify which LAMMPS version this issue was detected with. If this is not the latest development version, please stop and test that version, too, and report it here if the bug persists_ + +## Expected Behavior (Bug Report) + +_Describe the expected behavior. Quote from the LAMMPS manual where needed or explain why the expected behavior is meaningful, especially when it differs from the manual_ + +## Actual Behavior (Bug Report) + +_Describe the actual behavior, how it differs from the expected behavior, and how this can be observed. Try to be specific and do **not* use vague terms like "doesn't work" or "wrong result". Do not assume that the person reading this has any experience with or knowledge of your specific research._ + +## Steps to Reproduce (Bug Report) + +_Describe the steps required to quickly reproduce the issue. You can attach (small) files to the section below or add URLs where to download an archive with all necessary files. Please try to create input that are as small as possible and run as fast as possible. NOTE: the less effort and time it takes to reproduce your issue, the more likely, that somebody will look into it._ + +## Further Information, Files, and Links + +_Put any additional information here, attach relevant text or image files and URLs to external sites, e.g. relevant publications_ diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md new file mode 100644 index 0000000000..77c81ea69d --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -0,0 +1,29 @@ +## Purpose + +_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request. If this addresses an open GitHub Issue, mention the issue number, e.g. with `fixes #221` or `closes #135`, so that issue will be automatically closed when the pull request is merged_ + +## Author(s) + +_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_ + +## Backward Compatibility + +_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_ + +## Implementation Notes + +_Provide any relevant details about how the changes are implemented, how correctness was verified, how other features - if any - in LAMMPS are affected_ + +## Post Submission Checklist + +_Please check the fields below as they are completed_ +- [ ] The feature or features in this pull request is complete +- [ ] Suitable new documentation files and/or updates to the existing docs are included +- [ ] One or more example input decks are included +- [ ] The source code follows the LAMMPS formatting guidelines + +## Further Information, Files, and Links + +_Put any additional information here, attach relevant text or image files, and URLs to external sites (e.g. DOIs or webpages)_ + + diff --git a/doc/Makefile b/doc/Makefile index fd087f0344..2274ca5550 100644 --- a/doc/Makefile +++ b/doc/Makefile @@ -100,6 +100,7 @@ epub: $(OBJECTS) pdf: utils/txt2html/txt2html.exe @(\ + set -e; \ cd src; \ ../utils/txt2html/txt2html.exe -b *.txt; \ htmldoc --batch lammps.book; \ @@ -158,7 +159,7 @@ $(VENV): @( \ virtualenv -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ - pip install Sphinx; \ + pip install Sphinx==1.5.6; \ pip install sphinxcontrib-images; \ deactivate;\ ) diff --git a/doc/src/Eqs/cnp_cutoff.jpg b/doc/src/Eqs/cnp_cutoff.jpg new file mode 100644 index 0000000000..fae5c6b636 Binary files /dev/null and b/doc/src/Eqs/cnp_cutoff.jpg differ diff --git a/doc/src/Eqs/cnp_cutoff.tex b/doc/src/Eqs/cnp_cutoff.tex new file mode 100644 index 0000000000..f74166e608 --- /dev/null +++ b/doc/src/Eqs/cnp_cutoff.tex @@ -0,0 +1,14 @@ +\documentclass[12pt,article]{article} + +\usepackage{indentfirst} +\usepackage{amsmath} + +\begin{document} + +\begin{eqnarray*} + r_{c}^{fcc} & = & \frac{1}{2} \left(\frac{\sqrt{2}}{2} + 1\right) \mathrm{a} \simeq 0.8536 \:\mathrm{a} \\ + r_{c}^{bcc} & = & \frac{1}{2}(\sqrt{2} + 1) \mathrm{a} \simeq 1.207 \:\mathrm{a} \\ + r_{c}^{hcp} & = & \frac{1}{2}\left(1+\sqrt{\frac{4+2x^{2}}{3}}\right) \mathrm{a} +\end{eqnarray*} + +\end{document} diff --git a/doc/src/Eqs/cnp_cutoff2.jpg b/doc/src/Eqs/cnp_cutoff2.jpg new file mode 100644 index 0000000000..744b61e9b4 Binary files /dev/null and b/doc/src/Eqs/cnp_cutoff2.jpg differ diff --git a/doc/src/Eqs/cnp_cutoff2.tex b/doc/src/Eqs/cnp_cutoff2.tex new file mode 100644 index 0000000000..fcec31fd24 --- /dev/null +++ b/doc/src/Eqs/cnp_cutoff2.tex @@ -0,0 +1,12 @@ +\documentclass[12pt,article]{article} + +\usepackage{indentfirst} +\usepackage{amsmath} + +\begin{document} + +$$ + Rc + Rs > 2*{\rm cutoff} +$$ + +\end{document} diff --git a/doc/src/Eqs/cnp_eq.jpg b/doc/src/Eqs/cnp_eq.jpg new file mode 100644 index 0000000000..d421314442 Binary files /dev/null and b/doc/src/Eqs/cnp_eq.jpg differ diff --git a/doc/src/Eqs/cnp_eq.tex b/doc/src/Eqs/cnp_eq.tex new file mode 100644 index 0000000000..e5f157e6ba --- /dev/null +++ b/doc/src/Eqs/cnp_eq.tex @@ -0,0 +1,9 @@ +\documentclass[12pt]{article} + +\begin{document} + +$$ + Q_{i} = \frac{1}{n_i}\sum_{j = 1}^{n_i} | \sum_{k = 1}^{n_{ij}} \vec{R}_{ik} + \vec{R}_{jk} |^2 +$$ + +\end{document} diff --git a/doc/src/Eqs/pair_lj_sf.jpg b/doc/src/Eqs/pair_lj_sf.jpg deleted file mode 100644 index a702240003..0000000000 Binary files a/doc/src/Eqs/pair_lj_sf.jpg and /dev/null differ diff --git a/doc/src/Eqs/pair_lj_sf.tex b/doc/src/Eqs/pair_lj_sf.tex deleted file mode 100644 index e78e2ca75f..0000000000 --- a/doc/src/Eqs/pair_lj_sf.tex +++ /dev/null @@ -1,11 +0,0 @@ -\documentclass[12pt]{article} - -\begin{document} - -\begin{eqnarray*} - F & = & F_{\mathrm{LJ}}(r) - F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - E & = & E_{\mathrm{LJ}}(r) - E_{\mathrm{LJ}}(r_{\mathrm{c}}) + (r - r_{\mathrm{c}}) F_{\mathrm{LJ}}(r_{\mathrm{c}}) \qquad r < r_{\mathrm{c}} \\ - \mathrm{with} \qquad E_{\mathrm{LJ}}(r) & = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] \qquad \mathrm{and} \qquad F_{\mathrm{LJ}}(r) = - E^\prime_{\mathrm{LJ}}(r) -\end{eqnarray*} - -\end{document} diff --git a/doc/src/JPG/user_intel.png b/doc/src/JPG/user_intel.png index 0ebb2d1ae0..302b50124a 100755 Binary files a/doc/src/JPG/user_intel.png and b/doc/src/JPG/user_intel.png differ diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt index bceb174017..36391731d0 100644 --- a/doc/src/Manual.txt +++ b/doc/src/Manual.txt @@ -1,7 +1,7 @@ LAMMPS Users Manual - + @@ -21,7 +21,7 @@

LAMMPS Documentation :c,h3 -4 May 2017 version :c,h4 +6 Jul 2017 version :c,h4 Version info: :h4 diff --git a/doc/src/Section_commands.txt b/doc/src/Section_commands.txt index 771e830841..e17645e6d0 100644 --- a/doc/src/Section_commands.txt +++ b/doc/src/Section_commands.txt @@ -618,6 +618,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT. "press/berendsen"_fix_press_berendsen.html, "print"_fix_print.html, "property/atom"_fix_property_atom.html, +"python"_fix_python.html, "qeq/comb (o)"_fix_qeq_comb.html, "qeq/dynamic"_fix_qeq.html, "qeq/fire"_fix_qeq.html, @@ -716,7 +717,7 @@ package"_Section_start.html#start_3. "phonon"_fix_phonon.html, "pimd"_fix_pimd.html, "qbmsst"_fix_qbmsst.html, -"qeq/reax"_fix_qeq_reax.html, +"qeq/reax (ko)"_fix_qeq_reax.html, "qmmm"_fix_qmmm.html, "qtb"_fix_qtb.html, "reax/c/bonds"_fix_reax_bonds.html, @@ -830,6 +831,7 @@ package"_Section_start.html#start_3. "ackland/atom"_compute_ackland_atom.html, "basal/atom"_compute_basal_atom.html, +"cnp/atom"_compute_cnp_atom.html, "dpd"_compute_dpd.html, "dpd/atom"_compute_dpd_atom.html, "fep"_compute_fep.html, @@ -931,6 +933,8 @@ KOKKOS, o = USER-OMP, t = OPT. "gran/hertz/history (o)"_pair_gran.html, "gran/hooke (o)"_pair_gran.html, "gran/hooke/history (o)"_pair_gran.html, +"gw"_pair_gw.html, +"gw/zbl"_pair_gw.html, "hbond/dreiding/lj (o)"_pair_hbond_dreiding.html, "hbond/dreiding/morse (o)"_pair_hbond_dreiding.html, "kim"_pair_kim.html, @@ -960,7 +964,7 @@ KOKKOS, o = USER-OMP, t = OPT. "lj/expand (gko)"_pair_lj_expand.html, "lj/gromacs (gko)"_pair_gromacs.html, "lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html, -"lj/long/coul/long (o)"_pair_lj_long.html, +"lj/long/coul/long (io)"_pair_lj_long.html, "lj/long/dipole/long"_pair_dipole.html, "lj/long/tip4p/long"_pair_lj_long.html, "lj/smooth (o)"_pair_lj_smooth.html, @@ -982,6 +986,7 @@ KOKKOS, o = USER-OMP, t = OPT. "peri/pmb (o)"_pair_peri.html, "peri/ves"_pair_peri.html, "polymorphic"_pair_polymorphic.html, +"python"_pair_python.html, "reax"_pair_reax.html, "rebo (o)"_pair_airebo.html, "resquared (go)"_pair_resquared.html, @@ -1016,6 +1021,7 @@ package"_Section_start.html#start_3. "dpd/fdt/energy"_pair_dpd_fdt.html, "eam/cd (o)"_pair_eam.html, "edip (o)"_pair_edip.html, +"edip/multi"_pair_edip.html, "eff/cut"_pair_eff.html, "exp6/rx"_pair_exp6_rx.html, "gauss/cut"_pair_gauss.html, @@ -1033,7 +1039,7 @@ package"_Section_start.html#start_3. "lj/sdk (gko)"_pair_sdk.html, "lj/sdk/coul/long (go)"_pair_sdk.html, "lj/sdk/coul/msm (o)"_pair_sdk.html, -"lj/sf (o)"_pair_lj_sf.html, +"meam/c"_pair_meam.html, "meam/spline (o)"_pair_meam_spline.html, "meam/sw/spline"_pair_meam_sw_spline.html, "mgpt"_pair_mgpt.html, @@ -1052,7 +1058,7 @@ package"_Section_start.html#start_3. "oxdna2/excv"_pair_oxdna2.html, "oxdna2/stk"_pair_oxdna2.html, "quip"_pair_quip.html, -"reax/c (k)"_pair_reaxc.html, +"reax/c (ko)"_pair_reaxc.html, "smd/hertz"_pair_smd_hertz.html, "smd/tlsph"_pair_smd_tlsph.html, "smd/triangulated/surface"_pair_smd_triangulated_surface.html, @@ -1068,7 +1074,7 @@ package"_Section_start.html#start_3. "table/rx"_pair_table_rx.html, "tersoff/table (o)"_pair_tersoff.html, "thole"_pair_thole.html, -"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) +"tip4p/long/soft (o)"_pair_lj_soft.html :tb(c=4,ea=c) :line @@ -1220,7 +1226,7 @@ USER-OMP, t = OPT. "msm/cg (o)"_kspace_style.html, "pppm (go)"_kspace_style.html, "pppm/cg (o)"_kspace_style.html, -"pppm/disp"_kspace_style.html, +"pppm/disp (i)"_kspace_style.html, "pppm/disp/tip4p"_kspace_style.html, "pppm/stagger"_kspace_style.html, "pppm/tip4p (o)"_kspace_style.html :tb(c=4,ea=c) diff --git a/doc/src/Section_errors.txt b/doc/src/Section_errors.txt index 5e0574b390..40e61a248e 100644 --- a/doc/src/Section_errors.txt +++ b/doc/src/Section_errors.txt @@ -4696,9 +4696,9 @@ Self-explanatory. :dd {Fix bond/create induced too many angles/dihedrals/impropers per atom} :dt -See the read_data command for info on setting the "extra angle per -atom", etc header values to allow for additional angles, etc to be -formed. :dd +See the read_data command for info on using the "extra/angle/per/atom", +(or dihedral, improper) keywords to allow for additional +angles, dihedrals, and impropers to be formed. :dd {Fix bond/create needs ghost atoms from further away} :dt @@ -7876,18 +7876,20 @@ See the setting for tagint in the src/lmptype.h file. :dd {New bond exceeded bonds per atom in create_bonds} :dt -See the read_data command for info on setting the "extra bond per -atom" header value to allow for additional bonds to be formed. :dd +See the read_data command for info on using the "extra/bond/per/atom" +keyword to allow for additional bonds to be formed {New bond exceeded bonds per atom in fix bond/create} :dt -See the read_data command for info on setting the "extra bond per -atom" header value to allow for additional bonds to be formed. :dd +See the read_data command for info on using the "extra/bond/per/atom" +keyword to allow for additional bonds to be formed :dd {New bond exceeded special list size in fix bond/create} :dt -See the special_bonds extra command for info on how to leave space in -the special bonds list to allow for additional bonds to be formed. :dd +See the "special_bonds extra" command +(or the "read_data extra/special/per/atom" command) +for info on how to leave space in the special bonds +list to allow for additional bonds to be formed. :dd {Newton bond change after simulation box is defined} :dt @@ -8890,6 +8892,14 @@ This is a requirement to use this potential. :dd See the newton command. This is a restriction to use this potential. :dd +{Pair style vashishta/gpu requires atom IDs} :dt + +This is a requirement to use this potential. :dd + +{Pair style vashishta/gpu requires newton pair off} :dt + +See the newton command. This is a restriction to use this potential. :dd + {Pair style tersoff/gpu requires atom IDs} :dt This is a requirement to use the tersoff/gpu potential. :dd @@ -9656,9 +9666,10 @@ you are running. :dd {Special list size exceeded in fix bond/create} :dt -See the read_data command for info on setting the "extra special per -atom" header value to allow for additional special values to be -stored. :dd +See the special_bonds extra command +(or the read_data extra/special/per/atom command) +for info on how to leave space in the special bonds +list to allow for additional bonds to be formed. :dd {Specified processors != physical processors} :dt @@ -9675,23 +9686,23 @@ Self-explanatory. :dd {Subsequent read data induced too many angles per atom} :dt -See the create_box extra/angle/per/atom or read_data "extra angle per -atom" header value to set this limit larger. :dd +See the extra/angle/per/atom keyword for the create_box +or the read_data command to set this limit larger :dd {Subsequent read data induced too many bonds per atom} :dt -See the create_box extra/bond/per/atom or read_data "extra bond per -atom" header value to set this limit larger. :dd +See the extra/bond/per/atom keyword for the create_box +or the read_data command to set this limit larger :dd {Subsequent read data induced too many dihedrals per atom} :dt -See the create_box extra/dihedral/per/atom or read_data "extra -dihedral per atom" header value to set this limit larger. :dd +See the extra/dihedral/per/atom keyword for the create_box +or the read_data command to set this limit larger :dd {Subsequent read data induced too many impropers per atom} :dt -See the create_box extra/improper/per/atom or read_data "extra -improper per atom" header value to set this limit larger. :dd +See the extra/improper/per/atom keyword for the create_box +or the read_data command to set this limit larger :dd {Substitution for illegal variable} :dt diff --git a/doc/src/Section_howto.txt b/doc/src/Section_howto.txt index 579cb68474..f2f2561af8 100644 --- a/doc/src/Section_howto.txt +++ b/doc/src/Section_howto.txt @@ -1938,7 +1938,7 @@ documentation in the src/library.cpp file for details, including which quantities can be queried by name: void *lammps_extract_global(void *, char *) -void lammps_extract_box(void *, double *, double *, +void lammps_extract_box(void *, double *, double *, double *, double *, double *, int *, int *) void *lammps_extract_atom(void *, char *) void *lammps_extract_compute(void *, char *, int, int) @@ -2682,14 +2682,14 @@ bond_coeff 2 25.724 0.0 :pre When running dynamics with the adiabatic core/shell model, the following issues should be considered. The relative motion of -the core and shell particles corresponds to the polarization, -hereby an instantaneous relaxation of the shells is approximated +the core and shell particles corresponds to the polarization, +hereby an instantaneous relaxation of the shells is approximated and a fast core/shell spring frequency ensures a nearly constant -internal kinetic energy during the simulation. +internal kinetic energy during the simulation. Thermostats can alter this polarization behaviour, by scaling the -internal kinetic energy, meaning the shell will not react freely to -its electrostatic environment. -Therefore it is typically desirable to decouple the relative motion of +internal kinetic energy, meaning the shell will not react freely to +its electrostatic environment. +Therefore it is typically desirable to decouple the relative motion of the core/shell pair, which is an imaginary degree of freedom, from the real physical system. To do that, the "compute temp/cs"_compute_temp_cs.html command can be used, in conjunction with @@ -2721,13 +2721,13 @@ fix thermostatequ all nve # integrator as needed f fix_modify thermoberendsen temp CSequ thermo_modify temp CSequ # output of center-of-mass derived temperature :pre -The pressure for the core/shell system is computed via the regular -LAMMPS convention by "treating the cores and shells as individual -particles"_#MitchellFincham2. For the thermo output of the pressure -as well as for the application of a barostat, it is necessary to -use an additional "pressure"_compute_pressure compute based on the -default "temperature"_compute_temp and specifying it as a second -argument in "fix modify"_fix_modify.html and +The pressure for the core/shell system is computed via the regular +LAMMPS convention by "treating the cores and shells as individual +particles"_#MitchellFincham2. For the thermo output of the pressure +as well as for the application of a barostat, it is necessary to +use an additional "pressure"_compute_pressure compute based on the +default "temperature"_compute_temp and specifying it as a second +argument in "fix modify"_fix_modify.html and "thermo_modify"_thermo_modify.html resulting in: (...) @@ -2757,18 +2757,18 @@ temp/cs"_compute_temp_cs.html command to the {temp} keyword of the velocity all create 1427 134 bias yes temp CSequ velocity all scale 1427 temp CSequ :pre -To maintain the correct polarizability of the core/shell pairs, the -kinetic energy of the internal motion shall remain nearly constant. -Therefore the choice of spring force and mass ratio need to ensure -much faster relative motion of the 2 atoms within the core/shell pair -than their center-of-mass velocity. This allows the shells to -effectively react instantaneously to the electrostatic environment and +To maintain the correct polarizability of the core/shell pairs, the +kinetic energy of the internal motion shall remain nearly constant. +Therefore the choice of spring force and mass ratio need to ensure +much faster relative motion of the 2 atoms within the core/shell pair +than their center-of-mass velocity. This allows the shells to +effectively react instantaneously to the electrostatic environment and limits energy transfer to or from the core/shell oscillators. This fast movement also dictates the timestep that can be used. The primary literature of the adiabatic core/shell model suggests that the fast relative motion of the core/shell pairs only allows negligible -energy transfer to the environment. +energy transfer to the environment. The mentioned energy transfer will typically lead to a small drift in total energy over time. This internal energy can be monitored using the "compute chunk/atom"_compute_chunk_atom.html and "compute @@ -2790,7 +2790,7 @@ pairs as chunks. For example if core/shell pairs are the only molecules: -read_data NaCl_CS_x0.1_prop.data +read_data NaCl_CS_x0.1_prop.data compute prop all property/atom molecule compute cs_chunk all chunk/atom c_prop compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0 # note the chosen degrees of freedom for the core/shell pairs diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt index cc44c05906..76f88b8ab8 100644 --- a/doc/src/Section_packages.txt +++ b/doc/src/Section_packages.txt @@ -121,6 +121,7 @@ Package, Description, Doc page, Example, Library "USER-INTEL"_#USER-INTEL, optimized Intel CPU and KNL styles,"Section 5.3.2"_accelerate_intel.html, WWW bench, - "USER-LB"_#USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, - "USER-MANIFOLD"_#USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, - +"USER-MEAMC"_#USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, - "USER-MGPT"_#USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, - "USER-MISC"_#USER-MISC, single-file contributions, USER-MISC/README, USER/misc, - "USER-MOLFILE"_#USER-MOLFILE, "VMD"_vmd_home molfile plug-ins,"dump molfile"_dump_molfile.html, -, ext @@ -585,7 +586,7 @@ do not recommend building with other acceleration packages installed make yes-kokkos make machine :pre - + make no-kokkos make machine :pre @@ -839,13 +840,13 @@ written and read in parallel. Note that MPIIO is part of the standard message-passing interface (MPI) library, so you should not need any additional compiler or link settings, beyond what LAMMPS normally uses for MPI on your system. - + make yes-mpiio make machine :pre - + make no-mpiio make machine :pre - + [Supporting info:] src/MPIIO: filenames -> commands @@ -855,7 +856,7 @@ src/MPIIO: filenames -> commands "read_restart"_read_restart.html :ul :line - + MSCG package :link(mscg),h4 [Contents:] @@ -914,7 +915,7 @@ lib/mscg/README examples/mscg :ul :line - + OPT package :link(OPT),h4 [Contents:] @@ -1387,7 +1388,7 @@ atomic information to continuum fields. [Authors:] Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the ATC library in lib/atc. You can do this manually if you prefer; follow the instructions in lib/atc/README. You can also do it in one step @@ -1420,10 +1421,10 @@ usual manner: make yes-user-atc make machine :pre - + make no-user-atc make machine :pre - + [Supporting info:] src/USER-ATC: filenames -> commands @@ -1446,7 +1447,7 @@ model. [Author:] Ilya Valuev (JIHT, Russia). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the AWPMD library in lib/awpmd. You can do this manually if you prefer; follow the instructions in lib/awpmd/README. You can also do it in @@ -1479,10 +1480,10 @@ usual manner: make yes-user-awpmd make machine :pre - + make no-user-awpmd make machine :pre - + [Supporting info:] src/USER-AWPMD: filenames -> commands @@ -1502,16 +1503,16 @@ oxDNA model of Doye, Louis and Ouldridge at the University of Oxford. This includes Langevin-type rigid-body integrators with improved stability. -[Author:] Oliver Henrich (University of Edinburgh). +[Author:] Oliver Henrich (University of Strathclyde, Glasgow). [Install or un-install:] - + make yes-user-cgdna make machine :pre - + make no-user-cgdna make machine :pre - + [Supporting info:] src/USER-CGDNA: filenames -> commands @@ -1536,13 +1537,13 @@ acids. [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + make yes-user-cgsdk make machine :pre - + make no-user-cgsdk make machine :pre - + [Supporting info:] src/USER-CGSDK: filenames -> commands @@ -1570,7 +1571,7 @@ by Giacomo Fiorin (ICMS, Temple University, Philadelphia, PA, USA) and Jerome Henin (LISM, CNRS, Marseille, France). [Install or un-install:] - + Before building LAMMPS with this package, you must first build the COLVARS library in lib/colvars. You can do this manually if you prefer; follow the instructions in lib/colvars/README. You can also @@ -1594,10 +1595,10 @@ usual manner: make yes-user-colvars make machine :pre - + make no-user-colvars make machine :pre - + [Supporting info:] src/USER-COLVARS: filenames -> commands @@ -1619,13 +1620,13 @@ intensities based on kinematic diffraction theory. [Author:] Shawn Coleman while at the U Arkansas. [Install or un-install:] - + make yes-user-diffraction make machine :pre - + make no-user-diffraction make machine :pre - + [Supporting info:] src/USER-DIFFRACTION: filenames -> commands @@ -1654,13 +1655,13 @@ algorithm. Brennan (ARL). [Install or un-install:] - + make yes-user-dpd make machine :pre - + make no-user-dpd make machine :pre - + [Supporting info:] src/USER-DPD: filenames -> commands @@ -1696,13 +1697,13 @@ tools/drude. Devemy (CNRS), and Agilio Padua (U Blaise Pascal). [Install or un-install:] - + make yes-user-drude make machine :pre - + make no-user-drude make machine :pre - + [Supporting info:] src/USER-DRUDE: filenames -> commands @@ -1734,13 +1735,13 @@ tools/eff; see its README file. [Author:] Andres Jaramillo-Botero (CalTech). [Install or un-install:] - + make yes-user-eff make machine :pre - + make no-user-eff make machine :pre - + [Supporting info:] src/USER-EFF: filenames -> commands @@ -1773,13 +1774,13 @@ for using this package in tools/fep; see its README file. [Author:] Agilio Padua (Universite Blaise Pascal Clermont-Ferrand) [Install or un-install:] - + make yes-user-fep make machine :pre - + make no-user-fep make machine :pre - + [Supporting info:] src/USER-FEP: filenames -> commands @@ -1836,13 +1837,13 @@ file. You can then install/un-install the package and build LAMMPS in the usual manner: - + make yes-user-h5md make machine :pre - + make no-user-h5md make machine :pre - + [Supporting info:] src/USER-H5MD: filenames -> commands @@ -1908,7 +1909,7 @@ explained in "Section 5.3.2"_accelerate_intel.html. make yes-user-intel yes-user-omp make machine :pre - + make no-user-intel no-user-omp make machine :pre @@ -1938,13 +1939,13 @@ can be used to model MD particles influenced by hydrodynamic forces. Ontario). [Install or un-install:] - + make yes-user-lb make machine :pre - + make no-user-lb make machine :pre - + [Supporting info:] src/USER-LB: filenames -> commands @@ -1972,13 +1973,13 @@ matrix-MGPT algorithm due to Tomas Oppelstrup at LLNL. [Authors:] Tomas Oppelstrup and John Moriarty (LLNL). [Install or un-install:] - + make yes-user-mgpt make machine :pre - + make no-user-mgpt make machine :pre - + [Supporting info:] src/USER-MGPT: filenames -> commands @@ -2000,13 +2001,13 @@ dihedral, improper, or command style. src/USER-MISC/README file. [Install or un-install:] - + make yes-user-misc make machine :pre - + make no-user-misc make machine :pre - + [Supporting info:] src/USER-MISC: filenames -> commands @@ -2027,17 +2028,17 @@ algorithm to formulate single-particle constraint functions g(xi,yi,zi) = 0 and their derivative (i.e. the normal of the manifold) n = grad(g). -[Author:] Stefan Paquay (Eindhoven University of Technology (TU/e), The -Netherlands) +[Author:] Stefan Paquay (until 2017: Eindhoven University of Technology (TU/e), The +Netherlands; since 2017: Brandeis University, Waltham, MA, USA) [Install or un-install:] - + make yes-user-manifold make machine :pre - + make no-user-manifold make machine :pre - + [Supporting info:] src/USER-MANIFOLD: filenames -> commands @@ -2051,6 +2052,37 @@ http://lammps.sandia.gov/movies.html#manifold :ul :line +USER-MEAMC package :link(USER-MEAMC),h4 + +[Contents:] + +A pair style for the modified embedded atom (MEAM) potential +translated from the Fortran version in the "MEAM"_MEAM package +to plain C++. In contrast to the MEAM package, no library +needs to be compiled and the pair style can be instantiated +multiple times. + +[Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg) +based on the Fortran version of Greg Wagner (Northwestern U) while at +Sandia. + +[Install or un-install:] + +make yes-user-meamc +make machine :pre + +make no-user-meamc +make machine :pre + +[Supporting info:] + +src/USER-MEAMC: filenames -> commands +src/USER-MEAMC/README +"pair meam/c"_pair_meam.html +examples/meam :ul + +:line + USER-MOLFILE package :link(USER-MOLFILE),h4 [Contents:] @@ -2080,7 +2112,7 @@ at [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + Note that the lib/molfile/Makefile.lammps file has a setting for a dynamic loading library libdl.a that should is typically present on all systems, which is required for LAMMPS to link with this package. @@ -2090,10 +2122,10 @@ lib/molfile/Makefile.lammps for details. make yes-user-molfile make machine :pre - + make no-user-molfile make machine :pre - + [Supporting info:] src/USER-MOLFILE: filenames -> commands @@ -2128,7 +2160,7 @@ tools: [Author:] Lars Pastewka (Karlsruhe Institute of Technology). [Install or un-install:] - + Note that to follow these steps, you need the standard NetCDF software package installed on your system. The lib/netcdf/Makefile.lammps file has settings for NetCDF include and library files that LAMMPS needs to @@ -2138,7 +2170,7 @@ lib/netcdf/README for details. make yes-user-netcdf make machine :pre - + make no-user-netcdf make machine :pre @@ -2178,10 +2210,10 @@ Once you have an appropriate Makefile.machine, you can install/un-install the package and build LAMMPS in the usual manner: [Install or un-install:] - + make yes-user-omp make machine :pre - + make no-user-omp make machine :pre @@ -2213,13 +2245,13 @@ relations, directly from molecular dynamics simulations. [Author:] Ling-Ti Kong (Shanghai Jiao Tong University). [Install or un-install:] - + make yes-user-phonon make machine :pre - + make no-user-phonon make machine :pre - + [Supporting info:] src/USER-PHONON: filenames -> commands @@ -2235,7 +2267,7 @@ USER-QMMM package :link(USER-QMMM),h4 A "fix qmmm"_fix_qmmm.html command which allows LAMMPS to be used in a QM/MM simulation, currently only in combination with the "Quantum -ESPRESSO"_espresso package. +ESPRESSO"_espresso package. :link(espresso,http://www.quantum-espresso.org) @@ -2275,7 +2307,7 @@ usual manner: make yes-user-qmmm make machine :pre - + make no-user-qmmm make machine :pre @@ -2284,7 +2316,7 @@ for a QM/MM simulation. You must also build Quantum ESPRESSO and create a new executable which links LAMMPS and Quanutm ESPRESSO together. These are steps 3 and 4 described in the lib/qmmm/README file. - + [Supporting info:] src/USER-QMMM: filenames -> commands @@ -2312,13 +2344,13 @@ simulation. [Author:] Yuan Shen (Stanford U). [Install or un-install:] - + make yes-user-qtb make machine :pre - + make no-user-qtb make machine :pre - + [Supporting info:] src/USER-QTB: filenames -> commands @@ -2362,10 +2394,10 @@ usual manner: make yes-user-quip make machine :pre - + make no-user-quip make machine :pre - + [Supporting info:] src/USER-QUIP: filenames -> commands @@ -2388,13 +2420,13 @@ for monitoring molecules as bonds are created and destroyed. [Author:] Hasan Metin Aktulga (MSU) while at Purdue University. [Install or un-install:] - + make yes-user-reaxc make machine :pre - + make no-user-reaxc make machine :pre - + [Supporting info:] src/USER-REAXC: filenames -> commands @@ -2451,10 +2483,10 @@ usual manner: make yes-user-smd make machine :pre - + make no-user-smd make machine :pre - + [Supporting info:] src/USER-SMD: filenames -> commands @@ -2477,13 +2509,13 @@ ionocovalent bonds in oxides. Tetot (LAAS-CNRS, France). [Install or un-install:] - + make yes-user-smtbq make machine :pre - + make no-user-smtbq make machine :pre - + [Supporting info:] src/USER-SMTBQ: filenames -> commands @@ -2516,13 +2548,13 @@ property/atom"_compute_property_atom.html command. Dynamics, Ernst Mach Institute, Germany). [Install or un-install:] - + make yes-user-sph make machine :pre - + make no-user-sph make machine :pre - + [Supporting info:] src/USER-SPH: filenames -> commands @@ -2544,13 +2576,13 @@ stress, etc) about individual interactions. [Author:] Axel Kohlmeyer (Temple U). [Install or un-install:] - + make yes-user-tally make machine :pre - + make no-user-tally make machine :pre - + [Supporting info:] src/USER-TALLY: filenames -> commands @@ -2577,7 +2609,7 @@ system. [Authors:] Richard Berger (JKU) and Daniel Queteschiner (DCS Computing). [Install or un-install:] - + The lib/vtk/Makefile.lammps file has settings for accessing VTK files and its library, which are required for LAMMPS to build and link with this package. If the settings are not valid for your system, check if @@ -2590,10 +2622,10 @@ usual manner: make yes-user-vtk make machine :pre - + make no-user-vtk make machine :pre - + [Supporting info:] src/USER-VTK: filenames -> commands diff --git a/doc/src/Section_python.txt b/doc/src/Section_python.txt index 5d366f6b6c..1e67fca321 100644 --- a/doc/src/Section_python.txt +++ b/doc/src/Section_python.txt @@ -118,13 +118,21 @@ check which version of Python you have installed, by simply typing 11.2 Overview of using Python from a LAMMPS script :link(py_2),h4 -LAMMPS has a "python"_python.html command which can be used in an -input script to define and execute a Python function that you write -the code for. The Python function can also be assigned to a LAMMPS -python-style variable via the "variable"_variable.html command. Each -time the variable is evaluated, either in the LAMMPS input script -itself, or by another LAMMPS command that uses the variable, this will -trigger the Python function to be invoked. +LAMMPS has several commands which can be used to invoke Python +code directly from an input script: + +"python"_python.html +"variable python"_variable.html +"fix python"_fix_python.html +"pair_style python"_pair_python.html :ul + +The "python"_python.html command which can be used to define and +execute a Python function that you write the code for. The Python +function can also be assigned to a LAMMPS python-style variable via +the "variable"_variable.html command. Each time the variable is +evaluated, either in the LAMMPS input script itself, or by another +LAMMPS command that uses the variable, this will trigger the Python +function to be invoked. The Python code for the function can be included directly in the input script or in an auxiliary file. The function can have arguments which @@ -155,11 +163,18 @@ commands. See the "python"_python.html doc page and the "variable"_variable.html doc page for its python-style variables for more info, including examples of Python code you can write for both pure Python operations -and callbacks to LAMMPS. See "fix python"_fix_python.html to learn about -possibilities to execute Python code during each time step. +and callbacks to LAMMPS. -To run pure Python code from LAMMPS, you only need to build LAMMPS -with the PYTHON package installed: +The "fix python"_fix_python.html command can execute +Python code at selected timesteps during a simulation run. + +The "pair_style python"_pair_python command allows you to define +pairwise potentials as python code which encodes a single pairwise +interaction. This is useful for rapid-developement and debugging of a +new potential. + +To use any of these commands, you only need to build LAMMPS with the +PYTHON package installed: make yes-python make machine :pre @@ -699,7 +714,7 @@ stored in the "image" property. All three image flags are stored in a packed format in a single integer, so count would be 1 to retrieve that integer, however also a count value of 3 can be used and then the image flags will be unpacked into 3 individual integers, ordered -in a similar fashion as coordinates. +in a similar fashion as coordinates. Note that the data structure gather_atoms("x") returns is different from the data structure returned by extract_atom("x") in four ways. diff --git a/doc/src/accelerate_intel.txt b/doc/src/accelerate_intel.txt index d629828f12..155e29e367 100644 --- a/doc/src/accelerate_intel.txt +++ b/doc/src/accelerate_intel.txt @@ -30,8 +30,8 @@ Dihedral Styles: charmm, harmonic, opls :l Fixes: nve, npt, nvt, nvt/sllod :l Improper Styles: cvff, harmonic :l Pair Styles: buck/coul/cut, buck/coul/long, buck, eam, gayberne, -charmm/coul/long, lj/cut, lj/cut/coul/long, sw, tersoff :l -K-Space Styles: pppm :l +charmm/coul/long, lj/cut, lj/cut/coul/long, lj/long/coul/long, sw, tersoff :l +K-Space Styles: pppm, pppm/disp :l :ule [Speed-ups to expect:] @@ -42,62 +42,90 @@ precision mode. Performance improvements are shown compared to LAMMPS {without using other acceleration packages} as these are under active development (and subject to performance changes). The measurements were performed using the input files available in -the src/USER-INTEL/TEST directory. These are scalable in size; the -results given are with 512K particles (524K for Liquid Crystal). -Most of the simulations are standard LAMMPS benchmarks (indicated -by the filename extension in parenthesis) with modifications to the -run length and to add a warmup run (for use with offload -benchmarks). +the src/USER-INTEL/TEST directory with the provided run script. +These are scalable in size; the results given are with 512K +particles (524K for Liquid Crystal). Most of the simulations are +standard LAMMPS benchmarks (indicated by the filename extension in +parenthesis) with modifications to the run length and to add a +warmup run (for use with offload benchmarks). :c,image(JPG/user_intel.png) Results are speedups obtained on Intel Xeon E5-2697v4 processors (code-named Broadwell) and Intel Xeon Phi 7250 processors -(code-named Knights Landing) with "18 Jun 2016" LAMMPS built with -Intel Parallel Studio 2016 update 3. Results are with 1 MPI task +(code-named Knights Landing) with "June 2017" LAMMPS built with +Intel Parallel Studio 2017 update 2. Results are with 1 MPI task per physical core. See {src/USER-INTEL/TEST/README} for the raw simulation rates and instructions to reproduce. :line +[Accuracy and order of operations:] + +In most molecular dynamics software, parallelization parameters +(# of MPI, OpenMP, and vectorization) can change the results due +to changing the order of operations with finite-precision +calculations. The USER-INTEL package is deterministic. This means +that the results should be reproducible from run to run with the +{same} parallel configurations and when using determinstic +libraries or library settings (MPI, OpenMP, FFT). However, there +are differences in the USER-INTEL package that can change the +order of operations compared to LAMMPS without acceleration: + +Neighbor lists can be created in a different order :ulb,l +Bins used for sorting atoms can be oriented differently :l +The default stencil order for PPPM is 7. By default, LAMMPS will +calculate other PPPM parameters to fit the desired acuracy with +this order :l +The {newton} setting applies to all atoms, not just atoms shared +between MPI tasks :l +Vectorization can change the order for adding pairwise forces :l +:ule + +The precision mode (described below) used with the USER-INTEL +package can change the {accuracy} of the calculations. For the +default {mixed} precision option, calculations between pairs or +triplets of atoms are performed in single precision, intended to +be within the inherent error of MD simulations. All accumulation +is performed in double precision to prevent the error from growing +with the number of atoms in the simulation. {Single} precision +mode should not be used without appropriate validation. + +:line + [Quick Start for Experienced Users:] LAMMPS should be built with the USER-INTEL package installed. Simulations should be run with 1 MPI task per physical {core}, not {hardware thread}. -For Intel Xeon CPUs: - Edit src/MAKE/OPTIONS/Makefile.intel_cpu_intelmpi as necessary. :ulb,l -If using {kspace_style pppm} in the input script, add "neigh_modify binsize cutoff" and "kspace_modify diff ad" to the input script for better -performance. Cutoff should be roughly the neighbor list cutoff. By -default the binsize is half the neighbor list cutoff. :l -"-pk intel 0 omp 2 -sf intel" added to LAMMPS command-line :l +Set the environment variable KMP_BLOCKTIME=0 :l +"-pk intel 0 omp $t -sf intel" added to LAMMPS command-line :l +$t should be 2 for Intel Xeon CPUs and 2 or 4 for Intel Xeon Phi :l +For some of the simple 2-body potentials without long-range +electrostatics, performance and scalability can be better with +the "newton off" setting added to the input script :l +For simulations on higher node counts, add "processors * * * grid +numa" to the beginning of the input script for better scalability :l +If using {kspace_style pppm} in the input script, add +"kspace_modify diff ad" for better performance :l :ule -For Intel Xeon Phi CPUs for simulations without {kspace_style -pppm} in the input script : +For Intel Xeon Phi CPUs: -Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l -Runs should be performed using MCDRAM. :l -"-pk intel 0 omp 2 -sf intel" {or} "-pk intel 0 omp 4 -sf intel" -should be added to the LAMMPS command-line. Choice for best -performance will depend on the simulation. :l +Runs should be performed using MCDRAM. :ulb,l :ule -For Intel Xeon Phi CPUs for simulations with {kspace_style -pppm} in the input script: +For simulations using {kspace_style pppm} on Intel CPUs +supporting AVX-512: -Edit src/MAKE/OPTIONS/Makefile.knl as necessary. :ulb,l -Runs should be performed using MCDRAM. :l -Add "neigh_modify binsize 3" to the input script for better -performance. :l -Add "kspace_modify diff ad" to the input script for better -performance. :l -export KMP_AFFINITY=none :l -"-pk intel 0 omp 3 lrt yes -sf intel" or "-pk intel 0 omp 1 lrt yes --sf intel" added to LAMMPS command-line. Choice for best performance -will depend on the simulation. :l +Add "kspace_modify diff ad" to the input script :ulb,l +The command-line option should be changed to +"-pk intel 0 omp $r lrt yes -sf intel" where $r is the number of +threads minus 1. :l +Do not use thread affinity (set KMP_AFFINITY=none) :l +The "newton off" setting may provide better scalability :l :ule For Intel Xeon Phi coprocessors (Offload): @@ -169,6 +197,10 @@ cat /proc/cpuinfo :pre [Building LAMMPS with the USER-INTEL package:] +NOTE: See the src/USER-INTEL/README file for additional flags that +might be needed for best performance on Intel server processors +code-named "Skylake". + The USER-INTEL package must be installed into the source directory: make yes-user-intel :pre @@ -322,8 +354,8 @@ follow in the input script. NOTE: The USER-INTEL package will perform better with modifications to the input script when "PPPM"_kspace_style.html is used: -"kspace_modify diff ad"_kspace_modify.html and "neigh_modify binsize -3"_neigh_modify.html should be added to the input script. +"kspace_modify diff ad"_kspace_modify.html should be added to the +input script. Long-Range Thread (LRT) mode is an option to the "package intel"_package.html command that can improve performance when using @@ -342,6 +374,10 @@ would normally perform best with "-pk intel 0 omp 4", instead use environment variable "KMP_AFFINITY=none". LRT mode is not supported when using offload. +NOTE: Changing the "newton"_newton.html setting to off can improve +performance and/or scalability for simple 2-body potentials such as +lj/cut or when using LRT mode on processors supporting AVX-512. + Not all styles are supported in the USER-INTEL package. You can mix the USER-INTEL package with styles from the "OPT"_accelerate_opt.html package or the "USER-OMP package"_accelerate_omp.html. Of course, @@ -358,6 +394,10 @@ hybrid intel omp"_suffix.html command can also be used within the input script to automatically append the "omp" suffix to styles when USER-INTEL styles are not available. +NOTE: For simulations on higher node counts, add "processors * * * +grid numa"_processors.html" to the beginning of the input script for +better scalability. + When running on many nodes, performance might be better when using fewer OpenMP threads and more MPI tasks. This will depend on the simulation and the machine. Using the "verlet/split"_run_style.html @@ -467,7 +507,7 @@ supported. Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakker, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann. :ulb,l -Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. 2016 International Conference for High Performance Computing. In press. :l +Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. "Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency."_http://dl.acm.org/citation.cfm?id=3014915 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95). :l Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101. :l :ule diff --git a/doc/src/bond_oxdna.txt b/doc/src/bond_oxdna.txt index f9b35a167c..2add6f4c2f 100644 --- a/doc/src/bond_oxdna.txt +++ b/doc/src/bond_oxdna.txt @@ -30,7 +30,7 @@ The {oxdna/fene} and {oxdna2/fene} bond styles use the potential to define a modified finite extensible nonlinear elastic (FENE) potential "(Ouldridge)"_#oxdna_fene to model the connectivity of the phosphate backbone -in the oxDNA force field for coarse-grained modelling of DNA. +in the oxDNA force field for coarse-grained modelling of DNA. The following coefficients must be defined for the bond type via the "bond_coeff"_bond_coeff.html command as given in the above example, or in @@ -43,8 +43,8 @@ r0 (distance) :ul NOTE: The oxDNA bond style has to be used together with the corresponding oxDNA pair styles for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacking {oxdna/xstk} -and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of -"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair +and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of +"pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair style {oxdna2/dh} have to be defined. The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. @@ -66,7 +66,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html +"pair_style oxdna/excv"_pair_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "bond_coeff"_bond_coeff.html [Default:] none diff --git a/doc/src/compute_cna_atom.txt b/doc/src/compute_cna_atom.txt index 74240b515d..23289b0132 100644 --- a/doc/src/compute_cna_atom.txt +++ b/doc/src/compute_cna_atom.txt @@ -26,7 +26,7 @@ Define a computation that calculates the CNA (Common Neighbor Analysis) pattern for each atom in the group. In solid-state systems the CNA pattern is a useful measure of the local crystal structure around an atom. The CNA methodology is described in "(Faken)"_#Faken -and "(Tsuzuki)"_#Tsuzuki. +and "(Tsuzuki)"_#Tsuzuki1. Currently, there are five kinds of CNA patterns LAMMPS recognizes: @@ -93,5 +93,5 @@ above. :link(Faken) [(Faken)] Faken, Jonsson, Comput Mater Sci, 2, 279 (1994). -:link(Tsuzuki) +:link(Tsuzuki1) [(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_cnp_atom.txt b/doc/src/compute_cnp_atom.txt new file mode 100644 index 0000000000..16a51f5241 --- /dev/null +++ b/doc/src/compute_cnp_atom.txt @@ -0,0 +1,111 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute cnp/atom command :h3 + +[Syntax:] + +compute ID group-ID cnp/atom cutoff :pre + +ID, group-ID are documented in "compute"_compute.html command +cnp/atom = style name of this compute command +cutoff = cutoff distance for nearest neighbors (distance units) :ul + +[Examples:] + +compute 1 all cnp/atom 3.08 :pre + +[Description:] + +Define a computation that calculates the Common Neighborhood +Parameter (CNP) for each atom in the group. In solid-state systems +the CNP is a useful measure of the local crystal structure +around an atom and can be used to characterize whether the +atom is part of a perfect lattice, a local defect (e.g. a dislocation +or stacking fault), or at a surface. + +The value of the CNP parameter will be 0.0 for atoms not in the +specified compute group. Note that normally a CNP calculation should +only be performed on single component systems. + +This parameter is computed using the following formula from +"(Tsuzuki)"_#Tsuzuki2 + +:c,image(Eqs/cnp_eq.jpg) + +where the index {j} goes over the {n}i nearest neighbors of atom +{i}, and the index {k} goes over the {n}ij common nearest neighbors +between atom {i} and atom {j}. Rik and Rjk are the vectors connecting atom +{k} to atoms {i} and {j}. The quantity in the double sum is computed +for each atom. + +The CNP calculation is sensitive to the specified cutoff value. +You should ensure that the appropriate nearest neighbors of an atom are +found within the cutoff distance for the presumed crystal structure. +E.g. 12 nearest neighbor for perfect FCC and HCP crystals, 14 nearest +neighbors for perfect BCC crystals. These formulas can be used to +obtain a good cutoff distance: + +:c,image(Eqs/cnp_cutoff.jpg) + +where a is the lattice constant for the crystal structure concerned +and in the HCP case, x = (c/a) / 1.633, where 1.633 is the ideal c/a +for HCP crystals. + +Also note that since the CNP calculation in LAMMPS uses the neighbors +of an owned atom to find the nearest neighbors of a ghost atom, the +following relation should also be satisfied: + +:c,image(Eqs/cnp_cutoff2.jpg) + +where Rc is the cutoff distance of the potential, Rs is the skin +distance as specified by the "neighbor"_neighbor.html command, and +cutoff is the argument used with the compute cnp/atom command. LAMMPS +will issue a warning if this is not the case. + +The neighbor list needed to compute this quantity is constructed each +time the calculation is performed (e.g. each time a snapshot of atoms +is dumped). Thus it can be inefficient to compute/dump this quantity +too frequently or to have multiple compute/dump commands, each with a +{cnp/atom} style. + +[Output info:] + +This compute calculates a per-atom vector, which can be accessed by +any command that uses per-atom values from a compute as input. See +"Section 6.15"_Section_howto.html#howto_15 for an overview of +LAMMPS output options. + +The per-atom vector values will be real positive numbers. Some typical CNP +values: + +FCC lattice = 0.0 +BCC lattice = 0.0 +HCP lattice = 4.4 :pre + +FCC (111) surface ~ 13.0 +FCC (100) surface ~ 26.5 +FCC dislocation core ~ 11 :pre + +[Restrictions:] + +This compute is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"compute cna/atom"_compute_cna_atom.html +"compute centro/atom"_compute_centro_atom.html + +[Default:] none + +:line + +:link(Tsuzuki2) +[(Tsuzuki)] Tsuzuki, Branicio, Rino, Comput Phys Comm, 177, 518 (2007). diff --git a/doc/src/compute_pair_local.txt b/doc/src/compute_pair_local.txt index 0121210994..16aaba4667 100644 --- a/doc/src/compute_pair_local.txt +++ b/doc/src/compute_pair_local.txt @@ -76,7 +76,9 @@ command for the types of the two atoms is used. For the {radius} setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are overlapping, as computed by "granular pair -styles"_pair_gran.txt. +styles"_pair_gran.txt. Note that if a granular model defines atom +types such that all particles of a specific type are monodisperse +(same diameter), then the two settings are effectively identical. Note that as atoms migrate from processor to processor, there will be no consistent ordering of the entries within the local vector or array diff --git a/doc/src/compute_property_local.txt b/doc/src/compute_property_local.txt index f7851e864b..39106a39c8 100644 --- a/doc/src/compute_property_local.txt +++ b/doc/src/compute_property_local.txt @@ -79,6 +79,9 @@ the two atoms is used. For the {radius} setting, the sum of the radii of the two particles is used as a cutoff. For example, this is appropriate for granular particles which only interact when they are overlapping, as computed by "granular pair styles"_pair_gran.html. +Note that if a granular model defines atom types such that all +particles of a specific type are monodisperse (same diameter), then +the two settings are effectively identical. If the inputs are bond, angle, etc attributes, the local data is generated by looping over all the atoms owned on a processor and diff --git a/doc/src/compute_saed.txt b/doc/src/compute_saed.txt index aadda49533..020f72f565 100644 --- a/doc/src/compute_saed.txt +++ b/doc/src/compute_saed.txt @@ -111,26 +111,26 @@ Coefficients parameterized by "(Fox)"_#Fox are assigned for each atom type designating the chemical symbol and charge of each atom type. Valid chemical symbols for compute saed are: - H: He: Li: Be: B: - C: N: O: F: Ne: - Na: Mg: Al: Si: P: - S: Cl: Ar: K: Ca: - Sc: Ti: V: Cr: Mn: - Fe: Co: Ni: Cu: Zn: - Ga: Ge: As: Se: Br: - Kr: Rb: Sr: Y: Zr: - Nb: Mo: Tc: Ru: Rh: - Pd: Ag: Cd: In: Sn: - Sb: Te: I: Xe: Cs: - Ba: La: Ce: Pr: Nd: - Pm: Sm: Eu: Gd: Tb: - Dy: Ho: Er: Tm: Yb: - Lu: Hf: Ta: W: Re: - Os: Ir: Pt: Au: Hg: - Tl: Pb: Bi: Po: At: - Rn: Fr: Ra: Ac: Th: - Pa: U: Np: Pu: Am: - Cm: Bk: Cf:tb(c=5,s=:) +H: He: Li: Be: B: +C: N: O: F: Ne: +Na: Mg: Al: Si: P: +S: Cl: Ar: K: Ca: +Sc: Ti: V: Cr: Mn: +Fe: Co: Ni: Cu: Zn: +Ga: Ge: As: Se: Br: +Kr: Rb: Sr: Y: Zr: +Nb: Mo: Tc: Ru: Rh: +Pd: Ag: Cd: In: Sn: +Sb: Te: I: Xe: Cs: +Ba: La: Ce: Pr: Nd: +Pm: Sm: Eu: Gd: Tb: +Dy: Ho: Er: Tm: Yb: +Lu: Hf: Ta: W: Re: +Os: Ir: Pt: Au: Hg: +Tl: Pb: Bi: Po: At: +Rn: Fr: Ra: Ac: Th: +Pa: U: Np: Pu: Am: +Cm: Bk: Cf:tb(c=5,s=:) If the {echo} keyword is specified, compute saed will provide extra diff --git a/doc/src/compute_sna_atom.txt b/doc/src/compute_sna_atom.txt index f82df0d816..defd98d520 100644 --- a/doc/src/compute_sna_atom.txt +++ b/doc/src/compute_sna_atom.txt @@ -231,11 +231,12 @@ the numbers of columns are 930, 2790, and 5580, respectively. If the {quadratic} keyword value is set to 1, then additional columns are appended to each per-atom array, corresponding to -a matrix of quantities that are products of two bispectrum components. If the -number of bispectrum components is {K}, then the number of matrix elements -is {K}^2. These are output in subblocks of {K}^2 columns, using the same -ordering of columns and sub-blocks as was used for the bispectrum -components. +the products of all distinct pairs of bispectrum components. If the +number of bispectrum components is {K}, then the number of distinct pairs +is {K}({K}+1)/2. These are output in subblocks of {K}({K}+1)/2 columns, using the same +ordering of sub-blocks as was used for the bispectrum +components. Within each sub-block, the ordering is upper-triangular, +(1,1),(1,2)...(1,{K}),(2,1)...({K}-1,{K}-1),({K}-1,{K}),({K},{K}) These values can be accessed by any command that uses per-atom values from a compute as input. See "Section diff --git a/doc/src/computes.txt b/doc/src/computes.txt index 1d01798791..5a6ca66c46 100644 --- a/doc/src/computes.txt +++ b/doc/src/computes.txt @@ -17,6 +17,7 @@ Computes :h1 compute_chunk_atom compute_cluster_atom compute_cna_atom + compute_cnp_atom compute_com compute_com_chunk compute_contact_atom diff --git a/doc/src/create_bonds.txt b/doc/src/create_bonds.txt index f5a4c1f505..5a87852169 100644 --- a/doc/src/create_bonds.txt +++ b/doc/src/create_bonds.txt @@ -10,53 +10,93 @@ create_bonds command :h3 [Syntax:] -create_bonds group-ID group2-ID btype rmin rmax :pre +create_bonds style args ... keyword value ... :pre -group-ID = ID of first group -group2-ID = ID of second group, bonds will be between atoms in the 2 groups -btype = bond type of created bonds -rmin = minimum distance between pair of atoms to bond together -rmax = minimum distance between pair of atoms to bond together :ul +style = {many} or {single/bond} or {single/angle} or {single/dihedral} :ule,l + {many} args = group-ID group2-ID btype rmin rmax + group-ID = ID of first group + group2-ID = ID of second group, bonds will be between atoms in the 2 groups + btype = bond type of created bonds + rmin = minimum distance between pair of atoms to bond together + rmax = minimum distance between pair of atoms to bond together + {single/bond} args = btype batom1 batom2 + btype = bond type of new bond + batom1,batom2 = atom IDs for two atoms in bond + {single/angle} args = atype aatom1 aatom2 aatom3 + atype = bond type of new angle + aatom1,aatom2,aatom3 = atom IDs for three atoms in angle + {single/dihedral} args = dtype datom1 datom2 datom3 datom4 + dtype = bond type of new dihedral + datom1,datom2,datom3,datom4 = atom IDs for four atoms in dihedral :pre +zero or more keyword/value pairs may be appended :l +keyword = {special} :l + {special} value = {yes} or {no} :pre +:ule [Examples:] -create_bonds all all 1 1.0 1.2 -create_bonds surf solvent 3 2.0 2.4 :pre +create_bonds many all all 1 1.0 1.2 +create_bonds many surf solvent 3 2.0 2.4 +create_bond single/bond 1 1 2 +create_bond single/angle 5 52 98 107 special no :pre [Description:] -Create bonds between pairs of atoms that meet specified distance -criteria. The bond interactions can then be computed during a -simulation by the bond potential defined by the -"bond_style"_bond_style.html and "bond_coeff"_bond_coeff.html -commands. This command is useful for adding bonds to a system, -e.g. between nearest neighbors in a lattice of atoms, without having -to enumerate all the bonds in the data file read by the -"read_data"_read_data.html command. +Create bonds between pairs of atoms that meet a specified distance +criteria. Or create a single bond, angle, or dihedral between 2, 3, +or 4 specified atoms. -Note that the flexibility of this command is limited. It can be used -several times to create different types of bond at different -distances. But it cannot typically create all the bonds that would -normally be defined in a complex system of molecules. Also note that -this command does not add any 3-body or 4-body interactions which, -depending on your model, may be induced by added bonds, -e.g. "angle"_angle_style.html, "dihedral"_dihedral_style.html, or -"improper"_improper_style.html interactions. +The new bond (angle, dihedral) interactions will then be computed +during a simulation by the bond (angle, dihedral) potential defined by +the "bond_style"_bond_style.html, "bond_coeff"_bond_coeff.html, +"angle_style"_angle_style.html, "angle_coeff"_angle_coeff.html, +"dihedral_style"_dihedral_style.html, +"dihedral_coeff"_dihedral_coeff.html commands. -All created bonds will be between pairs of atoms I,J where I is in one -of the two specified groups, and J is in the other. The two groups -can be the same, e.g. group "all". The created bonds will be of bond -type {btype}, where {btype} must be a value between 1 and the number -of bond types defined. This maximum value is set by the "bond types" -field in the header of the data file read by the -"read_data"_read_data.html command, or via the optional "bond/types" -argument of the "create_box"_create_box.html command. +The {many} style is useful for adding bonds to a system, e.g. between +nearest neighbors in a lattice of atoms, without having to enumerate +all the bonds in the data file read by the "read_data"_read_data.html +command. + +The {single} styles are useful for adding bonds, angles, dihedrals +to a system incrementally, then continuing a simulation. + +Note that this command does not auto-create any angle or dihedral +interactions when a bond is added. Nor does it auto-create any bonds +when an angle or dihedral is added. Or auto-create any angles when a +dihedral is added. Thus the flexibility of this command is limited. +It can be used several times to create different types of bond at +different distances. But it cannot typically auto-create all the +bonds or angles or dihedral that would normally be defined in a data +file for a complex system of molecules. + +NOTE: If the system has no bonds (angles, dihedrals) to begin with, or +if more bonds per atom are being added than currently exist, then you +must insure that the number of bond types and the maximum number of +bonds per atom are set to large enough values. And similarly for +angles and dihedrals. Otherwise an error may occur when too many +bonds (angles, dihedrals) are added to an atom. If the +"read_data"_read_data.html command is used to define the system, these +parameters can be set via the "bond types" and "extra bond per atom" +fields in the header section of the data file. If the +"create_box"_create_box.html command is used to define the system, +these 2 parameters can be set via its optional "bond/types" and +"extra/bond/per/atom" arguments. And similarly for angles and +dihedrals. See the doc pages for these 2 commands for details. + +:line + +The {many} style will create bonds between pairs of atoms I,J where I +is in one of the two specified groups, and J is in the other. The two +groups can be the same, e.g. group "all". The created bonds will be +of bond type {btype}, where {btype} must be a value between 1 and the +number of bond types defined. For a bond to be created, an I,J pair of atoms must be a distance D apart such that {rmin} <= D <= {rmax}. -The following settings must have been made in an input -script before this command is used: +The following settings must have been made in an input script before +this style is used: special_bonds weight for 1-2 interactions must be 0.0 a "pair_style"_pair_style.html must be defined @@ -69,8 +109,8 @@ cannot appear in the neighbor list, to avoid creation of duplicate bonds. The neighbor list for all atom type pairs must also extend to a distance that encompasses the {rmax} for new bonds to create. -An additional requirement is that your system must be ready to perform -a simulation. This means, for example, that all +An additional requirement for this style is that your system must be +ready to perform a simulation. This means, for example, that all "pair_style"_pair_style.html coefficients be set via the "pair_coeff"_pair_coeff.html command. A "bond_style"_bond_style.html command and all bond coefficients must also be set, even if no bonds @@ -83,17 +123,58 @@ executes, e.g. if you wish to use long-range Coulombic interactions via the "kspace_style"_kspace_style.html command for your subsequent simulation. -NOTE: If the system has no bonds to begin with, or if more bonds per -atom are being added than currently exist, then you must insure that -the number of bond types and the maximum number of bonds per atom are -set to large enough values. Otherwise an error may occur when too -many bonds are added to an atom. If the "read_data"_read_data.html -command is used to define the system, these 2 parameters can be set -via the "bond types" and "extra bond per atom" fields in the header -section of the data file. If the "create_box"_create_box.html command -is used to define the system, these 2 parameters can be set via its -optional "bond/types" and "extra/bond/per/atom" arguments. See the -doc pages for the 2 commands for details. +:line + +The {single/bond} style creates a single bond of type {btype} between +two atoms with IDs {batom1} and {batom2}. {Btype} must be a value +between 1 and the number of bond types defined. + +The {single/angle} style creates a single angle of type {atype} +between three atoms with IDs {aatom1}, {aatom2}, and {aatom3}. The +ordering of the atoms is the same as in the {Angles} section of a data +file read by the "read_data"_read_data command. I.e. the 3 atoms are +ordered linearly within the angle; the central atom is {aatom2}. +{Atype} must be a value between 1 and the number of angle types +defined. + +The {single/dihedral} style creates a single dihedral of type {btype} +between two atoms with IDs {batom1} and {batom2}. The ordering of the +atoms is the same as in the {Dihedrals} section of a data file read by +the "read_data"_read_data command. I.e. the 4 atoms are ordered +linearly within the dihedral. {Dtype} must be a value between 1 and +the number of dihedral types defined. + +:line + +The keyword {special} controls whether an internal list of special +bonds is created after one or more bonds, or a single angle or +dihedral is added to the system. + +The default value is {yes}. A value of {no} cannot be used +with the {many} style. + +This is an expensive operation since the bond topology for the system +must be walked to find all 1-2, 1-3, 1-4 interactions to store in an +internal list, which is used when pairwise interactions are weighted; +see the "special_bonds"_special_bonds.html command for details. + +Thus if you are adding a few bonds or a large list of angles all at +the same time, by using this command repeatedly, it is more efficient +to only trigger the internal list to be created once, after the last +bond (or angle, or dihedral) is added: + +create_bonds single/bond 5 52 98 special no +create_bonds single/bond 5 73 74 special no +... +create_bonds single/bond 5 17 386 special no +create_bonds single/bond 4 112 183 special yes :pre + +Note that you MUST insure the internal list is re-built after the last +bond (angle, dihedral) is added, before performing a simulation. +Otherwise pairwise interactions will not be properly excluded or +weighted. LAMMPS does NOT check that you have done this correctly. + +:line [Restrictions:] @@ -105,4 +186,6 @@ molecule template files via the "molecule"_molecule.html and "create_atoms"_create_atoms.html, "delete_bonds"_delete_bonds.html -[Default:] none +[Default:] + +The keyword default is special = yes. diff --git a/doc/src/dihedral_charmm.txt b/doc/src/dihedral_charmm.txt index 918755ec38..73dc67cdef 100644 --- a/doc/src/dihedral_charmm.txt +++ b/doc/src/dihedral_charmm.txt @@ -138,7 +138,15 @@ more instructions on how to use the accelerated styles effectively. [Restrictions:] -This dihedral style can only be used if LAMMPS was built with the +When using run_style "respa"_run_style.html, these dihedral styles +must be assigned to the same r-RESPA level as {pair} or {outer}. + +When used in combination with CHARMM pair styles, the 1-4 +"special_bonds"_special_bonds.html scaling factors must be set to 0.0. +Otherwise non-bonded contributions for these 1-4 pairs will be +computed multiple times. + +These dihedral styles can only be used if LAMMPS was built with the MOLECULE package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. diff --git a/doc/src/dihedral_spherical.txt b/doc/src/dihedral_spherical.txt index 3f888db01b..7c17fbf5ef 100644 --- a/doc/src/dihedral_spherical.txt +++ b/doc/src/dihedral_spherical.txt @@ -14,10 +14,11 @@ dihedral_style spherical :pre [Examples:] -dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 -dihedral_coeff 1 3 286.1 1 114 1 1 90 0 1 90.0 0 & - 17.3 0 0.0 0 1 158 1 0 0.0 0 & - 15.1 0 0.0 0 0 0.0 0 1 167.3 1 :pre +dihedral_coeff 1 1 286.1 1 124 1 1 90.0 0 1 90.0 0 +dihedral_coeff 1 3 69.3 1 93.9 1 1 90 0 1 90 0 & + 49.1 0 0.00 0 1 74.4 1 0 0.00 0 & + 25.2 0 0.00 0 0 0.00 0 1 48.1 1 +:pre [Description:] @@ -35,13 +36,14 @@ the dihedral interaction even if it requires adding additional terms to the expansion (as was done in the second example). A careful choice of parameters can prevent singularities that occur with traditional force-fields whenever theta1 or theta2 approach 0 or 180 degrees. + The last example above corresponds to an interaction with a single energy -minima located at phi=114, theta1=158, theta2=167.3 degrees, and it remains +minima located near phi=93.9, theta1=74.4, theta2=48.1 degrees, and it remains numerically stable at all angles (phi, theta1, theta2). In this example, -the coefficients 17.3, and 15.1 can be physically interpreted as the +the coefficients 49.1, and 25.2 can be physically interpreted as the harmonic spring constants for theta1 and theta2 around their minima. -The coefficient 286.1 is the harmonic spring constant for phi after -division by sin(158)*sin(167.3) (the minima positions for theta1 and theta2). +The coefficient 69.3 is the harmonic spring constant for phi after +division by sin(74.4)*sin(48.1) (the minima positions for theta1 and theta2). The following coefficients must be defined for each dihedral type via the "dihedral_coeff"_dihedral_coeff.html command as in the example above, or in diff --git a/doc/src/dump_modify.txt b/doc/src/dump_modify.txt index b5daa6416e..2ea1da3db3 100644 --- a/doc/src/dump_modify.txt +++ b/doc/src/dump_modify.txt @@ -16,7 +16,8 @@ dump-ID = ID of dump to modify :ulb,l one or more keyword/value pairs may be appended :l these keywords apply to various dump styles :l keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} or {flush} or {format} or {image} or {label} or {nfile} or {pad} or {precision} or {region} or {scale} or {sort} or {thresh} or {unwrap} :l - {append} arg = {yes} or {no} + {append} arg = {yes} or {no} or {at} N + N = index of frame written upon first dump {buffer} arg = {yes} or {no} {element} args = E1 E2 ... EN, where N = # of atom types E1,...,EN = element name, e.g. C or Fe or Ga @@ -41,6 +42,7 @@ keyword = {append} or {buffer} or {element} or {every} or {fileper} or {first} o {region} arg = region-ID or "none" {scale} arg = {yes} or {no} {sfactor} arg = coordinate scaling factor (> 0.0) + {thermo} arg = {yes} or {no} {tfactor} arg = time scaling factor (> 0.0) {sort} arg = {off} or {id} or N or -N off = no sorting of per-atom lines within a snapshot @@ -139,12 +141,13 @@ and {dcd}. It also applies only to text output files, not to binary or gzipped or image/movie files. If specified as {yes}, then dump snapshots are appended to the end of an existing dump file. If specified as {no}, then a new dump file will be created which will -overwrite an existing file with the same name. This keyword can only -take effect if the dump_modify command is used after the -"dump"_dump.html command, but before the first command that causes -dump snapshots to be output, e.g. a "run"_run.html or -"minimize"_minimize.html command. Once the dump file has been opened, -this keyword has no further effect. +overwrite an existing file with the same name. If the {at} option is present +({netcdf} only), then the frame to append to can be specified. Negative values +are counted from the end of the file. This keyword can only take effect if the +dump_modify command is used after the "dump"_dump.html command, but before the +first command that causes dump snapshots to be output, e.g. a "run"_run.html or +"minimize"_minimize.html command. Once the dump file has been opened, this +keyword has no further effect. :line @@ -413,6 +416,13 @@ most effective when the typical magnitude of position data is between :line +The {thermo} keyword ({netcdf} only) triggers writing of "thermo"_thermo.html +information to the dump file alongside per-atom data. The data included in the +dump file is identical to the data specified by +"thermo_style"_thermo_style.html. + +:line + The {region} keyword only applies to the dump {custom}, {cfg}, {image}, and {movie} styles. If specified, only atoms in the region will be written to the dump file or included in the image/movie. Only diff --git a/doc/src/dump_netcdf.txt b/doc/src/dump_netcdf.txt index 4e82656698..63568137a6 100644 --- a/doc/src/dump_netcdf.txt +++ b/doc/src/dump_netcdf.txt @@ -24,7 +24,7 @@ args = list of atom attributes, same as for "dump_style custom"_dump.html :l,ule [Examples:] dump 1 all netcdf 100 traj.nc type x y z vx vy vz -dump_modify 1 append yes at -1 global c_thermo_pe c_thermo_temp c_thermo_press +dump_modify 1 append yes at -1 thermo yes dump 1 all netcdf/mpiio 1000 traj.nc id type x y z :pre [Description:] @@ -44,7 +44,7 @@ rank. NetCDF files can be directly visualized via the following tools: Ovito (http://www.ovito.org/). Ovito supports the AMBER convention and -all of the above extensions. :ule,b +all extensions of this dump style. :ule,b VMD (http://www.ks.uiuc.edu/Research/vmd/). :l @@ -52,15 +52,9 @@ AtomEye (http://www.libatoms.org/). The libAtoms version of AtomEye contains a NetCDF reader that is not present in the standard distribution of AtomEye. :l,ule -In addition to per-atom data, global data can be included in the dump -file, which are the kinds of values output by the -"thermo_style"_thermo_style.html command . See "Section howto -6.15"_Section_howto.html#howto_15 for an explanation of per-atom -versus global data. The global output written into the dump file can -be from computes, fixes, or variables, by prefixing the compute/fix ID -or variable name with "c_" or "f_" or "v_" respectively, as in the -example above. These global values are specified via the "dump_modify -global"_dump_modify.html command. +In addition to per-atom data, "thermo"_thermo.html data can be included in the +dump file. The data included in the dump file is identical to the data specified +by "thermo_style"_thermo_style.html. :link(netcdf-home,http://www.unidata.ucar.edu/software/netcdf/) :link(pnetcdf-home,http://trac.mcs.anl.gov/projects/parallel-netcdf/) diff --git a/doc/src/dump_vtk.txt b/doc/src/dump_vtk.txt index 21502e7f49..d4d28c81fc 100644 --- a/doc/src/dump_vtk.txt +++ b/doc/src/dump_vtk.txt @@ -16,7 +16,7 @@ ID = user-assigned name for the dump group-ID = ID of the group of atoms to be dumped vtk = style of dump command (other styles {atom} or {cfg} or {dcd} or {xtc} or {xyz} or {local} or {custom} are discussed on the "dump"_dump.html doc page) N = dump every this many timesteps -file = name of file to write dump info to +file = name of file to write dump info to args = same as arguments for "dump_style custom"_dump.html :ul [Examples:] @@ -83,7 +83,7 @@ Triclinic simulation boxes (non-orthogonal) are saved as hexahedrons in either legacy .vtk or .vtu XML format. Style {vtk} allows you to specify a list of atom attributes to be -written to the dump file for each atom. The list of possible attributes +written to the dump file for each atom. The list of possible attributes is the same as for the "dump_style custom"_dump.html command; see its doc page for a listing and an explanation of each attribute. diff --git a/doc/src/fix_adapt.txt b/doc/src/fix_adapt.txt index d7c32bef3d..19d1009b8a 100644 --- a/doc/src/fix_adapt.txt +++ b/doc/src/fix_adapt.txt @@ -47,7 +47,7 @@ keyword = {scale} or {reset} :l fix 1 all adapt 1 pair soft a 1 1 v_prefactor fix 1 all adapt 1 pair soft a 2* 3 v_prefactor fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes -fix 1 all adapt 10 atom diameter v_size +fix 1 all adapt 10 atom diameter v_size :pre variable ramp_up equal "ramp(0.01,0.5)" fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre diff --git a/doc/src/fix_box_relax.txt b/doc/src/fix_box_relax.txt index 54decd6282..e3d75ee858 100644 --- a/doc/src/fix_box_relax.txt +++ b/doc/src/fix_box_relax.txt @@ -245,7 +245,7 @@ appear the system is converging to your specified pressure. The solution for this is to either (a) zero the velocities of all atoms before performing the minimization, or (b) make sure you are monitoring the pressure without its kinetic component. The latter can -be done by outputting the pressure from the pressure compute this +be done by outputting the pressure from the pressure compute this command creates (see below) or a pressure compute you define yourself. NOTE: Because pressure is often a very sensitive function of volume, diff --git a/doc/src/fix_deform.txt b/doc/src/fix_deform.txt index 8c3a9fa499..d3254eece6 100644 --- a/doc/src/fix_deform.txt +++ b/doc/src/fix_deform.txt @@ -565,8 +565,10 @@ more instructions on how to use the accelerated styles effectively. [Restart, fix_modify, output, run start/stop, minimize info:] -No information about this fix is written to "binary restart -files"_restart.html. None of the "fix_modify"_fix_modify.html options +This fix will restore the initial box settings from "binary restart +files"_restart.html, which allows the fix to be properly continue +deformation, when using the start/stop options of the "run"_run.html +command. None of the "fix_modify"_fix_modify.html options are relevant to this fix. No global or per-atom quantities are stored by this fix for access by various "output commands"_Section_howto.html#howto_15. diff --git a/doc/src/fix_eos_table_rx.txt b/doc/src/fix_eos_table_rx.txt index e8d515e1f3..e5e4f772f6 100644 --- a/doc/src/fix_eos_table_rx.txt +++ b/doc/src/fix_eos_table_rx.txt @@ -45,14 +45,14 @@ species {j} in particle {i}, {u_j} is the internal energy of species j, {DeltaH_f,j} is the heat of formation of species {j}, N is the number of molecules represented by the coarse-grained particle, kb is the Boltzmann constant, and T is the temperature of the system. Additionally, -it is possible to modify the concentration-dependent particle internal -energy relation by adding an energy correction, temperature-dependent +it is possible to modify the concentration-dependent particle internal +energy relation by adding an energy correction, temperature-dependent correction, and/or a molecule-dependent correction. An energy correction can -be specified as a constant (in energy units). A temperature correction can be -specified by multiplying a temperature correction coefficient by the -internal temperature. A molecular correction can be specified by -by multiplying a molecule correction coefficient by the average number of -product gas particles in the coarse-grain particle. +be specified as a constant (in energy units). A temperature correction can be +specified by multiplying a temperature correction coefficient by the +internal temperature. A molecular correction can be specified by +by multiplying a molecule correction coefficient by the average number of +product gas particles in the coarse-grain particle. Fix {eos/table/rx} creates interpolation tables of length {N} from {m} internal energy values of each species {u_j} listed in a file as a @@ -72,12 +72,12 @@ The second filename specifies a file containing heat of formation {DeltaH_f,j} for each species. In cases where the coarse-grain particle represents a single molecular -species (i.e., no reactions occur and fix {rx} is not present in the input file), -fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} -within a non-reactive DPD simulation. In this case, the heat of formation +species (i.e., no reactions occur and fix {rx} is not present in the input file), +fix {eos/table/rx} can be applied in a similar manner to fix {eos/table} +within a non-reactive DPD simulation. In this case, the heat of formation filename is replaced with the heat of formation value for the single species. -Additionally, the energy correction and temperature correction coefficients may -also be specified as fix arguments. +Additionally, the energy correction and temperature correction coefficients may +also be specified as fix arguments. :line @@ -138,8 +138,8 @@ used as the species name must correspond with the tags used to define the reactions with the "fix rx"_fix_rx.html command. Alternatively, corrections to the EOS can be included by specifying -three additional columns that correspond to the energy correction, -the temperature correction coefficient and molecule correction +three additional columns that correspond to the energy correction, +the temperature correction coefficient and molecule correction coefficient. In this case, the format of the file is as follows: # HEAT OF FORMATION TABLE (one or more comment or blank lines) :pre diff --git a/doc/src/fix_filter_corotate.txt b/doc/src/fix_filter_corotate.txt index a3339648fa..b782d285c7 100644 --- a/doc/src/fix_filter_corotate.txt +++ b/doc/src/fix_filter_corotate.txt @@ -70,8 +70,8 @@ minimization"_minimize.html. [Restrictions:] -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. Currently, it does not support "molecule templates"_molecule.html. diff --git a/doc/src/fix_gcmc.txt b/doc/src/fix_gcmc.txt index 7ac607a2f1..41ec38cffb 100644 --- a/doc/src/fix_gcmc.txt +++ b/doc/src/fix_gcmc.txt @@ -406,7 +406,7 @@ the user for each subsequent fix gcmc command. [Default:] The option defaults are mol = no, maxangle = 10, overlap_cutoff = 0.0, -fugacity_coeff = 1, and full_energy = no, +fugacity_coeff = 1, and full_energy = no, except for the situations where full_energy is required, as listed above. diff --git a/doc/src/fix_gle.txt b/doc/src/fix_gle.txt index b8d3cc9b34..6568060f0c 100644 --- a/doc/src/fix_gle.txt +++ b/doc/src/fix_gle.txt @@ -68,7 +68,7 @@ matrix that gives canonical sampling for a given A is computed automatically. However, the GLE framework also allow for non-equilibrium sampling, that can be used for instance to model inexpensively zero-point energy effects "(Ceriotti2)"_#Ceriotti2. This is achieved specifying the {noneq} - keyword followed by the name of the file that contains the static covariance +keyword followed by the name of the file that contains the static covariance matrix for the non-equilibrium dynamics. Please note, that the covariance matrix is expected to be given in [temperature units]. diff --git a/doc/src/fix_grem.txt b/doc/src/fix_grem.txt index 3fc5c1a10e..661f68ed99 100644 --- a/doc/src/fix_grem.txt +++ b/doc/src/fix_grem.txt @@ -85,13 +85,13 @@ No information about this fix is written to "binary restart files"_restart.html. The "thermo_modify"_thermo_modify.html {press} option is supported -by this fix to add the rescaled kinetic pressure as part of +by this fix to add the rescaled kinetic pressure as part of "thermodynamic output"_thermo_style.html. [Restrictions:] -This fix is part of the USER-MISC package. It is only enabled if -LAMMPS was built with that package. See the "Making +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/fix_ipi.txt b/doc/src/fix_ipi.txt index b1533830bc..07e8025d77 100644 --- a/doc/src/fix_ipi.txt +++ b/doc/src/fix_ipi.txt @@ -58,14 +58,14 @@ input are listed in the same order as in the data file of LAMMPS. The initial configuration is ignored, as it will be substituted with the coordinates received from i-PI before forces are ever evaluated. -A note of caution when using potentials that contain long-range +A note of caution when using potentials that contain long-range electrostatics, or that contain parameters that depend on box size: all of these options will be initialized based on the cell size in the -LAMMPS-side initial configuration and kept constant during the run. -This is required to e.g. obtain reproducible and conserved forces. -If the cell varies too wildly, it may be advisable to reinitialize -these interactions at each call. This behavior can be requested by -setting the {reset} switch. +LAMMPS-side initial configuration and kept constant during the run. +This is required to e.g. obtain reproducible and conserved forces. +If the cell varies too wildly, it may be advisable to reinitialize +these interactions at each call. This behavior can be requested by +setting the {reset} switch. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_langevin_drude.txt b/doc/src/fix_langevin_drude.txt index 04437e7f36..afc9c5f257 100644 --- a/doc/src/fix_langevin_drude.txt +++ b/doc/src/fix_langevin_drude.txt @@ -67,11 +67,11 @@ The Langevin forces are computed as \(F_r'\) is a random force proportional to \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tcom\}\, m'\} \{\mathrm dt\, \mathtt\{damp\_com\} \} - \} \). :b + \} \). \(f_r'\) is a random force proportional to \(\sqrt \{ \frac \{2\, k_B \mathtt\{Tdrude\}\, m'\} \{\mathrm dt\, \mathtt\{damp\_drude\} \} - \} \). :b + \} \). Then the real forces acting on the particles are computed from the inverse transform: \begin\{equation\} F = \frac M \{M'\}\, F' - f' \end\{equation\} diff --git a/doc/src/fix_mscg.txt b/doc/src/fix_mscg.txt index 0e09f8a9c5..7d16967955 100644 --- a/doc/src/fix_mscg.txt +++ b/doc/src/fix_mscg.txt @@ -57,7 +57,7 @@ simulations is as follows: Perform all-atom simulations on the system to be coarse grained. Generate a trajectory mapped to the coarse-grained model. Create input files for the MS-CG library. -Run the range finder functionality of the MS-CG library. +Run the range finder functionality of the MS-CG library. Run the force matching functionality of the MS-CG library. Check the results of the force matching. Run coarse-grained simulations using the new coarse-grained potentials. :ol @@ -70,7 +70,7 @@ Step 2 can be performed using a Python script (what is the name?) provided with the MS-CG library which defines the coarse-grained model and converts a standard LAMMPS dump file for an all-atom simulation (step 1) into a LAMMPS dump file which has the positions of and forces -on the coarse-grained beads. +on the coarse-grained beads. In step 3, an input file named "control.in" is needed by the MS-CG library which sets parameters for the range finding and force matching diff --git a/doc/src/fix_msst.txt b/doc/src/fix_msst.txt index bd1edd805a..43f35d6880 100644 --- a/doc/src/fix_msst.txt +++ b/doc/src/fix_msst.txt @@ -17,19 +17,22 @@ msst = style name of this fix :l dir = {x} or {y} or {z} :l shockvel = shock velocity (strictly positive, distance/time units) :l zero or more keyword value pairs may be appended :l -keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} :l +keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l {q} value = cell mass-like parameter (mass^2/distance^4 units) {mu} value = artificial viscosity (mass/length/time units) {p0} value = initial pressure in the shock equations (pressure units) {v0} value = initial simulation cell volume in the shock equations (distance^3 units) {e0} value = initial total energy (energy units) - {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) :pre + {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) + {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+ + {beta} value = scale factor on energy contribution of DFTB+ :pre :ule [Examples:] fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 -fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 :pre +fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4 v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 +fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 dftb yes beta 0.5 :pre [Description:] @@ -58,11 +61,11 @@ oscillations have physical significance in some cases. The optional symmetry to equilibrate to the shock Hugoniot and Rayleigh line more rapidly in such cases. -{tscale} is a factor between 0 and 1 that determines what fraction of -thermal kinetic energy is converted to compressive strain kinetic -energy at the start of the simulation. Setting this parameter to a -non-zero value may assist in compression at the start of simulations -where it is slow to occur. +The keyword {tscale} is a factor between 0 and 1 that determines what +fraction of thermal kinetic energy is converted to compressive strain +kinetic energy at the start of the simulation. Setting this parameter +to a non-zero value may assist in compression at the start of +simulations where it is slow to occur. If keywords {e0}, {p0},or {v0} are not supplied, these quantities will be calculated on the first step, after the energy specified by @@ -77,17 +80,40 @@ For all pressure styles, the simulation box stays orthogonal in shape. Parrinello-Rahman boundary conditions (tilted box) are supported by LAMMPS, but are not implemented for MSST. -This fix computes a temperature and pressure each timestep. To do -this, the fix creates its own computes of style "temp" and "pressure", -as if these commands had been issued: +This fix computes a temperature and pressure and potential energy each +timestep. To do this, the fix creates its own computes of style "temp" +"pressure", and "pe", as if these commands had been issued: -compute fix-ID_temp group-ID temp -compute fix-ID_press group-ID pressure fix-ID_temp :pre +compute fix-ID_MSST_temp all temp +compute fix-ID_MSST_press all pressure fix-ID_MSST_temp :pre +compute fix-ID_MSST_pe all pe :pre See the "compute temp"_compute_temp.html and "compute pressure"_compute_pressure.html commands for details. Note that the -IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID -+ underscore + "press". The group for the new computes is "all". +IDs of the new computes are the fix-ID + "_MSST_temp" or "_MSST_press" +or "_MSST_pe". The group for the new computes is "all". + +:line + +The {dftb} and {beta} keywords are to allow this fix to be used when +LAMMPS is being driven by DFTB+, a density-functional tight-binding +code. + +If the keyword {dftb} is used with a value of {yes}, then the MSST +equations are altered to account for an energy contribution compute by +DFTB+. In this case, you must define a "fix +external"_fix_external.html command in your input script, which is +used to callback to DFTB+ during the LAMMPS timestepping. DFTB+ will +communicate its info to LAMMPS via that fix. + +The keyword {beta} is a scale factor on the DFTB+ energy contribution. +The value of {beta} must be between 0.0 and 1.0 inclusive. A value of +0.0 means no contribution, a value of 1.0 means a full contribution. + +(July 2017) More information about these keywords and the use of +LAMMPS with DFTB+ will be added to the LAMMMPS documention soon. + +:line [Restart, fix_modify, output, run start/stop, minimize info:] @@ -149,8 +175,9 @@ all. [Default:] -The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0 -are calculated on the first step. +The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no, +beta = 0.0. Note that p0, v0, and e0 are calculated on the first +timestep. :line diff --git a/doc/src/fix_neb.txt b/doc/src/fix_neb.txt index 9d11b7289e..52d8a7df84 100644 --- a/doc/src/fix_neb.txt +++ b/doc/src/fix_neb.txt @@ -10,68 +10,183 @@ fix neb command :h3 [Syntax:] -fix ID group-ID neb Kspring :pre +fix ID group-ID neb Kspring keyword value :pre -ID, group-ID are documented in "fix"_fix.html command -neb = style name of this fix command -Kspring = inter-replica spring constant (force/distance units) :ul +ID, group-ID are documented in "fix"_fix.html command :ulb,l +neb = style name of this fix command :l +Kspring = spring constant for parallel nudging force (force/distance units or force units, see parallel keyword) :l +zero or more keyword/value pairs may be appended :l +keyword = {parallel} or {perp} or {end} :l + {parallel} value = {neigh} or {ideal} + {neigh} = parallel nudging force based on distance to neighbor replicas (Kspring = force/distance units) + {ideal} = parallel nudging force based on interpolated ideal position (Kspring = force units) + {perp} value = {Kspring2} + {Kspring2} = spring constant for perpendicular nudging force (force/distance units) + {end} values = estyle Kspring3 + {estyle} = {first} or {last} or {last/efirst} or {last/efirst/middle} + {first} = apply force to first replica + {last} = apply force to last replica + {last/efirst} = apply force to last replica and set its target energy to that of first replica + {last/efirst/middle} = same as {last/efirst} plus prevent middle replicas having lower energy than first replica + {Kspring3} = spring constant for target energy term (1/distance units) :pre,ule [Examples:] -fix 1 active neb 10.0 :pre +fix 1 active neb 10.0 +fix 2 all neb 1.0 perp 1.0 end last +fix 2 all neb 1.0 perp 1.0 end first 1.0 end last 1.0 +fix 1 all neb 1.0 nudge ideal end last/efirst 1 :pre [Description:] -Add inter-replica forces to atoms in the group for a multi-replica +Add nudging forces to atoms in the group for a multi-replica simulation run via the "neb"_neb.html command to perform a nudged -elastic band (NEB) calculation for transition state finding. Hi-level -explanations of NEB are given with the "neb"_neb.html command and in -"Section 6.5"_Section_howto.html#howto_5 of the manual. The fix -neb command must be used with the "neb" command to define how -inter-replica forces are computed. +elastic band (NEB) calculation for finding the transition state. +Hi-level explanations of NEB are given with the "neb"_neb.html command +and in "Section_howto 5"_Section_howto.html#howto_5 of the manual. +The fix neb command must be used with the "neb" command and defines +how inter-replica nudging forces are computed. A NEB calculation is +divided in two stages. In the first stage n replicas are relaxed +toward a MEP until convergence. In the second stage, the climbing +image scheme (see "(Henkelman2)"_#Henkelman2) is enabled, so that the +replica having the highest energy relaxes toward the saddle point +(i.e. the point of highest energy along the MEP), and a second +relaxation is performed. -Only the N atoms in the fix group experience inter-replica forces. -Atoms in the two end-point replicas do not experience these forces, -but those in intermediate replicas do. During the initial stage of -NEB, the 3N-length vector of interatomic forces Fi = -Grad(V) acting -on the atoms of each intermediate replica I is altered, as described -in the "(Henkelman1)"_#Henkelman1 paper, to become: +A key purpose of the nudging forces is to keep the replicas equally +spaced. During the NEB calculation, the 3N-length vector of +interatomic force Fi = -Grad(V) for each replica I is altered. For +all intermediate replicas (i.e. for 1 < I < N, except the climbing +replica) the force vector becomes: -Fi = -Grad(V) + (Grad(V) dot That) That + Kspring (| Ri+i - Ri | - | Ri - Ri-1 |) That :pre +Fi = -Grad(V) + (Grad(V) dot T') T' + Fnudge_parallel + Fnudge_perp :pre -Ri are the atomic coordinates of replica I; Ri-1 and Ri+1 are the -coordinates of its neighbor replicas. That (t with a hat over it) is -the unit "tangent" vector for replica I which is a function of Ri, +T' is the unit "tangent" vector for replica I and is a function of Ri, Ri-1, Ri+1, and the potential energy of the 3 replicas; it points roughly in the direction of (Ri+i - Ri-1); see the -"(Henkelman1)"_#Henkelman1 paper for details. +"(Henkelman1)"_#Henkelman1 paper for details. Ri are the atomic +coordinates of replica I; Ri-1 and Ri+1 are the coordinates of its +neighbor replicas. The term (Grad(V) dot T') is used to remove the +component of the gradient parallel to the path which would tend to +distribute the replica unevenly along the path. Fnudge_parallel is an +artificial nudging force which is applied only in the tangent +direction and which maintains the equal spacing between replicas (see +below for more information). Fnudge_perp is an optional artificial +spring which is applied in a direction perpendicular to the tangent +direction and which prevent the paths from forming acute kinks (see +below for more information). -The first two terms in the above equation are the component of the -interatomic forces perpendicular to the tangent vector. The last term -is a spring force between replica I and its neighbors, parallel to the -tangent vector direction with the specified spring constant {Kspring}. +In the second stage of the NEB calculation, the interatomic force Fi +for the climbing replica (the replica of highest energy after the +first stage) is changed to: -The effect of the first two terms is to push the atoms of each replica -toward the minimum energy path (MEP) of conformational states that -transition over the energy barrier. The MEP for an energy barrier is -defined as a sequence of 3N-dimensional states which cross the barrier -at its saddle point, each of which has a potential energy gradient -parallel to the MEP itself. +Fi = -Grad(V) + 2 (Grad(V) dot T') T' :pre -The effect of the last term is to push each replica away from its two -neighbors in a direction along the MEP, so that the final set of -states are equidistant from each other. +and the relaxation procedure is continued to a new converged MEP. -During the second stage of NEB, the forces on the N atoms in the -replica nearest the top of the energy barrier are altered so that it -climbs to the top of the barrier and finds the saddle point. The -forces on atoms in this replica are described in the -"(Henkelman2)"_#Henkelman2 paper, and become: +:line -Fi = -Grad(V) + 2 (Grad(V) dot That) That :pre +The keyword {parallel} specifies how the parallel nudging force is +computed. With a value of {neigh}, the parallel nudging force is +computed as in "(Henkelman1)"_#Henkelman1 by connecting each +intermediate replica with the previous and the next image: -The inter-replica forces for the other replicas are unchanged from the -first equation. +Fnudge_parallel = {Kspring} * (|Ri+1 - Ri| - |Ri - Ri-1|) :pre + +Note that in this case the specified {Kspring) is in force/distance +units. + +With a value of {ideal}, the spring force is computed as suggested in +"(WeinenE)"_#WeinenE : + +Fnudge_parallel = -{Kspring} * (RD-RDideal) / (2 * meanDist) :pre + +where RD is the "reaction coordinate" see "neb"_neb.html section, and +RDideal is the ideal RD for which all the images are equally spaced. +I.e. RDideal = (I-1)*meanDist when the climbing replica is off, where +I is the replica number). The meanDist is the average distance +between replicas. Note that in this case the specified {Kspring) is +in force units. + +Note that the {ideal} form of nudging can often be more effective at +keeping the replicas equally spaced. + +:line + +The keyword {perp} specifies if and how a perpendicual nudging force +is computed. It adds a spring force perpendicular to the path in +order to prevent the path from becoming too kinky. It can +significantly improve the convergence of the NEB calculation when the +resolution is poor. I.e. when few replicas are used; see +"(Maras)"_#Maras1 for details. + +The perpendicular spring force is given by + +Fnudge_perp = {Kspring2} * F(Ri-1,Ri,Ri+1) (Ri+1 + Ri-1 - 2 Ri) :pre + +where {Kspring2} is the specified value. F(Ri-1 Ri R+1) is a smooth +scalar function of the angle Ri-1 Ri Ri+1. It is equal to 0.0 when +the path is straight and is equal to 1 when the angle Ri-1 Ri Ri+1 is +acute. F(Ri-1 Ri R+1) is defined in "(Jonsson)"_#Jonsson. + +If {Kspring2} is set to 0.0 (the default) then no perpendicular spring +force is added. + +:line + +By default, no additional forces act on the first and last replicas +during the NEB relaxation, so these replicas simply relax toward their +respective local minima. By using the key word {end}, additional +forces can be applied to the first and/or last replicas, to enable +them to relax toward a MEP while constraining their energy. + +The interatomic force Fi for the specified replica becomes: + +Fi = -Grad(V) + (Grad(V) dot T' + (E-ETarget)*Kspring3) T', {when} Grad(V) dot T' < 0 +Fi = -Grad(V) + (Grad(V) dot T' + (ETarget- E)*Kspring3) T', {when} Grad(V) dot T' > 0 +:pre + +where E is the current energy of the replica and ETarget is the target +energy. The "spring" constant on the difference in energies is the +specified {Kspring3} value. + +When {estyle} is specified as {first}, the force is applied to the +first replica. When {estyle} is specified as {last}, the force is +applied to the last replica. Note that the {end} keyword can be used +twice to add forces to both the first and last replicas. + +For both these {estyle} settings, the target energy {ETarget} is set +to the initial energy of the replica (at the start of the NEB +calculation). + +If the {estyle} is specified as {last/efirst} or {last/efirst/middle}, +force is applied to the last replica, but the target energy {ETarget} +is continuously set to the energy of the first replica, as it evolves +during the NEB relaxation. + +The difference between these two {estyle} options is as follows. When +{estyle} is specified as {last/efirst}, no change is made to the +inter-replica force applied to the intermediate replicas (neither +first or last). If the initial path is too far from the MEP, an +intermediate repilica may relax "faster" and reach a lower energy than +the last replica. In this case the intermediate replica will be +relaxing toward its own local minima. This behavior can be prevented +by specifying {estyle} as {last/efirst/middle} which will alter the +inter-replica force applied to intermediate replicas by removing the +contribution of the gradient to the inter-replica force. This will +only be done if a particular intermediate replica has a lower energy +than the first replica. This should effectively prevent the +intermediate replicas from over-relaxing. + +After converging a NEB calculation using an {estyle} of +{last/efirst/middle}, you should check that all intermediate replicas +have a larger energy than the first replica. If this is not the case, +the path is probably not a MEP. + +Finally, note that if the last replica converges toward a local +minimum which has a larger energy than the energy of the first +replica, a NEB calculation using an {estyle} of {last/efirst} or +{last/efirst/middle} cannot reach final convergence. [Restart, fix_modify, output, run start/stop, minimize info:] @@ -96,7 +211,12 @@ for more info on packages. "neb"_neb.html -[Default:] none +[Default:] + +The option defaults are nudge = neigh, perp = 0.0, ends is not +specified (no inter-replica force on the end replicas). + +:line :link(Henkelman1) [(Henkelman1)] Henkelman and Jonsson, J Chem Phys, 113, 9978-9985 (2000). @@ -104,3 +224,15 @@ for more info on packages. :link(Henkelman2) [(Henkelman2)] Henkelman, Uberuaga, Jonsson, J Chem Phys, 113, 9901-9904 (2000). + +:link(WeinenE) +[(WeinenE)] E, Ren, Vanden-Eijnden, Phys Rev B, 66, 052301 (2002). + +:link(Jonsson) +[(Jonsson)] Jonsson, Mills and Jacobsen, in Classical and Quantum +Dynamics in Condensed Phase Simulations, edited by Berne, Ciccotti, +and Coker World Scientific, Singapore, 1998, p 385. + +:link(Maras1) +[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, +Comp Phys Comm, 205, 13-21 (2016). diff --git a/doc/src/fix_nve_dot.txt b/doc/src/fix_nve_dot.txt index b1c00cd25c..7ad51f3768 100644 --- a/doc/src/fix_nve_dot.txt +++ b/doc/src/fix_nve_dot.txt @@ -23,13 +23,13 @@ fix 1 all nve/dot :pre [Description:] Apply a rigid-body integrator as described in "(Davidchack)"_#Davidchack1 -to a group of atoms, but without Langevin dynamics. +to a group of atoms, but without Langevin dynamics. This command performs Molecular dynamics (MD) -via a velocity-Verlet algorithm and an evolution operator that rotates -the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. +via a velocity-Verlet algorithm and an evolution operator that rotates +the quaternion degrees of freedom, similar to the scheme outlined in "(Miller)"_#Miller1. This command is the equivalent of the "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html -without damping and noise and can be used to determine the stability range +without damping and noise and can be used to determine the stability range in a NVE ensemble prior to using the Langevin-type DOTC-integrator (see also "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html). The command is equivalent to the "fix nve"_fix_nve.html. diff --git a/doc/src/fix_nve_dotc_langevin.txt b/doc/src/fix_nve_dotc_langevin.txt index 19d5b233ce..5de8e663c4 100644 --- a/doc/src/fix_nve_dotc_langevin.txt +++ b/doc/src/fix_nve_dotc_langevin.txt @@ -28,20 +28,20 @@ fix 1 all nve/dotc/langevin 1.0 1.0 0.03 457145 angmom 10 :pre [Description:] -Apply a rigid-body Langevin-type integrator of the kind "Langevin C" +Apply a rigid-body Langevin-type integrator of the kind "Langevin C" as described in "(Davidchack)"_#Davidchack2 to a group of atoms, which models an interaction with an implicit background solvent. This command performs Brownian dynamics (BD) -via a technique that splits the integration into a deterministic Hamiltonian -part and the Ornstein-Uhlenbeck process for noise and damping. +via a technique that splits the integration into a deterministic Hamiltonian +part and the Ornstein-Uhlenbeck process for noise and damping. The quaternion degrees of freedom are updated though an evolution operator which performs a rotation in quaternion space, preserves the quaternion norm and is akin to "(Miller)"_#Miller2. -In terms of syntax this command has been closely modelled on the -"fix langevin"_fix_langevin.html and its {angmom} option. But it combines -the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in -one single command. The main feature is improved stability +In terms of syntax this command has been closely modelled on the +"fix langevin"_fix_langevin.html and its {angmom} option. But it combines +the "fix nve"_fix_nve.html and the "fix langevin"_fix_langevin.html in +one single command. The main feature is improved stability over the standard integrator, permitting slightly larger timestep sizes. NOTE: Unlike the "fix langevin"_fix_langevin.html this command performs @@ -57,7 +57,7 @@ Fc is the conservative force computed via the usual inter-particle interactions ("pair_style"_pair_style.html, "bond_style"_bond_style.html, etc). -The Ff and Fr terms are implicitly taken into account by this fix +The Ff and Fr terms are implicitly taken into account by this fix on a per-particle basis. Ff is a frictional drag or viscous damping term proportional to the @@ -77,7 +77,7 @@ a Gaussian random number) for speed. :line -{Tstart} and {Tstop} have to be constant values, i.e. they cannot +{Tstart} and {Tstop} have to be constant values, i.e. they cannot be variables. The {damp} parameter is specified in time units and determines how @@ -98,16 +98,16 @@ different numbers of processors. The keyword/value option has to be used in the following way: -This fix has to be used together with the {angmom} keyword. The -particles are always considered to have a finite size. -The keyword {angmom} enables thermostatting of the rotational degrees of -freedom in addition to the usual translational degrees of freedom. +This fix has to be used together with the {angmom} keyword. The +particles are always considered to have a finite size. +The keyword {angmom} enables thermostatting of the rotational degrees of +freedom in addition to the usual translational degrees of freedom. -The scale factor after the {angmom} keyword gives the ratio of the rotational to +The scale factor after the {angmom} keyword gives the ratio of the rotational to the translational friction coefficient. An example input file can be found in /examples/USER/cgdna/examples/duplex2/. -A technical report with more information on this integrator can be found +A technical report with more information on this integrator can be found "here"_PDF/USER-CGDNA-overview.pdf. :line @@ -120,7 +120,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, +"fix nve"_fix_nve.html, "fix langevin"_fix_langevin.html, "fix nve/dot"_fix_nve_dot.html, [Default:] none diff --git a/doc/src/fix_nvk.txt b/doc/src/fix_nvk.txt index 271483b441..49fd8217ab 100644 --- a/doc/src/fix_nvk.txt +++ b/doc/src/fix_nvk.txt @@ -27,7 +27,7 @@ timestep. V is volume; K is kinetic energy. This creates a system trajectory consistent with the isokinetic ensemble. The equations of motion used are those of Minary et al in -"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in +"(Minary)"_#nvk-Minary, a variant of those initially given by Zhang in "(Zhang)"_#nvk-Zhang. The kinetic energy will be held constant at its value given when fix diff --git a/doc/src/fix_qeq_reax.txt b/doc/src/fix_qeq_reax.txt index aed043f6c0..a1a19b7368 100644 --- a/doc/src/fix_qeq_reax.txt +++ b/doc/src/fix_qeq_reax.txt @@ -8,17 +8,19 @@ fix qeq/reax command :h3 fix qeq/reax/kk command :h3 +fix qeq/reax/omp command :h3 [Syntax:] -fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params :pre +fix ID group-ID qeq/reax Nevery cutlo cuthi tolerance params args :pre ID, group-ID are documented in "fix"_fix.html command qeq/reax = style name of this fix command Nevery = perform QEq every this many steps cutlo,cuthi = lo and hi cutoff for Taper radius tolerance = precision to which charges will be equilibrated -params = reax/c or a filename :ul +params = reax/c or a filename +args = {dual} (optional) :ul [Examples:] @@ -59,6 +61,10 @@ potential file, except that eta is defined here as twice the eta value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units of this fix are hard-coded to be A, eV, and electronic charge. +The optional {dual} keyword allows to perform the optimization +of the S and T matrices in parallel. This is only supported for +the {qeq/reax/omp} style. Otherwise they are processed separately. + [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart diff --git a/doc/src/fix_reax_bonds.txt b/doc/src/fix_reax_bonds.txt index a874fa3d16..aadb0a9cbc 100644 --- a/doc/src/fix_reax_bonds.txt +++ b/doc/src/fix_reax_bonds.txt @@ -34,7 +34,20 @@ written to {filename} on timesteps that are multiples of {Nevery}, including timestep 0. For time-averaged chemical species analysis, please see the "fix reaxc/c/species"_fix_reaxc_species.html command. -The format of the output file should be self-explanatory. +The format of the output file should be reasonably self-explanatory. +The meaning of the column header abbreviations is as follows: + +id = atom id +type = atom type +nb = number of bonds +id_1 = atom id of first bond +id_nb = atom id of Nth bond +mol = molecule id +bo_1 = bond order of first bond +bo_nb = bond order of Nth bond +abo = atom bond order (sum of all bonds) +nlp = number of lone pairs +q = atomic charge :ul If the filename ends with ".gz", the output file is written in gzipped format. A gzipped dump file will be about 3x smaller than the text diff --git a/doc/src/fix_rigid.txt b/doc/src/fix_rigid.txt index 03edf61ed8..dbadd3fa63 100644 --- a/doc/src/fix_rigid.txt +++ b/doc/src/fix_rigid.txt @@ -31,11 +31,12 @@ bodystyle = {single} or {molecule} or {group} :l groupID1, groupID2, ... = list of N group IDs :pre zero or more keyword/value pairs may be appended :l -keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l +keyword = {langevin} or {reinit} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {couple} or {tparam} or {pchain} or {dilate} or {force} or {torque} or {infile} :l {langevin} values = Tstart Tstop Tperiod seed Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) seed = random number seed to use for white noise (positive integer) + {reinit} = {yes} or {no} {temp} values = Tstart Tstop Tdamp Tstart,Tstop = desired temperature at start/stop of run (temperature units) Tdamp = temperature damping parameter (time units) @@ -68,10 +69,10 @@ keyword = {langevin} or {temp} or {iso} or {aniso} or {x} or {y} or {z} or {coup [Examples:] -fix 1 clump rigid single +fix 1 clump rigid single reinit yes fix 1 clump rigid/small molecule fix 1 clump rigid single force 1 off off on langevin 1.0 1.0 1.0 428984 -fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 +fix 1 polychains rigid/nvt molecule temp 1.0 1.0 5.0 reinit no fix 1 polychains rigid molecule force 1*5 off off off force 6*10 off off on fix 1 polychains rigid/small molecule langevin 1.0 1.0 1.0 428984 fix 2 fluid rigid group 3 clump1 clump2 clump3 torque * off off off @@ -87,7 +88,12 @@ means that each timestep the total force and torque on each rigid body is computed as the sum of the forces and torques on its constituent particles. The coordinates, velocities, and orientations of the atoms in each body are then updated so that the body moves and rotates as a -single entity. +single entity. This is implemented by creating internal data structures +for each rigid body and performing time integration on these data +structures. Positions, velocities, and orientations of the constituent +particles are regenerated from the rigid body data structures in every +time step. This restricts which operations and fixes can be applied to +rigid bodies. See below for a detailed discussion. Examples of large rigid bodies are a colloidal particle, or portions of a biomolecule such as a protein. @@ -148,8 +154,9 @@ differences may accumulate to produce divergent trajectories. NOTE: You should not update the atoms in rigid bodies via other time-integration fixes (e.g. "fix nve"_fix_nve.html, "fix -nvt"_fix_nh.html, "fix npt"_fix_nh.html), or you will be integrating -their motion more than once each timestep. When performing a hybrid +nvt"_fix_nh.html, "fix npt"_fix_nh.html, "fix move"_fix_move.html), +or you will have conflicting updates to positions and velocities +resulting in unphysical behavior in most cases. When performing a hybrid simulation with some atoms in rigid bodies, and some not, a separate time integration fix like "fix nve"_fix_nve.html or "fix nvt"_fix_nh.html should be used for the non-rigid particles. @@ -165,23 +172,29 @@ setting the force on them to 0.0 (via the "fix setforce"_fix_setforce.html command), and integrating them as usual (e.g. via the "fix nve"_fix_nve.html command). -NOTE: The aggregate properties of each rigid body are calculated one -time at the start of the first simulation run after these fixes are -specified. The properties include the position and velocity of the -center-of-mass of the body, its moments of inertia, and its angular -momentum. This is done using the properties of the constituent atoms -of the body at that point in time (or see the {infile} keyword -option). Thereafter, changing properties of individual atoms in the -body will have no effect on a rigid body's dynamics, unless they -affect the "pair_style"_pair_style.html interactions that individual -particles are part of. For example, you might think you could -displace the atoms in a body or add a large velocity to each atom in a -body to make it move in a desired direction before a 2nd run is +IMPORTANT NOTE: The aggregate properties of each rigid body are +calculated at the start of a simulation run and are maintained in +internal data structures. The properties include the position and +velocity of the center-of-mass of the body, its moments of inertia, and +its angular momentum. This is done using the properties of the +constituent atoms of the body at that point in time (or see the {infile} +keyword option). Thereafter, changing these properties of individual +atoms in the body will have no effect on a rigid body's dynamics, unless +they effect any computation of per-atom forces or torques. If the +keyword {reinit} is set to {yes} (the default), the rigid body data +structures will be recreated at the beginning of each {run} command; +if the keyword {reinit} is set to {no}, the rigid body data structures +will be built only at the very first {run} command and maintained for +as long as the rigid fix is defined. For example, you might think you +could displace the atoms in a body or add a large velocity to each atom +in a body to make it move in a desired direction before a 2nd run is performed, using the "set"_set.html or "displace_atoms"_displace_atoms.html or "velocity"_velocity.html -command. But these commands will not affect the internal attributes -of the body, and the position and velocity of individual atoms in the -body will be reset when time integration starts. +commands. But these commands will not affect the internal attributes +of the body unless {reinit} is set to {yes}. With {reinit} set to {no} +(or using the {infile} option, which implies {reinit} {no}) the position +and velocity of individual atoms in the body will be reset when time +integration starts again. :line @@ -401,6 +414,14 @@ couple none :pre The keyword/value option pairs are used in the following ways. +The {reinit} keyword determines, whether the rigid body properties +are reinitialized between run commands. With the option {yes} (the +default) this is done, with the option {no} this is not done. Turning +off the reinitialization can be helpful to protect rigid bodies against +unphysical manipulations between runs or when properties cannot be +easily recomputed (e.g. when read from a file). When using the {infile} +keyword, the {reinit} option is automatically set to {no}. + The {langevin} and {temp} and {tparam} keywords perform thermostatting of the rigid bodies, altering both their translational and rotational degrees of freedom. What is meant by "temperature" of a collection of @@ -778,7 +799,7 @@ exclude, "fix shake"_fix_shake.html The option defaults are force * on on on and torque * on on on, meaning all rigid bodies are acted on by center-of-mass force and -torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3. +torque. Also Tchain = Pchain = 10, Titer = 1, Torder = 3, reinit = yes. :line diff --git a/doc/src/fix_spring.txt b/doc/src/fix_spring.txt index 5f94f4cdae..014a43aacc 100644 --- a/doc/src/fix_spring.txt +++ b/doc/src/fix_spring.txt @@ -89,7 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in group can straddle a periodic boundary. See the "dump"_dump.html doc page for a discussion of unwrapped coordinates. It also means that a spring connecting two groups or a group and the tether point can cross -a periodic boundary and its length be calculated correctly. +a periodic boundary and its length be calculated correctly. [Restart, fix_modify, output, run start/stop, minimize info:] diff --git a/doc/src/fix_ti_spring.txt b/doc/src/fix_ti_spring.txt index 40e595e21e..afb1dcf8ff 100644 --- a/doc/src/fix_ti_spring.txt +++ b/doc/src/fix_ti_spring.txt @@ -144,7 +144,11 @@ this fix. "fix spring"_fix_spring.html, "fix adapt"_fix_adapt.html -[Restrictions:] none +[Restrictions:] + +This fix is part of the USER-MISC package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. [Default:] diff --git a/doc/src/kspace_modify.txt b/doc/src/kspace_modify.txt index b488df9627..6d27bb7076 100644 --- a/doc/src/kspace_modify.txt +++ b/doc/src/kspace_modify.txt @@ -219,10 +219,10 @@ instead of using the virial equation. This option cannot be used to access individual components of the pressure tensor, to compute per-atom virial, or with suffix kspace/pair styles of MSM, like OMP or GPU. -The {fftbench} keyword applies only to PPPM. It is on by default. If -this option is turned off, LAMMPS will not take the time at the end -of a run to give FFT benchmark timings, and will finish a few seconds -faster than it would if this option were on. +The {fftbench} keyword applies only to PPPM. It is off by default. If +this option is turned on, LAMMPS will perform a short FFT benchmark +computation and report its timings, and will thus finish a some seconds +later than it would if this option were off. The {collective} keyword applies only to PPPM. It is set to {no} by default, except on IBM BlueGene machines. If this option is set to @@ -306,9 +306,10 @@ parameters, see the "How-To"_Section_howto.html#howto_24 discussion. The option defaults are mesh = mesh/disp = 0 0 0, order = order/disp = 5 (PPPM), order = 10 (MSM), minorder = 2, overlap = yes, force = -1.0, gewald = gewald/disp = 0.0, slab = 1.0, compute = yes, cutoff/adjust = -yes (MSM), pressure/scalar = yes (MSM), fftbench = yes (PPPM), diff = ik +yes (MSM), pressure/scalar = yes (MSM), fftbench = no (PPPM), diff = ik (PPPM), mix/disp = pair, force/disp/real = -1.0, force/disp/kspace = -1.0, -split = 0, tol = 1.0e-6, and disp/auto = no. +split = 0, tol = 1.0e-6, and disp/auto = no. For pppm/intel, order = +order/disp = 7. :line diff --git a/doc/src/kspace_style.txt b/doc/src/kspace_style.txt index 371540bd68..4f27c9aa78 100644 --- a/doc/src/kspace_style.txt +++ b/doc/src/kspace_style.txt @@ -33,12 +33,16 @@ style = {none} or {ewald} or {ewald/disp} or {ewald/omp} or {pppm} or {pppm/cg} accuracy = desired relative error in forces {pppm/gpu} value = accuracy accuracy = desired relative error in forces + {pppm/intel} value = accuracy + accuracy = desired relative error in forces {pppm/kk} value = accuracy accuracy = desired relative error in forces {pppm/omp} value = accuracy accuracy = desired relative error in forces {pppm/cg/omp} value = accuracy accuracy = desired relative error in forces + {pppm/disp/intel} value = accuracy + accuracy = desired relative error in forces {pppm/tip4p/omp} value = accuracy accuracy = desired relative error in forces {pppm/stagger} value = accuracy diff --git a/doc/src/lammps.book b/doc/src/lammps.book index 6b3ca8aa07..d901ef3f77 100644 --- a/doc/src/lammps.book +++ b/doc/src/lammps.book @@ -237,6 +237,7 @@ fix_pour.html fix_press_berendsen.html fix_print.html fix_property_atom.html +fix_python.html fix_qbmsst.html fix_qeq.html fix_qeq_comb.html @@ -300,6 +301,7 @@ compute_centro_atom.html compute_chunk_atom.html compute_cluster_atom.html compute_cna_atom.html +compute_cnp_atom.html compute_com.html compute_com_chunk.html compute_contact_atom.html @@ -432,6 +434,7 @@ pair_gauss.html pair_gayberne.html pair_gran.html pair_gromacs.html +pair_gw.html pair_hbond_dreiding.html pair_hybrid.html pair_kim.html @@ -444,7 +447,6 @@ pair_lj96.html pair_lj_cubic.html pair_lj_expand.html pair_lj_long.html -pair_lj_sf.html pair_lj_smooth.html pair_lj_smooth_linear.html pair_lj_soft.html @@ -467,6 +469,7 @@ pair_oxdna.html pair_oxdna2.html pair_peri.html pair_polymorphic.html +pair_python.html pair_quip.html pair_reax.html pair_reaxc.html diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt index 9f0082d5dc..c9bb1ce57f 100644 --- a/doc/src/manifolds.txt +++ b/doc/src/manifolds.txt @@ -24,14 +24,15 @@ to the relevant fixes. {manifold} @ {parameters} @ {equation} @ {description} cylinder @ R @ x^2 + y^2 - R^2 = 0 @ Cylinder along z-axis, axis going through (0,0,0) cylinder_dent @ R l a @ x^2 + y^2 - r(z)^2 = 0, r(x) = R if | z | > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise @ A cylinder with a dent around z = 0 -dumbbell @ a A B c @ -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell @ +dumbbell @ a A B c @ -( x^2 + y^2 ) + (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 @ A dumbbell ellipsoid @ a b c @ (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 @ An ellipsoid +gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0. plane @ a b c x0 y0 z0 @ a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 @ A plane with normal (a,b,c) going through point (x0,y0,z0) plane_wiggle @ a w @ z - a*sin(w*x) = 0 @ A plane with a sinusoidal modulation on z along x. sphere @ R @ x^2 + y^2 + z^2 - R^2 = 0 @ A sphere of radius R supersphere @ R q @ | x |^q + | y |^q + | z |^q - R^q = 0 @ A supersphere of hyperradius R -spine @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine -spine_two @ a, A, B, B2, c @ -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine +spine @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ An approximation to a dendtritic spine +spine_two @ a, A, B, B2, c @ -(x^2 + y^2) + (a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^2), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise @ Another approximation to a dendtritic spine thylakoid @ wB LB lB @ Various, see "(Paquay)"_#Paquay1 @ A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB torus @ R r @ (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 @ A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=@) diff --git a/doc/src/neb.txt b/doc/src/neb.txt index 3a62a77a6e..d2e8be3f03 100644 --- a/doc/src/neb.txt +++ b/doc/src/neb.txt @@ -10,28 +10,31 @@ neb command :h3 [Syntax:] -neb etol ftol N1 N2 Nevery file-style arg :pre +neb etol ftol N1 N2 Nevery file-style arg keyword :pre etol = stopping tolerance for energy (energy units) :ulb,l ftol = stopping tolerance for force (force units) :l N1 = max # of iterations (timesteps) to run initial NEB :l N2 = max # of iterations (timesteps) to run barrier-climbing NEB :l Nevery = print replica energies and reaction coordinates every this many timesteps :l -file-style= {final} or {each} or {none} :l +file-style = {final} or {each} or {none} :l {final} arg = filename filename = file with initial coords for final replica - coords for intermediate replicas are linearly interpolated between first and last replica + coords for intermediate replicas are linearly interpolated + between first and last replica {each} arg = filename - filename = unique filename for each replica (except first) with its initial coords - {none} arg = no argument - all replicas assumed to already have their initial coords :pre + filename = unique filename for each replica (except first) + with its initial coords + {none} arg = no argument all replicas assumed to already have + their initial coords :pre +keyword = {verbose} :ule [Examples:] neb 0.1 0.0 1000 500 50 final coords.final neb 0.0 0.001 1000 500 50 each coords.initial.$i -neb 0.0 0.001 1000 500 50 none :pre +neb 0.0 0.001 1000 500 50 none verbose :pre [Description:] @@ -43,8 +46,8 @@ NEB is a method for finding both the atomic configurations and height of the energy barrier associated with a transition state, e.g. for an atom to perform a diffusive hop from one energy basin to another in a coordinated fashion with its neighbors. The implementation in LAMMPS -follows the discussion in these 3 papers: "(HenkelmanA)"_#HenkelmanA, -"(HenkelmanB)"_#HenkelmanB, and "(Nakano)"_#Nakano3. +follows the discussion in these 4 papers: "(HenkelmanA)"_#HenkelmanA, +"(HenkelmanB)"_#HenkelmanB, "(Nakano)"_#Nakano3 and "(Maras)"_#Maras2. Each replica runs on a partition of one or more processors. Processor partitions are defined at run-time using the -partition command-line @@ -70,18 +73,17 @@ I.e. the simulation domain, the number of atoms, the interaction potentials, and the starting configuration when the neb command is issued should be the same for every replica. -In a NEB calculation each atom in a replica is connected to the same -atom in adjacent replicas by springs, which induce inter-replica -forces. These forces are imposed by the "fix neb"_fix_neb.html -command, which must be used in conjunction with the neb command. The -group used to define the fix neb command defines the NEB atoms which -are the only ones that inter-replica springs are applied to. If the -group does not include all atoms, then non-NEB atoms have no -inter-replica springs and the forces they feel and their motion is -computed in the usual way due only to other atoms within their -replica. Conceptually, the non-NEB atoms provide a background force -field for the NEB atoms. They can be allowed to move during the NEB -minimization procedure (which will typically induce different +In a NEB calculation each replica is connected to other replicas by +inter-replica nudging forces. These forces are imposed by the "fix +neb"_fix_neb.html command, which must be used in conjunction with the +neb command. The group used to define the fix neb command defines the +NEB atoms which are the only ones that inter-replica springs are +applied to. If the group does not include all atoms, then non-NEB +atoms have no inter-replica springs and the forces they feel and their +motion is computed in the usual way due only to other atoms within +their replica. Conceptually, the non-NEB atoms provide a background +force field for the NEB atoms. They can be allowed to move during the +NEB minimization procedure (which will typically induce different coordinates for non-NEB atoms in different replicas), or held fixed using other LAMMPS commands such as "fix setforce"_fix_setforce.html. Note that the "partition"_partition.html command can be used to invoke @@ -93,33 +95,18 @@ specified in different manners via the {file-style} setting, as discussed below. Only atoms whose initial coordinates should differ from the current configuration need be specified. -Conceptually, the initial configuration for the first replica should -be a state with all the atoms (NEB and non-NEB) having coordinates on -one side of the energy barrier. A perfect energy minimum is not -required, since atoms in the first replica experience no spring forces -from the 2nd replica. Thus the damped dynamics minimization will -drive the first replica to an energy minimum if it is not already -there. However, you will typically get better convergence if the -initial state is already at a minimum. For example, for a system with -a free surface, the surface should be fully relaxed before attempting -a NEB calculation. - -Likewise, the initial configuration of the final replica should be a -state with all the atoms (NEB and non-NEB) on the other side of the -energy barrier. Again, a perfect energy minimum is not required, -since the atoms in the last replica also experience no spring forces -from the next-to-last replica, and thus the damped dynamics -minimization will drive it to an energy minimum. +Conceptually, the initial and final configurations for the first +replica should be states on either side of an energy barrier. As explained below, the initial configurations of intermediate replicas can be atomic coordinates interpolated in a linear fashion -between the first and last replicas. This is often adequate state for +between the first and last replicas. This is often adequate for simple transitions. For more complex transitions, it may lead to slow convergence or even bad results if the minimum energy path (MEP, see below) of states over the barrier cannot be correctly converged to -from such an initial configuration. In this case, you will want to -generate initial states for the intermediate replicas that are -geometrically closer to the MEP and read them in. +from such an initial path. In this case, you will want to generate +initial states for the intermediate replicas that are geometrically +closer to the MEP and read them in. :line @@ -135,10 +122,11 @@ is assigned to be a fraction of the distance. E.g. if there are 10 replicas, the 2nd replica will assign a position that is 10% of the distance along a line between the starting and final point, and the 9th replica will assign a position that is 90% of the distance along -the line. Note that this procedure to produce consistent coordinates -across all the replicas, the current coordinates need to be the same -in all replicas. LAMMPS does not check for this, but invalid initial -configurations will likely result if it is not the case. +the line. Note that for this procedure to produce consistent +coordinates across all the replicas, the current coordinates need to +be the same in all replicas. LAMMPS does not check for this, but +invalid initial configurations will likely result if it is not the +case. NOTE: The "distance" between the starting and final point is calculated in a minimum-image sense for a periodic simulation box. @@ -150,8 +138,8 @@ interpolation is outside the periodic box, the atom will be wrapped back into the box when the NEB calculation begins. For a {file-style} setting of {each}, a filename is specified which is -assumed to be unique to each replica. This can be done by -using a variable in the filename, e.g. +assumed to be unique to each replica. This can be done by using a +variable in the filename, e.g. variable i equal part neb 0.0 0.001 1000 500 50 each coords.initial.$i :pre @@ -198,11 +186,10 @@ The minimizer tolerances for energy and force are set by {etol} and A non-zero {etol} means that the NEB calculation will terminate if the energy criterion is met by every replica. The energies being compared to {etol} do not include any contribution from the inter-replica -forces, since these are non-conservative. A non-zero {ftol} means -that the NEB calculation will terminate if the force criterion is met -by every replica. The forces being compared to {ftol} include the -inter-replica forces between an atom and its images in adjacent -replicas. +nudging forces, since these are non-conservative. A non-zero {ftol} +means that the NEB calculation will terminate if the force criterion +is met by every replica. The forces being compared to {ftol} include +the inter-replica nudging forces. The maximum number of iterations in each stage is set by {N1} and {N2}. These are effectively timestep counts since each iteration of @@ -220,27 +207,27 @@ finding a good energy barrier. {N1} and {N2} must both be multiples of {Nevery}. In the first stage of NEB, the set of replicas should converge toward -the minimum energy path (MEP) of conformational states that transition -over the barrier. The MEP for a barrier is defined as a sequence of -3N-dimensional states that cross the barrier at its saddle point, each -of which has a potential energy gradient parallel to the MEP itself. -The replica states will also be roughly equally spaced along the MEP -due to the inter-replica spring force added by the "fix -neb"_fix_neb.html command. +a minimum energy path (MEP) of conformational states that transition +over a barrier. The MEP for a transition is defined as a sequence of +3N-dimensional states, each of which has a potential energy gradient +parallel to the MEP itself. The configuration of highest energy along +a MEP corresponds to a saddle point. The replica states will also be +roughly equally spaced along the MEP due to the inter-replica nugding +force added by the "fix neb"_fix_neb.html command. -In the second stage of NEB, the replica with the highest energy -is selected and the inter-replica forces on it are converted to a -force that drives its atom coordinates to the top or saddle point of -the barrier, via the barrier-climbing calculation described in +In the second stage of NEB, the replica with the highest energy is +selected and the inter-replica forces on it are converted to a force +that drives its atom coordinates to the top or saddle point of the +barrier, via the barrier-climbing calculation described in "(HenkelmanB)"_#HenkelmanB. As before, the other replicas rearrange themselves along the MEP so as to be roughly equally spaced. When both stages are complete, if the NEB calculation was successful, -one of the replicas should be an atomic configuration at the top or -saddle point of the barrier, the potential energies for the set of -replicas should represent the energy profile of the barrier along the -MEP, and the configurations of the replicas should be a sequence of -configurations along the MEP. +the configurations of the replicas should be along (close to) the MEP +and the replica with the highest energy should be an atomic +configuration at (close to) the saddle point of the transition. The +potential energies for the set of replicas represents the energy +profile of the transition along the MEP. :line @@ -284,9 +271,9 @@ ID2 x2 y2 z2 ... IDN xN yN zN :pre -The fields are the atom ID, followed by the x,y,z coordinates. -The lines can be listed in any order. Additional trailing information -on the line is OK, such as a comment. +The fields are the atom ID, followed by the x,y,z coordinates. The +lines can be listed in any order. Additional trailing information on +the line is OK, such as a comment. Note that for a typical NEB calculation you do not need to specify initial coordinates for very many atoms to produce differing starting @@ -310,38 +297,54 @@ this case), the print-out to the screen and master log.lammps file contains a line of output, printed once every {Nevery} timesteps. It contains the timestep, the maximum force per replica, the maximum force per atom (in any replica), potential gradients in the initial, -final, and climbing replicas, the forward and backward energy barriers, -the total reaction coordinate (RDT), and the normalized reaction -coordinate and potential energy of each replica. +final, and climbing replicas, the forward and backward energy +barriers, the total reaction coordinate (RDT), and the normalized +reaction coordinate and potential energy of each replica. -The "maximum force per replica" is -the two-norm of the 3N-length force vector for the atoms in each -replica, maximized across replicas, which is what the {ftol} setting -is checking against. In this case, N is all the atoms in each -replica. The "maximum force per atom" is the maximum force component -of any atom in any replica. The potential gradients are the two-norm -of the 3N-length force vector solely due to the interaction potential i.e. -without adding in inter-replica forces. Note that inter-replica forces -are zero in the initial and final replicas, and only affect -the direction in the climbing replica. For this reason, the "maximum -force per replica" is often equal to the potential gradient in the -climbing replica. In the first stage of NEB, there is no climbing -replica, and so the potential gradient in the highest energy replica -is reported, since this replica will become the climbing replica -in the second stage of NEB. +The "maximum force per replica" is the two-norm of the 3N-length force +vector for the atoms in each replica, maximized across replicas, which +is what the {ftol} setting is checking against. In this case, N is +all the atoms in each replica. The "maximum force per atom" is the +maximum force component of any atom in any replica. The potential +gradients are the two-norm of the 3N-length force vector solely due to +the interaction potential i.e. without adding in inter-replica +forces. -The "reaction coordinate" (RD) for each -replica is the two-norm of the 3N-length vector of distances between -its atoms and the preceding replica's atoms, added to the RD of the -preceding replica. The RD of the first replica RD1 = 0.0; -the RD of the final replica RDN = RDT, the total reaction coordinate. -The normalized RDs are divided by RDT, -so that they form a monotonically increasing sequence -from zero to one. When computing RD, N only includes the atoms -being operated on by the fix neb command. +The "reaction coordinate" (RD) for each replica is the two-norm of the +3N-length vector of distances between its atoms and the preceding +replica's atoms, added to the RD of the preceding replica. The RD of +the first replica RD1 = 0.0; the RD of the final replica RDN = RDT, +the total reaction coordinate. The normalized RDs are divided by RDT, +so that they form a monotonically increasing sequence from zero to +one. When computing RD, N only includes the atoms being operated on by +the fix neb command. + +The forward (reverse) energy barrier is the potential energy of the +highest replica minus the energy of the first (last) replica. + +Supplementary informations for all replicas can be printed out to the +screen and master log.lammps file by adding the verbose keyword. These +informations include the following. The "path angle" (pathangle) for +the replica i which is the angle between the 3N-length vectors (Ri-1 - +Ri) and (Ri+1 - Ri) (where Ri is the atomic coordinates of replica +i). A "path angle" of 180 indicates that replicas i-1, i and i+1 are +aligned. "angletangrad" is the angle between the 3N-length tangent +vector and the 3N-length force vector at image i. The tangent vector +is calculated as in "(HenkelmanA)"_#HenkelmanA for all intermediate +replicas and at R2 - R1 and RM - RM-1 for the first and last replica, +respectively. "anglegrad" is the angle between the 3N-length energy +gradient vector of replica i and that of replica i+1. It is not +defined for the final replica and reads nan. gradV is the norm of the +energy gradient of image i. ReplicaForce is the two-norm of the +3N-length force vector (including nudging forces) for replica i. +MaxAtomForce is the maximum force component of any atom in replica i. + +When a NEB calculation does not converge properly, these suplementary +informations can help understanding what is going wrong. For instance +when the path angle becomes accute the definition of tangent used in +the NEB calculation is questionable and the NEB cannot may diverge +"(Maras)"_#Maras2. -The forward (reverse) energy barrier is the potential energy of the highest -replica minus the energy of the first (last) replica. When running on multiple partitions, LAMMPS produces additional log files for each partition, e.g. log.lammps.0, log.lammps.1, etc. For a @@ -396,12 +399,16 @@ This command can only be used if LAMMPS was built with the REPLICA package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. +:line + [Related commands:] -"prd"_prd.html, "temper"_temper.html, "fix -langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html +"prd"_prd.html, "temper"_temper.html, "fix langevin"_fix_langevin.html, +"fix viscous"_fix_viscous.html -[Default:] none +[Default:] + +none :line @@ -414,3 +421,7 @@ langevin"_fix_langevin.html, "fix viscous"_fix_viscous.html :link(Nakano3) [(Nakano)] Nakano, Comp Phys Comm, 178, 280-289 (2008). + +:link(Maras2) +[(Maras)] Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, +Comp Phys Comm, 205, 13-21 (2016) diff --git a/doc/src/package.txt b/doc/src/package.txt index a0894b3128..18a26bd55c 100644 --- a/doc/src/package.txt +++ b/doc/src/package.txt @@ -574,9 +574,9 @@ is used. If it is not used, you must invoke the package intel command in your input script or or via the "-pk intel" "command-line switch"_Section_start.html#start_7. -For the KOKKOS package, the option defaults neigh = full, neigh/qeq - = full, newton = off, binsize = 0.0, and comm = device. These settings - are made automatically by the required "-k on" "command-line +For the KOKKOS package, the option defaults neigh = full, +neigh/qeq = full, newton = off, binsize = 0.0, and comm = device. +These settings are made automatically by the required "-k on" "command-line switch"_Section_start.html#start_7. You can change them bu using the package kokkos command in your input script or via the "-pk kokkos" "command-line switch"_Section_start.html#start_7. diff --git a/doc/src/pair_agni.txt b/doc/src/pair_agni.txt index 27fb6c10fe..06dcccb9d9 100644 --- a/doc/src/pair_agni.txt +++ b/doc/src/pair_agni.txt @@ -40,8 +40,8 @@ vectorial atomic forces. Only a single pair_coeff command is used with the {agni} style which specifies an AGNI potential file containing the parameters of the -force field for the needed elements. These are mapped to LAMMPS atom -types by specifying N additional arguments after the filename in the +force field for the needed elements. These are mapped to LAMMPS atom +types by specifying N additional arguments after the filename in the pair_coeff command, where N is the number of LAMMPS atom types: filename @@ -52,13 +52,13 @@ to specify the path for the force field file. An AGNI force field is fully specified by the filename which contains the parameters of the force field, i.e., the reference training environments -used to construct the machine learning force field. Example force field -and input files are provided in the examples/USER/misc/agni directory. +used to construct the machine learning force field. Example force field +and input files are provided in the examples/USER/misc/agni directory. :line -Styles with {omp} suffix is functionally the same as the corresponding -style without the suffix. They have been optimized to run faster, depending +Styles with {omp} suffix is functionally the same as the corresponding +style without the suffix. They have been optimized to run faster, depending on your available hardware, as discussed in "Section 5"_Section_accelerate.html of the manual. The accelerated style takes the same arguments and should produce the same results, except for round-off and precision diff --git a/doc/src/pair_buck.txt b/doc/src/pair_buck.txt index 49161404c3..e705e735fb 100644 --- a/doc/src/pair_buck.txt +++ b/doc/src/pair_buck.txt @@ -75,7 +75,7 @@ Lennard-Jones 12/6) given by :c,image(Eqs/pair_buck.jpg) where rho is an ionic-pair dependent length parameter, and Rc is the -cutoff on both terms. +cutoff on both terms. The styles with {coul/cut} or {coul/long} or {coul/msm} add a Coulombic term as described for the "lj/cut"_pair_lj.html pair styles. diff --git a/doc/src/pair_charmm.txt b/doc/src/pair_charmm.txt index 9c5973c725..1e78607c08 100644 --- a/doc/src/pair_charmm.txt +++ b/doc/src/pair_charmm.txt @@ -104,7 +104,15 @@ charmmfsw"_dihedral_charmm.html command. Eventually code from the new styles will propagate into the related pair styles (e.g. implicit, accelerator, free energy variants). -The general CHARMM formulas are as follows +NOTE: The newest CHARMM pair styles reset the Coulombic energy +conversion factor used internally in the code, from the LAMMPS value +to the CHARMM value, as if it were effectively a parameter of the +force field. This is because the CHARMM code uses a slightly +different value for the this conversion factor in "real +units"_units.html (Kcal/mole), namely CHARMM = 332.0716, LAMMPS = +332.06371. This is to enable more precise agreement by LAMMPS with +the CHARMM force field energies and forces, when using one of these +two CHARMM pair styles. :c,image(Eqs/pair_charmm.jpg) diff --git a/doc/src/pair_dipole.txt b/doc/src/pair_dipole.txt index a9622b32fd..985581cac8 100644 --- a/doc/src/pair_dipole.txt +++ b/doc/src/pair_dipole.txt @@ -71,6 +71,14 @@ and force, Fij = -Fji as symmetric forces, and Tij != -Tji since the torques do not act symmetrically. These formulas are discussed in "(Allen)"_#Allen2 and in "(Toukmaji)"_#Toukmaji2. +Also note, that in the code, all of these terms (except Elj) have a +C/epsilon prefactor, the same as the Coulombic term in the LJ + +Coulombic pair styles discussed "here"_pair_lj.html. C is an +energy-conversion constant and epsilon is the dielectric constant +which can be set by the "dielectric"_dielectric.html command. The +same is true of the equations that follow for other dipole pair +styles. + Style {lj/sf/dipole/sf} computes "shifted-force" interactions between pairs of particles that each have a charge and/or a point dipole moment. In general, a shifted-force potential is a (sligthly) modified diff --git a/doc/src/pair_edip.txt b/doc/src/pair_edip.txt index cdfc265752..86453859d3 100644 --- a/doc/src/pair_edip.txt +++ b/doc/src/pair_edip.txt @@ -7,11 +7,13 @@ :line pair_style edip command :h3 +pair_style edip/multi command :h3 [Syntax:] -pair_style edip :pre -pair_style edip/omp :pre +pair_style style :pre + +style = {edip} or {edip/multi} :ul [Examples:] @@ -20,11 +22,14 @@ pair_coeff * * Si.edip Si [Description:] -The {edip} style computes a 3-body "EDIP"_#EDIP potential which is -popular for modeling silicon materials where it can have advantages -over other models such as the "Stillinger-Weber"_pair_sw.html or -"Tersoff"_pair_tersoff.html potentials. In EDIP, the energy E of a -system of atoms is +The {edip} and {edip/multi} styles compute a 3-body "EDIP"_#EDIP +potential which is popular for modeling silicon materials where +it can have advantages over other models such as the +"Stillinger-Weber"_pair_sw.html or "Tersoff"_pair_tersoff.html +potentials. The {edip} style has been programmed for single element +potentials, while {edip/multi} supports multi-element EDIP runs. + +In EDIP, the energy E of a system of atoms is :c,image(Eqs/pair_edip.jpg) @@ -142,7 +147,7 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This angle style can only be used if LAMMPS was built with the +This pair style can only be used if LAMMPS was built with the USER-MISC package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info on packages. @@ -151,7 +156,7 @@ for pair interactions. The EDIP potential files provided with LAMMPS (see the potentials directory) are parameterized for metal "units"_units.html. -You can use the SW potential with any LAMMPS units, but you would need +You can use the EDIP potential with any LAMMPS units, but you would need to create your own EDIP potential file with coefficients listed in the appropriate units if your simulation doesn't use "metal" units. @@ -164,4 +169,4 @@ appropriate units if your simulation doesn't use "metal" units. :line :link(EDIP) -[(EDIP)] J. F. Justo et al., Phys. Rev. B 58, 2539 (1998). +[(EDIP)] J F Justo et al, Phys Rev B 58, 2539 (1998). diff --git a/doc/src/pair_exp6_rx.txt b/doc/src/pair_exp6_rx.txt index 47045a5933..cbc17d357d 100644 --- a/doc/src/pair_exp6_rx.txt +++ b/doc/src/pair_exp6_rx.txt @@ -55,33 +55,33 @@ defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. The interaction potential is -weighted by the geometric average of either the mole fraction concentrations -or the number of molecules associated with the interacting coarse-grained -particles (see the {fractional} or {molecular} weighting pair style options). +weighted by the geometric average of either the mole fraction concentrations +or the number of molecules associated with the interacting coarse-grained +particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). -The fourth argument specifies the type of scaling that will be used +The fourth argument specifies the type of scaling that will be used to scale the EXP-6 parameters as reactions occur. Currently, there are three scaling options: {exponent}, {polynomial} and {none}. -Exponent scaling requires two additional arguments for scaling +Exponent scaling requires two additional arguments for scaling the {Rm} and {epsilon} parameters, respectively. The scaling factor -is computed by phi^exponent, where phi is the number of molecules -represented by the coarse-grain particle and exponent is specified +is computed by phi^exponent, where phi is the number of molecules +represented by the coarse-grain particle and exponent is specified as a pair coefficient argument for {Rm} and {epsilon}, respectively. -The {Rm} and {epsilon} parameters are multiplied by the scaling +The {Rm} and {epsilon} parameters are multiplied by the scaling factor to give the scaled interaction parameters for the CG particle. -Polynomial scaling requires a filename to be specified as a pair +Polynomial scaling requires a filename to be specified as a pair coeff argument. The file contains the coefficients to a fifth order -polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend -upon phi (the number of molecules represented by the CG particle). +polynomial for the {alpha}, {epsilon} and {Rm} parameters that depend +upon phi (the number of molecules represented by the CG particle). The format of a polynomial file is provided below. The {none} option to the scaling does not have any additional pair coeff -arguments. This is equivalent to specifying the {exponent} option with +arguments. This is equivalent to specifying the {exponent} option with {Rm} and {epsilon} exponents of 0.0 and 0.0, respectively. The final argument specifies the interaction cutoff (optional). @@ -102,7 +102,7 @@ parenthesized comments): # POLYNOMIAL FILE (one or more comment or blank lines) :pre # General Functional Form: -# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F +# A*phi^5 + B*phi^4 + C*phi^3 + D*phi^2 + E*phi + F # # Parameter A B C D E F (blank) diff --git a/doc/src/pair_gauss.txt b/doc/src/pair_gauss.txt index 92d8b51d8b..f6f46a2de8 100644 --- a/doc/src/pair_gauss.txt +++ b/doc/src/pair_gauss.txt @@ -128,7 +128,7 @@ The B parameter is converted to a distance (sigma), before mixing afterwards (using B=sigma^2). Negative A values are converted to positive A values (using abs(A)) before mixing, and converted back after mixing -(by multiplying by sign(Ai)*sign(Aj)). +(by multiplying by min(sign(Ai),sign(Aj))). This way, if either particle is repulsive (if Ai<0 or Aj<0), then the default interaction between both particles will be repulsive. diff --git a/doc/src/pair_gw.txt b/doc/src/pair_gw.txt new file mode 100644 index 0000000000..fcf63b1bc4 --- /dev/null +++ b/doc/src/pair_gw.txt @@ -0,0 +1,120 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style gw command :h3 +pair_style gw/zbl command :h3 + +[Syntax:] + +pair_style style :pre + +style = {gw} or {gw/zbl} :ul + +[Examples:] + +pair_style gw +pair_coeff * * SiC.gw Si C C + +pair_style gw/zbl +pair_coeff * * SiC.gw.zbl C Si :pre + +[Description:] + +The {gw} style computes a 3-body "Gao-Weber"_#Gao potential; +similarly {gw/zbl} combines this potential with a modified +repulsive ZBL core function in a similar fashion as implemented +in the "tersoff/zbl"_pair_tersoff_zbl.html pair style. + +Unfortunately the author of this contributed code has not been +able to submit a suitable documentation explaining the details +of the potentials. The LAMMPS developers thus have finally decided +to release the code anyway with only the technical explanations. +For details of the model and the parameters, please refer to the +linked publication. + +Only a single pair_coeff command is used with the {gw} and {gw/zbl} +styles which specifies a Gao-Weber potential file with parameters +for all needed elements. These are mapped to LAMMPS atom types by +specifying N additional arguments after the filename in the pair_coeff +command, where N is the number of LAMMPS atom types: + +filename +N element names = mapping of GW elements to atom types :ul + +See the "pair_coeff"_pair_coeff.html doc page for alternate ways +to specify the path for the potential file. + +As an example, imagine a file SiC.gw has Gao-Weber values for Si and C. +If your LAMMPS simulation has 4 atoms types and you want the first 3 to +be Si, and the 4th to be C, you would use the following pair_coeff command: + +pair_coeff * * SiC.gw Si Si Si C :pre + +The first 2 arguments must be * * so as to span all LAMMPS atom types. +The first three Si arguments map LAMMPS atom types 1,2,3 to the Si +element in the GW file. The final C argument maps LAMMPS atom type 4 +to the C element in the GW file. If a mapping value is specified as +NULL, the mapping is not performed. This can be used when a {gw} +potential is used as part of the {hybrid} pair style. The NULL values +are placeholders for atom types that will be used with other +potentials. + +Gao-Weber files in the {potentials} directory of the LAMMPS +distribution have a ".gw" suffix. Gao-Weber with ZBL files +have a ".gz.zbl" suffix. The structure of the potential files +is similar to other many-body potentials supported by LAMMPS. +You have to refer to the comments in the files and the literature +to learn more details. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +For atom type pairs I,J and I != J, where types I and J correspond to +two different element types, mixing is performed by LAMMPS as +described above from values in the potential file. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style is part of the USER-MISC package. It is only enabled +if LAMMPS was built with that package. See +the "Making LAMMPS"_Section_start.html#start_3 section for more info. + +This pair style requires the "newton"_newton.html setting to be "on" +for pair interactions. + +The Gao-Weber potential files provided with LAMMPS (see the +potentials directory) are parameterized for metal "units"_units.html. +You can use the GW potential with any LAMMPS units, but you would need +to create your own GW potential file with coefficients listed in the +appropriate units if your simulation doesn't use "metal" units. + +[Related commands:] + +"pair_coeff"_pair_coeff.html + +[Default:] none + +:line + +:link(Gao) +[(Gao)] Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504. diff --git a/doc/src/pair_kolmogorov_crespi_z.txt b/doc/src/pair_kolmogorov_crespi_z.txt index 0879dc34d0..c7a6d4194f 100644 --- a/doc/src/pair_kolmogorov_crespi_z.txt +++ b/doc/src/pair_kolmogorov_crespi_z.txt @@ -24,25 +24,25 @@ pair_coeff 1 2 kolmogorov/crespi/z CC.KC C C :pre [Description:] -The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction -potential as described in "(KC05)"_#KC05. An important simplification is made, -which is to take all normals along the z-axis. +The {kolmogorov/crespi/z} style computes the Kolmogorov-Crespi interaction +potential as described in "(KC05)"_#KC05. An important simplification is made, +which is to take all normals along the z-axis. :c,image(Eqs/pair_kolmogorov_crespi_z.jpg) -It is important to have a suffiently large cutoff to ensure smooth forces. -Energies are shifted so that they go continously to zero at the cutoff assuming +It is important to have a suffiently large cutoff to ensure smooth forces. +Energies are shifted so that they go continously to zero at the cutoff assuming that the exponential part of {Vij} (first term) decays sufficiently fast. This shift is achieved by the last term in the equation for {Vij} above. -This potential is intended for interactions between two layers of graphene. -Therefore, to avoid interaction between layers in multi-layered materials, -each layer should have a separate atom type and interactions should only +This potential is intended for interactions between two layers of graphene. +Therefore, to avoid interaction between layers in multi-layered materials, +each layer should have a separate atom type and interactions should only be computed between atom types of neighbouring layers. -The parameter file (e.g. CC.KC), is intended for use with metal -"units"_units.html, with energies in meV. An additional parameter, {S}, -is available to facilitate scaling of energies in accordance with +The parameter file (e.g. CC.KC), is intended for use with metal +"units"_units.html, with energies in meV. An additional parameter, {S}, +is available to facilitate scaling of energies in accordance with "(vanWijk)"_#vanWijk. This potential must be used in combination with hybrid/overlay. @@ -64,7 +64,7 @@ LAMMPS"_Section_start.html#start_3 section for more info. :line -:link(KC05) +:link(KC05) [(KC05)] A. N. Kolmogorov, V. H. Crespi, Phys. Rev. B 71, 235415 (2005) :link(vanWijk) diff --git a/doc/src/pair_lj_long.txt b/doc/src/pair_lj_long.txt index d559871f9d..da9f37b9c3 100644 --- a/doc/src/pair_lj_long.txt +++ b/doc/src/pair_lj_long.txt @@ -7,6 +7,7 @@ :line pair_style lj/long/coul/long command :h3 +pair_style lj/long/coul/long/intel command :h3 pair_style lj/long/coul/long/omp command :h3 pair_style lj/long/coul/long/opt command :h3 pair_style lj/long/tip4p/long command :h3 diff --git a/doc/src/pair_lj_sf.txt b/doc/src/pair_lj_sf.txt deleted file mode 100644 index 65e28b6f51..0000000000 --- a/doc/src/pair_lj_sf.txt +++ /dev/null @@ -1,114 +0,0 @@ -"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c - -:link(lws,http://lammps.sandia.gov) -:link(ld,Manual.html) -:link(lc,Section_commands.html#comm) - -:line - -pair_style lj/sf command :h3 -pair_style lj/sf/omp command :h3 - -[Syntax:] - -pair_style lj/sf cutoff :pre - -cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul - -[Examples:] - -pair_style lj/sf 2.5 -pair_coeff * * 1.0 1.0 -pair_coeff 1 1 1.0 1.0 3.0 :pre - -[Description:] - -Style {lj/sf} computes a truncated and force-shifted LJ interaction -(Shifted Force Lennard-Jones), so that both the potential and the -force go continuously to zero at the cutoff "(Toxvaerd)"_#Toxvaerd: - -:c,image(Eqs/pair_lj_sf.jpg) - -The following coefficients must be defined for each pair of atoms -types via the "pair_coeff"_pair_coeff.html command as in the examples -above, or in the data file or restart files read by the -"read_data"_read_data.html or "read_restart"_read_restart.html -commands, or by mixing as described below: - -epsilon (energy units) -sigma (distance units) -cutoff (distance units) :ul - -The last coefficient is optional. If not specified, the global -LJ cutoff specified in the pair_style command is used. - -:line - -Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are -functionally the same as the corresponding style without the suffix. -They have been optimized to run faster, depending on your available -hardware, as discussed in "Section 5"_Section_accelerate.html -of the manual. The accelerated styles take the same arguments and -should produce the same results, except for round-off and precision -issues. - -These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, -USER-OMP and OPT packages, respectively. They are only enabled if -LAMMPS was built with those packages. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -You can specify the accelerated styles explicitly in your input script -by including their suffix, or you can use the "-suffix command-line -switch"_Section_start.html#start_7 when you invoke LAMMPS, or you can -use the "suffix"_suffix.html command in your input script. - -See "Section 5"_Section_accelerate.html of the manual for -more instructions on how to use the accelerated styles effectively. - -:line - -[Mixing, shift, table, tail correction, restart, rRESPA info]: - -For atom type pairs I,J and I != J, the epsilon and sigma -coefficients and cutoff distance for this pair style can be mixed. -Rin is a cutoff value and is mixed like the cutoff. The -default mix value is {geometric}. See the "pair_modify" command for -details. - -The "pair_modify"_pair_modify.html shift option is not relevant for -this pair style, since the pair interaction goes to 0.0 at the cutoff. - -The "pair_modify"_pair_modify.html table option is not relevant -for this pair style. - -This pair style does not support the "pair_modify"_pair_modify.html -tail option for adding long-range tail corrections to energy and -pressure, since the energy of the pair interaction is smoothed to 0.0 -at the cutoff. - -This pair style writes its information to "binary restart -files"_restart.html, so pair_style and pair_coeff commands do not need -to be specified in an input script that reads a restart file. - -This pair style can only be used via the {pair} keyword of the -"run_style respa"_run_style.html command. It does not support the -{inner}, {middle}, {outer} keywords. - -:line - -[Restrictions:] - -This pair style is part of the USER-MISC package. It is only enabled -if LAMMPS was built with that package. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. - -[Related commands:] - -"pair_coeff"_pair_coeff.html - -[Default:] none - -:line - -:link(Toxvaerd) -[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). diff --git a/doc/src/pair_lj_smooth_linear.txt b/doc/src/pair_lj_smooth_linear.txt index 8b9b9aa5fa..a48c441f54 100644 --- a/doc/src/pair_lj_smooth_linear.txt +++ b/doc/src/pair_lj_smooth_linear.txt @@ -11,26 +11,26 @@ pair_style lj/smooth/linear/omp command :h3 [Syntax:] -pair_style lj/smooth/linear Rc :pre +pair_style lj/smooth/linear cutoff :pre -Rc = cutoff for lj/smooth/linear interactions (distance units) :ul +cutoff = global cutoff for Lennard-Jones interactions (distance units) :ul [Examples:] -pair_style lj/smooth/linear 5.456108274435118 -pair_coeff * * 0.7242785984051078 2.598146797350056 -pair_coeff 1 1 20.0 1.3 9.0 :pre +pair_style lj/smooth/linear 2.5 +pair_coeff * * 1.0 1.0 +pair_coeff 1 1 0.3 3.0 9.0 :pre [Description:] -Style {lj/smooth/linear} computes a LJ interaction that combines the -standard 12/6 Lennard-Jones function and subtracts a linear term that -includes the cutoff distance Rc, as in this formula: +Style {lj/smooth/linear} computes a truncated and force-shifted LJ +interaction (aka Shifted Force Lennard-Jones) that combines the +standard 12/6 Lennard-Jones function and subtracts a linear term based +on the cutoff distance, so that both, the potential and the force, go +continuously to zero at the cutoff Rc "(Toxvaerd)"_#Toxvaerd: :c,image(Eqs/pair_lj_smooth_linear.jpg) -At the cutoff Rc, the energy and force (its 1st derivative) will be 0.0. - The following coefficients must be defined for each pair of atoms types via the "pair_coeff"_pair_coeff.html command as in the examples above, or in the data file or restart files read by the @@ -41,8 +41,8 @@ epsilon (energy units) sigma (distance units) cutoff (distance units) :ul -The last coefficient is optional. If not specified, the global value -for Rc is used. +The last coefficient is optional. If not specified, the global +LJ cutoff specified in the pair_style command is used. :line @@ -76,10 +76,11 @@ and cutoff distance can be mixed. The default mix value is geometric. See the "pair_modify" command for details. This pair style does not support the "pair_modify"_pair_modify.html -shift option for the energy of the pair interaction. +shift option for the energy of the pair interaction, since it goes +to 0.0 at the cutoff by construction. -The "pair_modify"_pair_modify.html table option is not relevant for -this pair style. +The "pair_modify"_pair_modify.html table option is not relevant +for this pair style. This pair style does not support the "pair_modify"_pair_modify.html tail option for adding long-range tail corrections to energy and @@ -103,3 +104,8 @@ This pair style can only be used via the {pair} keyword of the "pair_coeff"_pair_coeff.html, "pair lj/smooth"_pair_lj_smooth.html [Default:] none + +:line + +:link(Toxvaerd) +[(Toxvaerd)] Toxvaerd, Dyre, J Chem Phys, 134, 081102 (2011). diff --git a/doc/src/pair_meam.txt b/doc/src/pair_meam.txt index 4fcb7a2e6c..62fa59f406 100644 --- a/doc/src/pair_meam.txt +++ b/doc/src/pair_meam.txt @@ -7,10 +7,13 @@ :line pair_style meam command :h3 +pair_style meam/c command :h3 [Syntax:] -pair_style meam :pre +pair_style style :pre + +style = {meam} or {meam/c} [Examples:] @@ -30,7 +33,8 @@ using modified embedded-atom method (MEAM) potentials "EAM potentials"_pair_eam.html which adds angular forces. It is thus suitable for modeling metals and alloys with fcc, bcc, hcp and diamond cubic structures, as well as covalently bonded materials like -silicon and carbon. +silicon and carbon. Style {meam/c} is a translation of the {meam} code +from (mostly) Fortran to C++. It is functionally equivalent to {meam}. In the MEAM formulation, the total energy E of a system of atoms is given by: @@ -331,10 +335,14 @@ This pair style can only be used via the {pair} keyword of the [Restrictions:] -This style is part of the MEAM package. It is only enabled if LAMMPS +The {meam} style is part of the MEAM package. It is only enabled if LAMMPS was built with that package, which also requires the MEAM library be -built and linked with LAMMPS. See the "Making -LAMMPS"_Section_start.html#start_3 section for more info. +built and linked with LAMMPS. +The {meam/c} style is provided in the USER-MEAMC package. It is only enabled +if LAMMPS was built with that package. In contrast to the {meam} style, +{meam/c} does not require a separate library to be compiled and it can be +instantiated multiple times in a "hybrid"_pair_hybrid.html pair style. +See the "Making LAMMPS"_Section_start.html#start_3 section for more info. [Related commands:] diff --git a/doc/src/pair_meam_spline.txt b/doc/src/pair_meam_spline.txt index e4d86521c9..2295a6640b 100644 --- a/doc/src/pair_meam_spline.txt +++ b/doc/src/pair_meam_spline.txt @@ -33,7 +33,7 @@ atoms J, I, and K centered on atom I. The five functions Phi, U, rho, f, and g are represented by cubic splines. The {meam/spline} style also supports a new style multicomponent -modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang1, where +modified embedded-atom method (MEAM) potential "(Zhang)"_#Zhang4, where the total energy E is given by :c,image(Eqs/pair_meam_spline_multicomponent.jpg) @@ -164,5 +164,5 @@ for more info. Kress, Modelling Simulation Materials Science Engineering, 8, 825 (2000). -:link(Zhang1) +:link(Zhang4) [(Zhang)] Zhang and Trinkle, Computational Materials Science, 124, 204-210 (2016). diff --git a/doc/src/pair_morse.txt b/doc/src/pair_morse.txt index c5e3a3c399..5fbb6d5c0a 100644 --- a/doc/src/pair_morse.txt +++ b/doc/src/pair_morse.txt @@ -26,7 +26,7 @@ args = list of arguments for a particular style :ul {morse/smooth/linear} args = cutoff cutoff = global cutoff for Morse interactions (distance units) {morse/soft} args = n lf cutoff - n = soft-core parameter + n = soft-core parameter lf = transformation range is lf < lambda < 1 cutoff = global cutoff for Morse interactions (distance units) :pre @@ -36,7 +36,7 @@ args = list of arguments for a particular style :ul pair_style morse 2.5 pair_style morse/smooth/linear 2.5 pair_coeff * * 100.0 2.0 1.5 -pair_coeff 1 1 100.0 2.0 1.5 3.0 +pair_coeff 1 1 100.0 2.0 1.5 3.0 :pre pair_style morse/soft 4 0.9 10.0 pair_coeff * * 100.0 2.0 1.5 1.0 diff --git a/doc/src/pair_multi_lucy_rx.txt b/doc/src/pair_multi_lucy_rx.txt index bf5d5636fe..77ed223e2a 100644 --- a/doc/src/pair_multi_lucy_rx.txt +++ b/doc/src/pair_multi_lucy_rx.txt @@ -97,9 +97,9 @@ tags must either correspond to the species defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the +The interaction potential is weighted by the geometric average of +either the mole fraction concentrations or the number of molecules +associated with the interacting coarse-grained particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). diff --git a/doc/src/pair_nb3b_harmonic.txt b/doc/src/pair_nb3b_harmonic.txt index 86a535acf3..3f7066c826 100644 --- a/doc/src/pair_nb3b_harmonic.txt +++ b/doc/src/pair_nb3b_harmonic.txt @@ -80,10 +80,12 @@ For a given entry, if the first three arguments are all different, then the entry is for the {K} and {theta_0} parameters (the cutoff in this case is irrelevant). -It is {not} required that the potential file contain entries for all -of the elements listed in the pair_coeff command. It can also contain -entries for additional elements not being used in a particular -simulation; LAMMPS ignores those entries. +It is required that the potential file contains entries for {all} +permutations of the elements listed in the pair_coeff command. +If certain combinations are not parameterized the corresponding +parameters should be set to zero. The potential file can also +contain entries for additional elements which are not used in +a particular simulation; LAMMPS ignores those entries. :line diff --git a/doc/src/pair_oxdna.txt b/doc/src/pair_oxdna.txt index 0a07417fd0..d9734f122d 100644 --- a/doc/src/pair_oxdna.txt +++ b/doc/src/pair_oxdna.txt @@ -39,17 +39,17 @@ pair_coeff * * oxdna/coaxstk 46.0 0.4 0.6 0.22 0.58 2.0 2.541592653589793 0.65 1 [Description:] -The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +The {oxdna} pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction {oxdna/excv}, the stacking {oxdna/stk}, cross-stacking {oxdna/xstk} and coaxial stacking interaction {oxdna/coaxstk} as well as the hydrogen-bonding interaction {oxdna/hbond} between complementary pairs of nucleotides on opposite strands. -The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients -in the above example. The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +The exact functional form of the pair styles is rather complex, which manifests itself in the 144 coefficients +in the above example. The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Ouldridge-DPhil)"_#Ouldridge-DPhil1 and "(Ouldridge)"_#Ouldridge1 for a detailed description of the oxDNA force field. @@ -57,8 +57,8 @@ NOTE: These pair styles have to be used together with the related oxDNA bond sty {oxdna/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna/fene"_bond_oxdna.html). With one exception the coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). -When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html +The exception is the first coefficient after {oxdna/stk} (T=0.1 in the above example). +When using a Langevin thermostat, e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. @@ -79,7 +79,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] -"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, +"bond_style oxdna/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, "bond_style oxdna2/fene"_bond_oxdna.html, "pair_style oxdna2/excv"_pair_oxdna2.html [Default:] none diff --git a/doc/src/pair_oxdna2.txt b/doc/src/pair_oxdna2.txt index 1cc562d5f1..1728a0bc7b 100644 --- a/doc/src/pair_oxdna2.txt +++ b/doc/src/pair_oxdna2.txt @@ -45,17 +45,17 @@ pair_coeff * * oxdna2/dh 0.1 1.0 0.815 :pre [Description:] -The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field -for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the +The {oxdna2} pair styles compute the pairwise-additive parts of the oxDNA force field +for coarse-grained modelling of DNA. The effective interaction between the nucleotides consists of potentials for the excluded volume interaction {oxdna2/excv}, the stacking {oxdna2/stk}, cross-stacking {oxdna2/xstk} and coaxial stacking interaction {oxdna2/coaxstk}, electrostatic Debye-Hueckel interaction {oxdna2/dh} as well as the hydrogen-bonding interaction {oxdna2/hbond} between complementary pairs of nucleotides on opposite strands. -The exact functional form of the pair styles is rather complex. -The individual potentials consist of products of modulation factors, -which themselves are constructed from a number of more basic potentials -(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. +The exact functional form of the pair styles is rather complex. +The individual potentials consist of products of modulation factors, +which themselves are constructed from a number of more basic potentials +(Morse, Lennard-Jones, harmonic angle and distance) as well as quadratic smoothing and modulation terms. We refer to "(Snodin)"_#Snodin and the original oxDNA publications "(Ouldridge-DPhil)"_#Ouldridge-DPhil2 and "(Ouldridge)"_#Ouldridge2 for a detailed description of the oxDNA2 force field. @@ -63,7 +63,7 @@ NOTE: These pair styles have to be used together with the related oxDNA2 bond st {oxdna2/fene} for the connectivity of the phosphate backbone (see also documentation of "bond_style oxdna2/fene"_bond_oxdna.html). Almost all coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model. -Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients +Exceptions are the first coefficient after {oxdna2/stk} (T=0.1 in the above example) and the coefficients after {oxdna2/dh} (T=0.1, rhos=1.0, qeff=0.815 in the above example). When using a Langevin thermostat e.g. through "fix langevin"_fix_langevin.html or "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html the temperature coefficients have to be matched to the one used in the fix. @@ -86,7 +86,7 @@ LAMMPS"_Section_start.html#start_3 section for more info on packages. [Related commands:] "bond_style oxdna2/fene"_bond_oxdna.html, "fix nve/dotc/langevin"_fix_nve_dotc_langevin.html, "pair_coeff"_pair_coeff.html, -"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html +"bond_style oxdna/fene"_bond_oxdna.html, "pair_style oxdna/excv"_pair_oxdna.html [Default:] none diff --git a/doc/src/pair_python.txt b/doc/src/pair_python.txt new file mode 100644 index 0000000000..2f8ed7a27c --- /dev/null +++ b/doc/src/pair_python.txt @@ -0,0 +1,217 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +pair_style python command :h3 + +[Syntax:] + +pair_style python cutoff :pre + +cutoff = global cutoff for interactions in python potential classes + +[Examples:] + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj :pre + +pair_style hybrid/overlay coul/long 12.0 python 12.0 +pair_coeff * * coul/long +pair_coeff * * python py_pot.LJCutSPCE OW NULL :pre + +[Description:] + +The {python} pair style provides a way to define pairwise additive +potential functions as python script code that is loaded into LAMMPS +from a python file which must contain specific python class definitions. +This allows to rapidly evaluate different potential functions without +having to modify and recompile LAMMPS. Due to python being an +interpreted language, however, the performance of this pair style is +going to be significantly slower (often between 20x and 100x) than +corresponding compiled code. This penalty can be significantly reduced +through generating tabulations from the python code through the +"pair_write"_pair_write.html command, which is supported by this style. + +Only a single pair_coeff command is used with the {python} pair style +which specifies a python class inside a python module or file that +LAMMPS will look up in the current directory, the folder pointed to by +the LAMMPS_POTENTIALS environment variable or somewhere in your python +path. A single python module can hold multiple python pair class +definitions. The class definitions itself have to follow specific +rules that are explained below. + +Atom types in the python class are specified through symbolic +constants, typically strings. These are mapped to LAMMPS atom types by +specifying N additional arguments after the class name in the +pair_coeff command, where N must be the number of currently defined +atom types: + +As an example, imagine a file {py_pot.py} has a python potential class +names {LJCutMelt} with parameters and potential functions for a two +Lennard-Jones atom types labeled as 'LJ1' and 'LJ2'. In your LAMMPS +input and you would have defined 3 atom types, out of which the first +two are supposed to be using the 'LJ1' parameters and the third the +'LJ2' parameters, then you would use the following pair_coeff command: + +pair_coeff * * py_pot.LJCutMelt LJ1 LJ1 LJ2 :pre + +The first two arguments [must] be * * so as to span all LAMMPS atom +types. The first two LJ1 arguments map LAMMPS atom types 1 and 2 to +the LJ1 atom type in the LJCutMelt class of the py_pot.py file. The +final LJ2 argument maps LAMMPS atom type 3 to the LJ2 atom type the +python file. If a mapping value is specified as NULL, the mapping is +not performed, any pair interaction with this atom type will be +skipped. This can be used when a {python} potential is used as part of +the {hybrid} or {hybrid/overlay} pair style. The NULL values are then +placeholders for atom types that will be used with other potentials. + +:line + +The python potential file has to start with the following code: + +from __future__ import print_function +# +class LAMMPSPairPotential(object): + def __init__(self): + self.pmap=dict() + self.units='lj' + def map_coeff(self,name,ltype): + self.pmap\[ltype\]=name + def check_units(self,units): + if (units != self.units): + raise Exception("Conflicting units: %s vs. %s" % (self.units,units)) +:pre + +Any classes with definitions of specific potentials have to be derived +from this class and should be initialize in a similar fashion to the +example given below. + +NOTE: The class constructor has to set up a data structure containing +the potential parameters supported by this class. It should also +define a variable {self.units} containing a string matching one of the +options of LAMMPS' "units"_units.html command, which is used to +verify, that the potential definition in the python class and in the +LAMMPS input match. + +Here is an example for a single type Lennard-Jones potential class +{LJCutMelt} in reducted units, which defines an atom type {lj} for +which the parameters epsilon and sigma are both 1.0: + +class LJCutMelt(LAMMPSPairPotential): + def __init__(self): + super(LJCutMelt,self).__init__() + # set coeffs: 48*eps*sig**12, 24*eps*sig**6, + # 4*eps*sig**12, 4*eps*sig**6 + self.units = 'lj' + self.coeff = \{'lj' : \{'lj' : (48.0,24.0,4.0,4.0)\}\} +:pre + +The class also has to provide two methods for the computation of the +potential energy and forces, which have be named {compute_force}, +and {compute_energy}, which both take 3 numerical arguments: + + rsq = the square of the distance between a pair of atoms (float) :l + itype = the (numerical) type of the first atom :l + jtype = the (numerical) type of the second atom :ul + +This functions need to compute the force and the energy, respectively, +and use the result as return value. The functions need to use the +{pmap} dictionary to convert the LAMMPS atom type number to the symbolic +value of the internal potential parameter data structure. Following +the {LJCutMelt} example, here are the two functions: + + def compute_force(self,rsq,itype,jtype): + coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj1 = coeff\[0\] + lj2 = coeff\[1\] + return (r6inv * (lj1*r6inv - lj2))*r2inv :pre + + def compute_energy(self,rsq,itype,jtype): + coeff = self.coeff\[self.pmap\[itype\]\]\[self.pmap\[jtype\]\] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj3 = coeff\[2\] + lj4 = coeff\[3\] + return (r6inv * (lj3*r6inv - lj4)) :pre + +NOTE: for consistency with the C++ pair styles in LAMMPS, the +{compute_force} function follows the conventions of the Pair::single() +methods and does not return the full force, but the force scaled by +the distance between the two atoms, so this value only needs to be +multiplied by delta x, delta y, and delta z to conveniently obtain the +three components of the force vector between these two atoms. + +:line + +NOTE: The evaluation of scripted python code will slow down the +computation pair-wise interactions quite significantly. However, this +can be largely worked around through using the python pair style not +for the actual simulation, but to generate tabulated potentials on the +fly using the "pair_write"_pair_write.html command. Please see below +for an example LAMMPS input of how to build a table file: + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj +shell rm -f melt.table +pair_write 1 1 2000 rsq 0.01 2.5 lj1_lj2.table lj :pre + +Note that it is strongly recommended to try to [delete] the potential +table file before generating it. Since the {pair_write} command will +always [append] to a table file, while pair style table will use the +[first match]. Thus when changing the potential function in the python +class, the table pair style will still read the old variant unless the +table file is first deleted. + +After switching the pair style to {table}, the potential tables need +to be assigned to the LAMMPS atom types like this: + +pair_style table linear 2000 +pair_coeff 1 1 melt.table lj :pre + +This can also be done for more complex systems. Please see the +{examples/python} folders for a few more examples. + +:line + +[Mixing, shift, table, tail correction, restart, rRESPA info]: + +Mixing of potential parameters has to be handled inside the provided +python module. The python pair style simply assumes that force and +energy computation can be correctly performed for all pairs of atom +types as they are mapped to the atom type labels inside the python +potential class. + +This pair style does not support the "pair_modify"_pair_modify.html +shift, table, and tail options. + +This pair style does not write its information to "binary restart +files"_restart.html, since it is stored in potential files. Thus, you +need to re-specify the pair_style and pair_coeff commands in an input +script that reads a restart file. + +This pair style can only be used via the {pair} keyword of the +"run_style respa"_run_style.html command. It does not support the +{inner}, {middle}, {outer} keywords. + +:line + +[Restrictions:] + +This pair style is part of the PYTHON package. It is only enabled if +LAMMPS was built with that package. See the "Making +LAMMPS"_Section_start.html#start_3 section for more info. + +[Related commands:] + +"pair_coeff"_pair_coeff.html, "pair_write"_pair_write.html, +"pair style table"_pair_table.html + +[Default:] none + + diff --git a/doc/src/pair_reaxc.txt b/doc/src/pair_reaxc.txt index 76a8e6fd5c..cfa88673d7 100644 --- a/doc/src/pair_reaxc.txt +++ b/doc/src/pair_reaxc.txt @@ -8,6 +8,7 @@ pair_style reax/c command :h3 pair_style reax/c/kk command :h3 +pair_style reax/c/omp command :h3 [Syntax:] diff --git a/doc/src/pair_snap.txt b/doc/src/pair_snap.txt index ab7313832c..fa90dc34e9 100644 --- a/doc/src/pair_snap.txt +++ b/doc/src/pair_snap.txt @@ -10,7 +10,8 @@ pair_style snap command :h3 [Syntax:] -pair_style snap :pre +pair_style snap +:pre [Examples:] @@ -19,11 +20,11 @@ pair_coeff * * InP.snapcoeff In P InP.snapparam In In P P :pre [Description:] -Style {snap} computes interactions +Pair style {snap} computes interactions using the spectral neighbor analysis potential (SNAP) "(Thompson)"_#Thompson20142. Like the GAP framework of Bartok et al. "(Bartok2010)"_#Bartok20102, "(Bartok2013)"_#Bartok2013 -it uses bispectrum components +which uses bispectrum components to characterize the local neighborhood of each atom in a very general way. The mathematical definition of the bispectrum calculation used by SNAP is identical @@ -139,10 +140,15 @@ The default values for these keywords are {rmin0} = 0.0 {diagonalstyle} = 3 {switchflag} = 0 -{bzeroflag} = 1 :ul +{bzeroflag} = 1 +{quadraticflag} = 1 :ul -Detailed definitions of these keywords are given on the "compute +Detailed definitions for all the keywords are given on the "compute sna/atom"_compute_sna_atom.html doc page. +If {quadraticflag} is set to 1, then the SNAP energy expression includes the quadratic term, +0.5*B^t.alpha.B, where alpha is a symmetric {K} by {K} matrix. +The SNAP element file should contain {K}({K}+1)/2 additional coefficients +for each element, the upper-triangular elements of alpha. :line diff --git a/doc/src/pair_table_rx.txt b/doc/src/pair_table_rx.txt index d089a4f9da..f93af21da4 100644 --- a/doc/src/pair_table_rx.txt +++ b/doc/src/pair_table_rx.txt @@ -85,9 +85,9 @@ tags must either correspond to the species defined in the reaction kinetics files specified with the "fix rx"_fix_rx.html command or they must correspond to the tag "1fluid", signifying interaction with a product species mixture determined through a one-fluid approximation. -The interaction potential is weighted by the geometric average of -either the mole fraction concentrations or the number of molecules -associated with the interacting coarse-grained particles (see the +The interaction potential is weighted by the geometric average of +either the mole fraction concentrations or the number of molecules +associated with the interacting coarse-grained particles (see the {fractional} or {molecular} weighting pair style options). The coarse-grained potential is stored before and after the reaction kinetics solver is applied, where the difference is defined to be the internal chemical energy (uChem). diff --git a/doc/src/pair_tersoff.txt b/doc/src/pair_tersoff.txt index eb4a8993cf..23a20ad0fd 100644 --- a/doc/src/pair_tersoff.txt +++ b/doc/src/pair_tersoff.txt @@ -18,7 +18,7 @@ pair_style tersoff/table/omp command :h3 pair_style style :pre -style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} +style = {tersoff} or {tersoff/table} or {tersoff/gpu} or {tersoff/omp} or {tersoff/table/omp} :ul [Examples:] diff --git a/doc/src/pair_vashishta.txt b/doc/src/pair_vashishta.txt index 902e6012f8..9c275a61d3 100644 --- a/doc/src/pair_vashishta.txt +++ b/doc/src/pair_vashishta.txt @@ -7,6 +7,7 @@ :line pair_style vashishta command :h3 +pair_style vashishta/gpu command :h3 pair_style vashishta/omp command :h3 pair_style vashishta/kk command :h3 pair_style vashishta/table command :h3 diff --git a/doc/src/pair_yukawa_colloid.txt b/doc/src/pair_yukawa_colloid.txt index 3d5294bbdb..ecdc1496ab 100644 --- a/doc/src/pair_yukawa_colloid.txt +++ b/doc/src/pair_yukawa_colloid.txt @@ -35,7 +35,7 @@ cutoff. In contrast to "pair_style yukawa"_pair_yukawa.html, this functional form arises from the Coulombic interaction between two colloid particles, screened due to the presence of an electrolyte, see the -book by "Safran"_#Safran for a derivation in the context of DVLO +book by "Safran"_#Safran for a derivation in the context of DLVO theory. "Pair_style yukawa"_pair_yukawa.html is a screened Coulombic potential between two point-charges and uses no such approximation. diff --git a/doc/src/pair_zero.txt b/doc/src/pair_zero.txt index ffd40a977d..e58b33c75f 100644 --- a/doc/src/pair_zero.txt +++ b/doc/src/pair_zero.txt @@ -14,7 +14,7 @@ pair_style zero cutoff {nocoeff} :pre zero = style name of this pair style cutoff = global cutoff (distance units) -nocoeff = ignore all pair_coeff parameters (optional) :l +nocoeff = ignore all pair_coeff parameters (optional) :ul [Examples:] diff --git a/doc/src/pairs.txt b/doc/src/pairs.txt index 0898906e7c..2c1b20f4d3 100644 --- a/doc/src/pairs.txt +++ b/doc/src/pairs.txt @@ -36,6 +36,7 @@ Pair Styles :h1 pair_gayberne pair_gran pair_gromacs + pair_gw pair_hbond_dreiding pair_hybrid pair_kim @@ -48,7 +49,6 @@ Pair Styles :h1 pair_lj_cubic pair_lj_expand pair_lj_long - pair_lj_sf pair_lj_smooth pair_lj_smooth_linear pair_lj_soft @@ -71,6 +71,7 @@ Pair Styles :h1 pair_oxdna2 pair_peri pair_polymorphic + pair_python pair_quip pair_reax pair_reaxc diff --git a/doc/src/python.txt b/doc/src/python.txt index e00b90234c..c6538ded45 100644 --- a/doc/src/python.txt +++ b/doc/src/python.txt @@ -489,7 +489,7 @@ python"_Section_python.html. Note that it is important that the stand-alone LAMMPS executable and the LAMMPS shared library be consistent (built from the same source code files) in order for this to work. If the two have been built at different times using -different source files, problems may occur. +different source files, problems may occur. [Related commands:] diff --git a/doc/src/read_data.txt b/doc/src/read_data.txt index b9924989a6..6785eb1066 100644 --- a/doc/src/read_data.txt +++ b/doc/src/read_data.txt @@ -14,7 +14,7 @@ read_data file keyword args ... :pre file = name of data file to read in :ulb,l zero or more keyword/arg pairs may be appended :l -keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {group} or {nocoeff} or {fix} :l +keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/types} or {extra/angle/types} or {extra/dihedral/types} or {extra/improper/types} or {extra/bond/per/atom} or {extra/angle/per/atom} or {extra/dihedral/per/atom} or {extra/improper/per/atom} or {group} or {nocoeff} or {fix} :l {add} arg = {append} or {Nstart} or {merge} append = add new atoms with IDs appended to current IDs Nstart = add new atoms with IDs starting with Nstart @@ -32,6 +32,11 @@ keyword = {add} or {offset} or {shift} or {extra/atom/types} or {extra/bond/type {extra/angle/types} arg = # of extra angle types {extra/dihedral/types} arg = # of extra dihedral types {extra/improper/types} arg = # of extra improper types + {extra/bond/per/atom} arg = leave space for this many new bonds per atom + {extra/angle/per/atom} arg = leave space for this many new angles per atom + {extra/dihedral/per/atom} arg = leave space for this many new dihedrals per atom + {extra/improper/per/atom} arg = leave space for this many new impropers per atom + {extra/special/per/atom} arg = leave space for extra 1-2,1-3,1-4 interactions per atom {group} args = groupID groupID = add atoms in data file to this group {nocoeff} = ignore force field parameters @@ -264,11 +269,11 @@ is different than the default. {angle types} = # of angle types in system {dihedral types} = # of dihedral types in system {improper types} = # of improper types in system -{extra bond per atom} = leave space for this many new bonds per atom -{extra angle per atom} = leave space for this many new angles per atom -{extra dihedral per atom} = leave space for this many new dihedrals per atom -{extra improper per atom} = leave space for this many new impropers per atom -{extra special per atom} = leave space for this many new special bonds per atom +{extra bond per atom} = leave space for this many new bonds per atom (deprecated, use extra/bond/per/atom keyword) +{extra angle per atom} = leave space for this many new angles per atom (deprecated, use extra/angle/per/atom keyword) +{extra dihedral per atom} = leave space for this many new dihedrals per atom (deprecated, use extra/dihedral/per/atom keyword) +{extra improper per atom} = leave space for this many new impropers per atom (deprecated, use extra/improper/per/atom keyword) +{extra special per atom} = leave space for this many new special bonds per atom (deprecated, use extra/special/per/atom keyword) {ellipsoids} = # of ellipsoids in system {lines} = # of line segments in system {triangles} = # of triangles in system @@ -367,25 +372,32 @@ read_data command will generate an error in this case. The "extra bond per atom" setting (angle, dihedral, improper) is only needed if new bonds (angles, dihedrals, impropers) will be added to the system when a simulation runs, e.g. by using the "fix -bond/create"_fix_bond_create.html command. This will pre-allocate -space in LAMMPS data structures for storing the new bonds (angles, +bond/create"_fix_bond_create.html command. Using this header flag +is deprecated; please use the {extra/bond/per/atom} keyword (and +correspondingly for angles, dihedrals and impropers) in the +read_data command instead. Either will pre-allocate space in LAMMPS + data structures for storing the new bonds (angles, dihedrals, impropers). The "extra special per atom" setting is typically only needed if new bonds/angles/etc will be added to the system, e.g. by using the "fix bond/create"_fix_bond_create.html command. Or if entire new molecules -will be added to the system, e.g. by using the "fix -deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, which -will have more special 1-2,1-3,1-4 neighbors than any other molecules -defined in the data file. Using this setting will pre-allocate space -in the LAMMPS data structures for storing these neighbors. See the +will be added to the system, e.g. by using the +"fix deposit"_fix_deposit.html or "fix pour"_fix_pour.html commands, +which will have more special 1-2,1-3,1-4 neighbors than any other +molecules defined in the data file. Using this header flag is +deprecated; please use the {extra/special/per/atom} keyword instead. +Using this setting will pre-allocate space in the LAMMPS data +structures for storing these neighbors. See the "special_bonds"_special_bonds.html and "molecule"_molecule.html doc pages for more discussion of 1-2,1-3,1-4 neighbors. -NOTE: All of the "extra" settings are only used if they appear in the -first data file read; see the description of the {add} keyword above -for reading multiple data files. If they appear in later data files, -they are ignored. +NOTE: All of the "extra" settings are only applied in the first data +file read and when no simulation box has yet been created; as soon as +the simulation box is created (and read_data implies that), these +settings are {locked} and cannot be changed anymore. Please see the +description of the {add} keyword above for reading multiple data files. +If they appear in later data files, they are ignored. The "ellipsoids" and "lines" and "triangles" and "bodies" settings are only used with "atom_style ellipsoid or line or tri or diff --git a/doc/src/rerun.txt b/doc/src/rerun.txt index 860ee68033..edf94cc711 100644 --- a/doc/src/rerun.txt +++ b/doc/src/rerun.txt @@ -15,7 +15,7 @@ rerun file1 file2 ... keyword args ... :pre file1,file2,... = dump file(s) to read :ulb,l one or more keywords may be appended, keyword {dump} must appear and be last :l keyword = {first} or {last} or {every} or {skip} or {start} or {stop} or {dump} - {first} args = Nfirts + {first} args = Nfirst Nfirst = dump timestep to start on {last} args = Nlast Nlast = dumptimestep to stop on diff --git a/doc/src/run_style.txt b/doc/src/run_style.txt index 0e3c1a939f..a67899420b 100644 --- a/doc/src/run_style.txt +++ b/doc/src/run_style.txt @@ -17,7 +17,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l {verlet/split} args = none {respa} args = N n1 n2 ... keyword values ... N = # of levels of rRESPA - n1, n2, ... = loop factor between rRESPA levels (N-1 values) + n1, n2, ... = loop factors between rRESPA levels (N-1 values) zero or more keyword/value pairings may be appended to the loop factors keyword = {bond} or {angle} or {dihedral} or {improper} or {pair} or {inner} or {middle} or {outer} or {hybrid} or {kspace} @@ -55,7 +55,7 @@ style = {verlet} or {verlet/split} or {respa} or {respa/omp} :ulb,l run_style verlet run_style respa 4 2 2 2 bond 1 dihedral 2 pair 3 kspace 4 -run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 :pre +run_style respa 4 2 2 2 bond 1 dihedral 2 inner 3 5.0 6.0 outer 4 kspace 4 run_style respa 3 4 2 bond 1 hybrid 2 2 1 kspace 3 :pre [Description:] diff --git a/doc/src/set.txt b/doc/src/set.txt index 6b59bf1332..14460c9741 100644 --- a/doc/src/set.txt +++ b/doc/src/set.txt @@ -80,6 +80,7 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \ value can be an atom-style variable (see below) {image} nx ny nz nx,ny,nz = which periodic image of the simulation box the atom is in + any of nx,ny,nz can be an atom-style variable (see below) {bond} value = bond type for all bonds between selected atoms {angle} value = angle type for all angles between selected atoms {dihedral} value = dihedral type for all dihedrals between selected atoms @@ -363,9 +364,8 @@ A value of -1 means subtract 1 box length to get the true value. LAMMPS updates these flags as atoms cross periodic boundaries during the simulation. The flags can be output with atom snapshots via the "dump"_dump.html command. If a value of NULL is specified for any of -nx,ny,nz, then the current image value for that dimension is -unchanged. For non-periodic dimensions only a value of 0 can be -specified. This keyword does not allow use of atom-style variables. +nx,ny,nz, then the current image value for that dimension is unchanged. +For non-periodic dimensions only a value of 0 can be specified. This command can be useful after a system has been equilibrated and atoms have diffused one or more box lengths in various directions. This command can then reset the image values for atoms so that they diff --git a/doc/src/special_bonds.txt b/doc/src/special_bonds.txt index 6924b321a0..6a661015bd 100644 --- a/doc/src/special_bonds.txt +++ b/doc/src/special_bonds.txt @@ -65,7 +65,13 @@ sense to define permanent bonds between atoms that interact via these potentials, though such bonds may exist elsewhere in your system, e.g. when using the "pair_style hybrid"_pair_hybrid.html command. Thus LAMMPS ignores special_bonds settings when manybody potentials -are calculated. +are calculated. Please note, that the existence of explicit bonds +for atoms that are described by a manybody potential will alter the +neigborlist and thus can render the computation of those interactions +invalid, since those pairs are not only used to determine direct +pairwise interactions but also neighbors of neighbors and more. +The recommended course of action is to remove such bonds, or - if +that is not possible - use a special bonds setting of 1.0 1.0 1.0. NOTE: Unlike some commands in LAMMPS, you cannot use this command multiple times in an incremental fashion: e.g. to first set the LJ diff --git a/doc/src/tutorial_github.txt b/doc/src/tutorial_github.txt index d6ec22589b..3e10b821ae 100644 --- a/doc/src/tutorial_github.txt +++ b/doc/src/tutorial_github.txt @@ -86,7 +86,7 @@ machine via HTTPS: or, if you have set up your GitHub account for using SSH keys, via SSH: $ git clone git@github.com:/lammps.git :pre - + You can find the proper URL by clicking the "Clone or download"-button: :c,image(JPG/tutorial_https_block.png) diff --git a/doc/src/tutorial_pylammps.txt b/doc/src/tutorial_pylammps.txt index a4a7a4041e..78cdd241fb 100644 --- a/doc/src/tutorial_pylammps.txt +++ b/doc/src/tutorial_pylammps.txt @@ -10,6 +10,7 @@ PyLammps Tutorial :h1 Overview :h2 @@ -35,7 +36,7 @@ lammps.PyLammps :h4 higher-level abstraction built on top of original C-Types interface manipulation of Python objects -communication with LAMMPS is hidden from API user +communication with LAMMPS is hidden from API user shorter, more concise Python better IPython integration, designed for quick prototyping :ul @@ -327,7 +328,7 @@ IPyLammps Examples :h2 Examples of IPython notebooks can be found in the python/examples/pylammps subdirectory. To open these notebooks launch {jupyter notebook} inside this -directory and navigate to one of them. If you compiled and installed +directory and navigate to one of them. If you compiled and installed a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support you should be able to rerun all of these notebooks. @@ -398,19 +399,19 @@ natoms = L.system.natoms :pre for i in range(niterations): iatom = random.randrange(0, natoms) current_atom = L.atoms\[iatom\] :pre - + x0, y0 = current_atom.position :pre - + dx = deltamove * random.uniform(-1, 1) dy = deltamove * random.uniform(-1, 1) :pre - + current_atom.position = (x0+dx, y0+dy) :pre - + L.run(1, "pre no post no") :pre - + e = L.eval("pe") energies.append(e) :pre - + if e <= elast: naccept += 1 elast = e @@ -459,4 +460,4 @@ Feedback and Contributing :h2 If you find this Python interface useful, please feel free to provide feedback and ideas on how to improve it to Richard Berger (richard.berger@temple.edu). We also want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage -and maybe their latest research results. +and maybe their latest research results. diff --git a/doc/src/velocity.txt b/doc/src/velocity.txt index 70ddb559fa..b8299a5acf 100644 --- a/doc/src/velocity.txt +++ b/doc/src/velocity.txt @@ -61,7 +61,7 @@ keyword/value parameters. Not all options are used by each style. Each option has a default as listed below. The {create} style generates an ensemble of velocities using a random -number generator with the specified seed as the specified temperature. +number generator with the specified seed at the specified temperature. The {set} style sets the velocities of all atoms in the group to the specified values. If any component is specified as NULL, then it is diff --git a/examples/ASPHERE/poly/in.poly b/examples/ASPHERE/poly/in.poly index 77df095e15..3496a774bb 100644 --- a/examples/ASPHERE/poly/in.poly +++ b/examples/ASPHERE/poly/in.poly @@ -62,6 +62,7 @@ pair_coeff 3 3 1.0 1.5 pair_coeff 1 4 0.0 1.0 0.5 pair_coeff 2 4 0.0 1.0 1.0 pair_coeff 3 4 0.0 1.0 0.75 +pair_coeff 4 4 0.0 1.0 0.0 delete_atoms overlap 1.0 small big diff --git a/examples/ASPHERE/poly/in.poly.mp b/examples/ASPHERE/poly/in.poly.mp index 5ced616e7c..1c6a1faee3 100644 --- a/examples/ASPHERE/poly/in.poly.mp +++ b/examples/ASPHERE/poly/in.poly.mp @@ -62,6 +62,7 @@ pair_coeff 3 3 1.0 1.5 pair_coeff 1 4 0.0 1.0 0.5 pair_coeff 2 4 0.0 1.0 1.0 pair_coeff 3 4 0.0 1.0 0.75 +pair_coeff 4 4 0.0 1.0 0.0 delete_atoms overlap 1.0 small big diff --git a/examples/COUPLE/README b/examples/COUPLE/README index 7a62536239..c8c9e0e31b 100644 --- a/examples/COUPLE/README +++ b/examples/COUPLE/README @@ -41,5 +41,8 @@ fortran a simple wrapper on the LAMMPS library API that can be called from Fortran fortran2 a more sophisticated wrapper on the LAMMPS library API that can be called from Fortran +fortran3 wrapper written by Nir Goldman (LLNL), as an + extension to fortran2, used for calling LAMMPS + from Fortran DFTB+ code -Each sub-directory has its own README. +Each sub-directory has its own README with more details. diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper.cpp b/examples/COUPLE/fortran3/LAMMPS-wrapper.cpp new file mode 100644 index 0000000000..6e8bbec5ae --- /dev/null +++ b/examples/COUPLE/fortran3/LAMMPS-wrapper.cpp @@ -0,0 +1,236 @@ +/* ----------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing author: Karl D. Hammond + University of Tennessee, Knoxville (USA), 2012 +------------------------------------------------------------------------- */ + +/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself + provides a (I hope) robust Fortran interface to library.cpp and + library.h. All functions herein COULD be added to library.cpp instead of + including this as a separate file. See the README for instructions. */ + +#include +#include "LAMMPS-wrapper.h" +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +void lammps_open_fortran_wrapper (int argc, char **argv, + MPI_Fint communicator, void **ptr) +{ + MPI_Comm C_communicator = MPI_Comm_f2c (communicator); + lammps_open (argc, argv, C_communicator, ptr); +} + +int lammps_get_ntypes (void *ptr) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + int ntypes = lmp->atom->ntypes; + return ntypes; +} + +void lammps_error_all (void *ptr, const char *file, int line, const char *str) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + lmp->error->all (file, line, str); +} + +int lammps_extract_compute_vectorsize (void *ptr, char *id, int style) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + int icompute = lmp->modify->find_compute(id); + if ( icompute < 0 ) return 0; + class Compute *compute = lmp->modify->compute[icompute]; + + if ( style == 0 ) + { + if ( !compute->vector_flag ) + return 0; + else + return compute->size_vector; + } + else if ( style == 1 ) + { + return lammps_get_natoms (ptr); + } + else if ( style == 2 ) + { + if ( !compute->local_flag ) + return 0; + else + return compute->size_local_rows; + } + else + return 0; +} + +void lammps_extract_compute_arraysize (void *ptr, char *id, int style, + int *nrows, int *ncols) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + int icompute = lmp->modify->find_compute(id); + if ( icompute < 0 ) + { + *nrows = 0; + *ncols = 0; + } + class Compute *compute = lmp->modify->compute[icompute]; + + if ( style == 0 ) + { + if ( !compute->array_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = compute->size_array_rows; + *ncols = compute->size_array_cols; + } + } + else if ( style == 1 ) + { + if ( !compute->peratom_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = lammps_get_natoms (ptr); + *ncols = compute->size_peratom_cols; + } + } + else if ( style == 2 ) + { + if ( !compute->local_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = compute->size_local_rows; + *ncols = compute->size_local_cols; + } + } + else + { + *nrows = 0; + *ncols = 0; + } + + return; +} + +int lammps_extract_fix_vectorsize (void *ptr, char *id, int style) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + int ifix = lmp->modify->find_fix(id); + if ( ifix < 0 ) return 0; + class Fix *fix = lmp->modify->fix[ifix]; + + if ( style == 0 ) + { + if ( !fix->vector_flag ) + return 0; + else + return fix->size_vector; + } + else if ( style == 1 ) + { + return lammps_get_natoms (ptr); + } + else if ( style == 2 ) + { + if ( !fix->local_flag ) + return 0; + else + return fix->size_local_rows; + } + else + return 0; +} + +void lammps_extract_fix_arraysize (void *ptr, char *id, int style, + int *nrows, int *ncols) +{ + class LAMMPS *lmp = (class LAMMPS *) ptr; + int ifix = lmp->modify->find_fix(id); + if ( ifix < 0 ) + { + *nrows = 0; + *ncols = 0; + } + class Fix *fix = lmp->modify->fix[ifix]; + + if ( style == 0 ) + { + if ( !fix->array_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = fix->size_array_rows; + *ncols = fix->size_array_cols; + } + } + else if ( style == 1 ) + { + if ( !fix->peratom_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = lammps_get_natoms (ptr); + *ncols = fix->size_peratom_cols; + } + } + else if ( style == 2 ) + { + if ( !fix->local_flag ) + { + *nrows = 0; + *ncols = 0; + } + else + { + *nrows = fix->size_local_rows; + *ncols = fix->size_local_cols; + } + } + else + { + *nrows = 0; + *ncols = 0; + } + + return; + +} + +/* vim: set ts=3 sts=3 expandtab: */ diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper.h b/examples/COUPLE/fortran3/LAMMPS-wrapper.h new file mode 100644 index 0000000000..7d94362436 --- /dev/null +++ b/examples/COUPLE/fortran3/LAMMPS-wrapper.h @@ -0,0 +1,40 @@ +/* ----------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing author: Karl D. Hammond + University of Tennessee, Knoxville (USA), 2012 +------------------------------------------------------------------------- */ + +/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself + provides a (I hope) robust Fortran interface to library.cpp and + library.h. All prototypes herein COULD be added to library.h instead of + including this as a separate file. See the README for instructions. */ +#ifdef __cplusplus +extern "C" { +#endif + +/* Prototypes for auxiliary functions */ +void lammps_open_fortran_wrapper (int, char**, MPI_Fint, void**); +int lammps_get_ntypes (void*); +int lammps_extract_compute_vectorsize (void*, char*, int); +void lammps_extract_compute_arraysize (void*, char*, int, int*, int*); +int lammps_extract_fix_vectorsize (void*, char*, int); +void lammps_extract_fix_arraysize (void*, char*, int, int*, int*); +void lammps_error_all (void*, const char*, int, const char*); + +#ifdef __cplusplus +} +#endif + +/* vim: set ts=3 sts=3 expandtab: */ diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp b/examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp new file mode 100644 index 0000000000..f245c44d79 --- /dev/null +++ b/examples/COUPLE/fortran3/LAMMPS-wrapper2.cpp @@ -0,0 +1,57 @@ +/* ----------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing author: Karl D. Hammond + University of Tennessee, Knoxville (USA), 2012 +------------------------------------------------------------------------- */ + +/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself + provides a (I hope) robust Fortran interface to library.cpp and + library.h. All functions herein COULD be added to library.cpp instead of + including this as a separate file. See the README for instructions. */ + +#include +#include "LAMMPS-wrapper2.h" +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +using namespace LAMMPS_NS; + +extern "C" void f_callback(void *, bigint, int, tagint *, double **, double **); + +void lammps_set_callback (void *ptr) { + class LAMMPS *lmp = (class LAMMPS *) ptr; + int ifix = lmp->modify->find_fix_by_style("external"); + FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix]; + fix->set_callback(f_callback, ptr); + return; +} + +void lammps_set_user_energy (void *ptr, double energy) { + class LAMMPS *lmp = (class LAMMPS *) ptr; + int ifix = lmp->modify->find_fix_by_style("external"); + FixExternal *fix = (FixExternal *) lmp->modify->fix[ifix]; + fix->set_energy(energy); + return; +} + diff --git a/examples/COUPLE/fortran3/LAMMPS-wrapper2.h b/examples/COUPLE/fortran3/LAMMPS-wrapper2.h new file mode 100644 index 0000000000..794006e3af --- /dev/null +++ b/examples/COUPLE/fortran3/LAMMPS-wrapper2.h @@ -0,0 +1,34 @@ +/* ----------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + www.cs.sandia.gov/~sjplimp/lammps.html + Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories + + Copyright (2003) Sandia Corporation. Under the terms of Contract + DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains + certain rights in this software. This software is distributed under + the GNU General Public License. + + See the README file in the top-level LAMMPS directory. +------------------------------------------------------------------------- */ + +/* ------------------------------------------------------------------------ + Contributing author: Nir Goldman, ngoldman@llnl.gov, Oct. 19th, 2016 +------------------------------------------------------------------------- */ + +/* This is set of "wrapper" functions to assist LAMMPS.F90, which itself + provides a (I hope) robust Fortran interface to library.cpp and + library.h. All prototypes herein COULD be added to library.h instead of + including this as a separate file. See the README for instructions. */ +#ifdef __cplusplus +extern "C" { +#endif + +/* Prototypes for auxiliary functions */ +void lammps_set_callback (void *); +void lammps_set_user_energy (void*, double); + +#ifdef __cplusplus +} +#endif + +/* vim: set ts=3 sts=3 expandtab: */ diff --git a/examples/COUPLE/fortran3/LAMMPS.F90 b/examples/COUPLE/fortran3/LAMMPS.F90 new file mode 100644 index 0000000000..eb5b7f825b --- /dev/null +++ b/examples/COUPLE/fortran3/LAMMPS.F90 @@ -0,0 +1,956 @@ +!! ----------------------------------------------------------------------- +! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator +! www.cs.sandia.gov/~sjplimp/lammps.html +! Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories +! +! Copyright (2003) Sandia Corporation. Under the terms of Contract +! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains +! certain rights in this software. This software is distributed under +! the GNU General Public License. +! +! See the README file in the top-level LAMMPS directory. +!-------------------------------------------------------------------------- + +!! ------------------------------------------------------------------------ +! Contributing author: Karl D. Hammond +! University of Tennessee, Knoxville (USA), 2012 +!-------------------------------------------------------------------------- + +!! LAMMPS, a Fortran 2003 module containing an interface between Fortran +!! programs and the C-style functions in library.cpp that ship with LAMMPS. +!! This file should be accompanied by LAMMPS-wrapper.cpp and LAMMPS-wrapper.h, +!! which define wrapper functions that ease portability and enforce array +!! dimensions. +!! +!! Everything in this module should be 100% portable by way of Fortran 2003's +!! ISO_C_BINDING intrinsic module. See the README for instructions for +!! compilation and use. +!! +!! Here are the PUBLIC functions and subroutines included in this module. +!! subroutine lammps_open (command_line, communicator, ptr) +!! subroutine lammps_open_no_mpi (command_line, ptr) +!! subroutine lammps_close (ptr) +!! subroutine lammps_file (ptr, str) +!! subroutine lammps_command (ptr, str) +!! subroutine lammps_free (ptr) +!! subroutine lammps_extract_global (global, ptr, name) +!! subroutine lammps_extract_atom (atom, ptr, name) +!! subroutine lammps_extract_fix (fix, ptr, id, style, type, i, j) +!! subroutine lammps_extract_compute (compute, ptr, id, style, type) +!! subroutine lammps_extract_variable (variable, ptr, name, group) +!! function lammps_get_natoms (ptr) +!! subroutine lammps_gather_atoms (ptr, name, count, data) +!! subroutine lammps_scatter_atoms (ptr, name, data) + +#define FLERR __FILE__,__LINE__ +! The above line allows for similar error checking as is done with standard +! LAMMPS files. + +module LAMMPS + + use, intrinsic :: ISO_C_binding, only : C_double, C_int, C_ptr, C_char, & + C_NULL_CHAR, C_loc, C_F_pointer, lammps_instance => C_ptr + implicit none + private + public :: lammps_open, lammps_open_no_mpi, lammps_close, lammps_file, & + lammps_command, lammps_free, lammps_extract_global, & + lammps_extract_atom, lammps_extract_compute, lammps_extract_fix, & + lammps_extract_variable, lammps_get_natoms, lammps_gather_atoms, & + lammps_scatter_atoms, lammps_set_callback, lammps_set_user_energy + public :: lammps_instance, C_ptr, C_double, C_int + + !! Functions supplemental to the prototypes in library.h. {{{1 + !! The function definitions (in C++) are contained in LAMMPS-wrapper.cpp. + !! I would have written the first in Fortran, but the MPI libraries (which + !! were written in C) have C-based functions to convert from Fortran MPI + !! handles to C MPI handles, and there is no Fortran equivalent for those + !! functions. + interface + subroutine lammps_open_wrapper (argc, argv, communicator, ptr) & + bind (C, name='lammps_open_fortran_wrapper') + import :: C_int, C_ptr + integer (C_int), value :: argc + type (C_ptr), dimension(*) :: argv + integer, value :: communicator + type (C_ptr) :: ptr + end subroutine lammps_open_wrapper + subroutine lammps_actual_error_all (ptr, file, line, str) & + bind (C, name='lammps_error_all') + import :: C_int, C_char, C_ptr + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*), intent(in) :: file, str + integer (C_int), value :: line + end subroutine lammps_actual_error_all + function lammps_get_ntypes (ptr) result (ntypes) & + bind (C, name='lammps_get_ntypes') + import :: C_int, C_ptr + type (C_ptr), value :: ptr + integer (C_int) :: ntypes + end function lammps_get_ntypes + function lammps_actual_extract_compute_vectorsize (ptr, id, style) & + result (vectorsize) bind (C, name='lammps_extract_compute_vectorsize') + import :: C_int, C_char, C_ptr + integer (C_int) :: vectorsize + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style + end function lammps_actual_extract_compute_vectorsize + subroutine lammps_actual_extract_compute_arraysize (ptr, id, style, & + nrows, ncols) bind (C, name='lammps_extract_compute_arraysize') + import :: C_int, C_char, C_ptr + integer (C_int) :: arraysize + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style + integer (C_int) :: nrows, ncols + end subroutine lammps_actual_extract_compute_arraysize + function lammps_actual_extract_fix_vectorsize (ptr, id, style) & + result (vectorsize) bind (C, name='lammps_extract_fix_vectorsize') + import :: C_int, C_char, C_ptr + integer (C_int) :: vectorsize + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style + end function lammps_actual_extract_fix_vectorsize + subroutine lammps_actual_extract_fix_arraysize (ptr, id, style, & + nrows, ncols) bind (C, name='lammps_extract_fix_arraysize') + import :: C_int, C_char, C_ptr + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style + integer (C_int) :: nrows, ncols + end subroutine lammps_actual_extract_fix_arraysize + end interface + + !! Functions/subroutines defined in library.h and library.cpp {{{1 + interface + subroutine lammps_actual_open_no_mpi (argc, argv, ptr) & + bind (C, name='lammps_open_no_mpi') + import :: C_int, C_ptr + integer (C_int), value :: argc + type (C_ptr), dimension(*) :: argv + type (C_ptr) :: ptr + end subroutine lammps_actual_open_no_mpi + + subroutine lammps_close (ptr) bind (C, name='lammps_close') + import :: C_ptr + type (C_ptr), value :: ptr + end subroutine lammps_close + + subroutine lammps_actual_file (ptr, str) bind (C, name='lammps_file') + import :: C_ptr, C_char + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: str + end subroutine lammps_actual_file + + function lammps_actual_command (ptr, str) result (command) & + bind (C, name='lammps_command') + import :: C_ptr, C_char + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: str + type (C_ptr) :: command + end function lammps_actual_command + + subroutine lammps_free (ptr) bind (C, name='lammps_free') + import :: C_ptr + type (C_ptr), value :: ptr + end subroutine lammps_free + + function lammps_actual_extract_global (ptr, name) & + bind (C, name='lammps_extract_global') result (global) + import :: C_ptr, C_char + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: name + type (C_ptr) :: global + end function lammps_actual_extract_global + + function lammps_actual_extract_atom (ptr, name) & + bind (C, name='lammps_extract_atom') result (atom) + import :: C_ptr, C_char + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: name + type (C_ptr) :: atom + end function lammps_actual_extract_atom + + function lammps_actual_extract_compute (ptr, id, style, type) & + result (compute) bind (C, name='lammps_extract_compute') + import :: C_ptr, C_char, C_int + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style, type + type (C_ptr) :: compute + end function lammps_actual_extract_compute + + function lammps_actual_extract_fix (ptr, id, style, type, i, j) & + result (fix) bind (C, name='lammps_extract_fix') + import :: C_ptr, C_char, C_int + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: id + integer (C_int), value :: style, type, i, j + type (C_ptr) :: fix + end function lammps_actual_extract_fix + + function lammps_actual_extract_variable (ptr, name, group) & + result (variable) bind (C, name='lammps_extract_variable') + import :: C_ptr, C_char + type (C_ptr), value :: ptr + character (kind=C_char), dimension(*) :: name, group + type (C_ptr) :: variable + end function lammps_actual_extract_variable + + function lammps_get_natoms (ptr) result (natoms) & + bind (C, name='lammps_get_natoms') + import :: C_ptr, C_int + type (C_ptr), value :: ptr + integer (C_int) :: natoms + end function lammps_get_natoms + + subroutine lammps_set_callback (ptr) & + bind (C, name='lammps_set_callback') + import :: C_ptr + type (C_ptr), value :: ptr + end subroutine lammps_set_callback + + subroutine lammps_set_user_energy (ptr, energy) & + bind (C, name='lammps_set_user_energy') + import :: C_ptr, C_double + type (C_ptr), value :: ptr + real(C_double), value :: energy + end subroutine lammps_set_user_energy + + subroutine lammps_actual_gather_atoms (ptr, name, type, count, data) & + bind (C, name='lammps_gather_atoms') + import :: C_ptr, C_int, C_char + type (C_ptr), value :: ptr, data + character (kind=C_char), dimension(*) :: name + integer (C_int), value :: type, count + end subroutine lammps_actual_gather_atoms + + subroutine lammps_actual_scatter_atoms (ptr, name, type, count, data) & + bind (C, name='lammps_scatter_atoms') + import :: C_ptr, C_int, C_char + type (C_ptr), value :: ptr, data + character (kind=C_char), dimension(*) :: name + integer (C_int), value :: type, count + end subroutine lammps_actual_scatter_atoms + end interface + + ! Generic functions for the wrappers below {{{1 + + interface lammps_extract_global + module procedure lammps_extract_global_i, & + lammps_extract_global_dp + end interface lammps_extract_global + + interface lammps_extract_atom + module procedure lammps_extract_atom_ia, & + lammps_extract_atom_dpa, & + lammps_extract_atom_dp2a + end interface lammps_extract_atom + + interface lammps_extract_compute + module procedure lammps_extract_compute_dp, & + lammps_extract_compute_dpa, & + lammps_extract_compute_dp2a + end interface lammps_extract_compute + + interface lammps_extract_fix + module procedure lammps_extract_fix_dp, & + lammps_extract_fix_dpa, & + lammps_extract_fix_dp2a + end interface lammps_extract_fix + + interface lammps_extract_variable + module procedure lammps_extract_variable_dp, & + lammps_extract_variable_dpa + end interface lammps_extract_variable + + interface lammps_gather_atoms + module procedure lammps_gather_atoms_ia, lammps_gather_atoms_dpa + end interface lammps_gather_atoms + + interface lammps_scatter_atoms + module procedure lammps_scatter_atoms_ia, lammps_scatter_atoms_dpa + end interface lammps_scatter_atoms + +contains !! Wrapper functions local to this module {{{1 + + subroutine lammps_open (command_line, communicator, ptr) + character (len=*), intent(in) :: command_line + integer, intent(in) :: communicator + type (C_ptr) :: ptr + integer (C_int) :: argc + type (C_ptr), dimension(:), allocatable :: argv + character (kind=C_char), dimension(len_trim(command_line)+1), target :: & + c_command_line + c_command_line = string2Cstring (command_line) + call Cstring2argcargv (c_command_line, argc, argv) + call lammps_open_wrapper (argc, argv, communicator, ptr) + deallocate (argv) + end subroutine lammps_open + +!----------------------------------------------------------------------------- + + subroutine lammps_open_no_mpi (command_line, ptr) + character (len=*), intent(in) :: command_line + type (C_ptr) :: ptr + integer (C_int) :: argc + type (C_ptr), dimension(:), allocatable :: argv + character (kind=C_char), dimension(len_trim(command_line)+1), target :: & + c_command_line + c_command_line = string2Cstring (command_line) + call Cstring2argcargv (c_command_line, argc, argv) + call lammps_actual_open_no_mpi (argc, argv, ptr) + deallocate (argv) + end subroutine lammps_open_no_mpi + +!----------------------------------------------------------------------------- + + subroutine lammps_file (ptr, str) + type (C_ptr) :: ptr + character (len=*) :: str + character (kind=C_char), dimension(len_trim(str)+1) :: Cstr + Cstr = string2Cstring (str) + call lammps_actual_file (ptr, Cstr) + end subroutine lammps_file + +!----------------------------------------------------------------------------- + + subroutine lammps_command (ptr, str) + type (C_ptr) :: ptr + character (len=*) :: str + character (kind=C_char), dimension(len_trim(str)+1) :: Cstr + type (C_ptr) :: dummy + Cstr = string2Cstring (str) + dummy = lammps_actual_command (ptr, Cstr) + end subroutine lammps_command + +!----------------------------------------------------------------------------- + +! lammps_extract_global {{{2 + function lammps_extract_global_Cptr (ptr, name) result (global) + type (C_ptr) :: global + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + Cname = string2Cstring (name) + global = lammps_actual_extract_global (ptr, Cname) + end function lammps_extract_global_Cptr + subroutine lammps_extract_global_i (global, ptr, name) + integer (C_int), pointer, intent(out) :: global + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + type (C_ptr) :: Cptr + Cptr = lammps_extract_global_Cptr (ptr, name) + call C_F_pointer (Cptr, global) + end subroutine lammps_extract_global_i + subroutine lammps_extract_global_dp (global, ptr, name) + real (C_double), pointer, intent(out) :: global + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + type (C_ptr) :: Cptr + Cptr = lammps_extract_global_Cptr (ptr, name) + call C_F_pointer (Cptr, global) + end subroutine lammps_extract_global_dp + +!----------------------------------------------------------------------------- + +! lammps_extract_atom {{{2 + function lammps_extract_atom_Cptr (ptr, name) result (atom) + type (C_ptr) :: atom + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + Cname = string2Cstring (name) + atom = lammps_actual_extract_atom (ptr, Cname) + end function lammps_extract_atom_Cptr + subroutine lammps_extract_atom_ia (atom, ptr, name) + integer (C_int), dimension(:), pointer, intent(out) :: atom + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + type (C_ptr) :: Cptr + integer (C_int), pointer :: nelements + call lammps_extract_global_i (nelements, ptr, 'nlocal') + Cptr = lammps_extract_atom_Cptr (ptr, name) + call C_F_pointer (Cptr, atom, (/nelements/)) + end subroutine lammps_extract_atom_ia + subroutine lammps_extract_atom_dpa (atom, ptr, name) + real (C_double), dimension(:), pointer, intent(out) :: atom + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + type (C_ptr) :: Cptr + integer (C_int), pointer :: nlocal + integer :: nelements + real (C_double), dimension(:), pointer :: Fptr + if ( name == 'mass' ) then + nelements = lammps_get_ntypes (ptr) + 1 + else if ( name == 'x' .or. name == 'v' .or. name == 'f' .or. & + name == 'mu' .or. name == 'omega' .or. name == 'torque' .or. & + name == 'angmom' ) then + ! We should not be getting a rank-2 array here! + call lammps_error_all (ptr, FLERR, 'You cannot extract those atom& + & data (' // trim(name) // ') into a rank 1 array.') + return + else + ! Everything else we can get is probably nlocal units long + call lammps_extract_global_i (nlocal, ptr, 'nlocal') + nelements = nlocal + end if + Cptr = lammps_extract_atom_Cptr (ptr, name) + call C_F_pointer (Cptr, Fptr, (/nelements/)) + if ( name == 'mass' ) then + !atom(0:) => Fptr + atom => Fptr + else + atom => Fptr + end if + end subroutine lammps_extract_atom_dpa + subroutine lammps_extract_atom_dp2a (atom, ptr, name) + real (C_double), dimension(:,:), pointer, intent(out) :: atom + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + type (C_ptr) :: Cptr + type (C_ptr), pointer, dimension(:) :: Catom + integer (C_int), pointer :: nelements + if ( name /= 'x' .and. name /= 'v' .and. name /= 'f' .and. & + name /= 'mu' .and. name /= 'omega' .and. name /= 'tandque' .and. & + name /= 'angmom' .and. name /= 'fexternal' ) then + ! We should not be getting a rank-2 array here! + call lammps_error_all (ptr, FLERR, 'You cannot extract those atom& + & data (' // trim(name) // ') into a rank 2 array.') + return + end if + Cptr = lammps_extract_atom_Cptr (ptr, name) + call lammps_extract_global_i (nelements, ptr, 'nlocal') + ! Catom will now be the array of void* pointers that the void** pointer + ! pointed to. Catom(1) is now the pointer to the first element. + call C_F_pointer (Cptr, Catom, (/nelements/)) + ! Now get the actual array, which has its shape transposed from what we + ! might think of it in C + call C_F_pointer (Catom(1), atom, (/3, nelements/)) + end subroutine lammps_extract_atom_dp2a + +!----------------------------------------------------------------------------- + +! lammps_extract_compute {{{2 + function lammps_extract_compute_Cptr (ptr, id, style, type) result (compute) + type (C_ptr) :: compute + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type + integer (kind=C_int) :: Cstyle, Ctype + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + Cid = string2Cstring (id) + Cstyle = style + Ctype = type + compute = lammps_actual_extract_compute (ptr, Cid, Cstyle, Ctype) + end function lammps_extract_compute_Cptr + subroutine lammps_extract_compute_dp (compute, ptr, id, style, type) + real (C_double), pointer, intent(out) :: compute + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type + type (C_ptr) :: Cptr + ! The only valid values of (style,type) are (0,0) for scalar 'compute' + if ( style /= 0 ) then + call lammps_error_all (ptr, FLERR, 'You cannot pack per-atom/local& + & data into a scalar.') + return + end if + if ( type == 1 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & vector (rank 1) into a scalar.') + return + else if ( type == 2 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & array (rank 2) into a scalar.') + return + end if + Cptr = lammps_extract_compute_Cptr (ptr, id, style, type) + call C_F_pointer (Cptr, compute) + end subroutine lammps_extract_compute_dp + subroutine lammps_extract_compute_dpa (compute, ptr, id, style, type) + real (C_double), dimension(:), pointer, intent(out) :: compute + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type + type (C_ptr) :: Cptr + integer :: nelements + ! Check for the correct dimensionality + if ( type == 0 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & scalar (rank 0) into a rank 1 variable.') + return + else if ( type == 2 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & array (rank 2) into a rank 1 variable.') + return + end if + nelements = lammps_extract_compute_vectorsize (ptr, id, style) + Cptr = lammps_extract_compute_Cptr (ptr, id, style, type) + call C_F_pointer (Cptr, compute, (/nelements/)) + end subroutine lammps_extract_compute_dpa + subroutine lammps_extract_compute_dp2a (compute, ptr, id, style, type) + real (C_double), dimension(:,:), pointer, intent(out) :: compute + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type + type (C_ptr) :: Cptr + type (C_ptr), pointer, dimension(:) :: Ccompute + integer :: nr, nc + ! Check for the correct dimensionality + if ( type == 0 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & scalar (rank 0) into a rank 2 variable.') + return + else if ( type == 1 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a compute& + & array (rank 1) into a rank 2 variable.') + return + end if + call lammps_extract_compute_arraysize (ptr, id, style, nr, nc) + Cptr = lammps_extract_compute_Cptr (ptr, id, style, type) + call C_F_pointer (Cptr, Ccompute, (/nr/)) + ! Note that the matrix is transposed, from Fortran's perspective + call C_F_pointer (Ccompute(1), compute, (/nc, nr/)) + end subroutine lammps_extract_compute_dp2a + +!----------------------------------------------------------------------------- + +! lammps_extract_fix {{{2 + function lammps_extract_fix_Cptr (ptr, id, style, type, i, j) & + result (fix) + type (C_ptr) :: fix + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type, i, j + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + integer (kind=C_int) :: Cstyle, Ctype, Ci, Cj + Cid = string2Cstring (id) + Cstyle = style + Ctype = type + Ci = i - 1 ! This is for consistency with the values from f_ID[i], + Cj = j - 1 ! which is different from what library.cpp uses! + if ( (type >= 1 .and. Ci < 0) .or. & + (type == 2 .and. (Ci < 0 .or. Cj < 0) ) ) then + call lammps_error_all (ptr, FLERR, 'Index out of range in& + & lammps_extract_fix') + end if + fix = lammps_actual_extract_fix (ptr, Cid, Cstyle, Ctype, Ci, Cj) + end function lammps_extract_fix_Cptr + subroutine lammps_extract_fix_dp (fix, ptr, id, style, type, i, j) + real (C_double), intent(out) :: fix + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type, i, j + type (C_ptr) :: Cptr + real (C_double), pointer :: Fptr + ! Check for the correct dimensionality + if ( style /= 0 ) then + select case (type) + case (0) + call lammps_error_all (ptr, FLERR, 'There is no per-atom or local& + & scalar data available from fixes.') + case (1) + call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s & + &per-atom/local vector (rank 1) into a scalar.') + case (2) + call lammps_error_all (ptr, FLERR, 'You cannot extract a fix''s & + &per-atom/local array (rank 2) into a scalar.') + case default + call lammps_error_all (ptr, FLERR, 'Invalid extract_fix style/& + &type combination.') + end select + return + end if + Cptr = lammps_extract_fix_Cptr (ptr, id, style, type, i, j) + call C_F_pointer (Cptr, Fptr) + fix = Fptr + nullify (Fptr) + ! Memory is only allocated for "global" fix variables + if ( style == 0 ) call lammps_free (Cptr) + end subroutine lammps_extract_fix_dp + subroutine lammps_extract_fix_dpa (fix, ptr, id, style, type, i, j) + real (C_double), dimension(:), pointer, intent(out) :: fix + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type, i, j + type (C_ptr) :: Cptr + integer :: fix_len + ! Check for the correct dimensionality + if ( style == 0 ) then + call lammps_error_all (ptr, FLERR, 'You can''t extract the& + & whole vector from global fix data') + return + else if ( type == 0 ) then + call lammps_error_all (ptr, FLERR, 'You can''t extract a fix& + & scalar into a rank 1 variable') + return + else if ( type == 2 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a fix& + & array into a rank 1 variable.') + return + else if ( type /= 1 ) then + call lammps_error_all (ptr, FLERR, 'Invalid type for fix extraction.') + return + end if + fix_len = lammps_extract_fix_vectorsize (ptr, id, style) + call C_F_pointer (Cptr, fix, (/fix_len/)) + ! Memory is only allocated for "global" fix variables, which we should + ! never get here, so no need to call lammps_free! + end subroutine lammps_extract_fix_dpa + subroutine lammps_extract_fix_dp2a (fix, ptr, id, style, type, i, j) + real (C_double), dimension(:,:), pointer, intent(out) :: fix + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style, type, i, j + type (C_ptr) :: Cptr + type (C_ptr), pointer, dimension(:) :: Cfix + integer :: nr, nc + ! Check for the correct dimensionality + if ( style == 0 ) then + call lammps_error_all (ptr, FLERR, 'It is not possible to extract the& + & entire array from global fix data.') + return + else if ( type == 0 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a fix& + & scalar (rank 0) into a rank 2 variable.') + return + else if ( type == 1 ) then + call lammps_error_all (ptr, FLERR, 'You cannot extract a fix& + & vector (rank 1) into a rank 2 variable.') + return + end if + call lammps_extract_fix_arraysize (ptr, id, style, nr, nc) + ! Extract pointer to first element as Cfix(1) + call C_F_pointer (Cptr, Cfix, (/nr/)) + ! Now extract the array, which is transposed + call C_F_pointer (Cfix(1), fix, (/nc, nr/)) + end subroutine lammps_extract_fix_dp2a + +!----------------------------------------------------------------------------- + +! lammps_extract_variable {{{2 + function lammps_extract_variable_Cptr (ptr, name, group) result (variable) + type (C_ptr) :: ptr, variable + character (len=*) :: name + character (len=*), optional :: group + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + character (kind=C_char), dimension(:), allocatable :: Cgroup + Cname = string2Cstring (name) + if ( present(group) ) then + allocate (Cgroup(len_trim(group)+1)) + Cgroup = string2Cstring (group) + else + allocate (Cgroup(1)) + Cgroup(1) = C_NULL_CHAR + end if + variable = lammps_actual_extract_variable (ptr, Cname, Cgroup) + deallocate (Cgroup) + end function lammps_extract_variable_Cptr + subroutine lammps_extract_variable_dp (variable, ptr, name, group) + real (C_double), intent(out) :: variable + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + character (len=*), intent(in), optional :: group + type (C_ptr) :: Cptr + real (C_double), pointer :: Fptr + if ( present(group) ) then + Cptr = lammps_extract_variable_Cptr (ptr, name, group) + else + Cptr = lammps_extract_variable_Cptr (ptr, name) + end if + call C_F_pointer (Cptr, Fptr) + variable = Fptr + nullify (Fptr) + call lammps_free (Cptr) + end subroutine lammps_extract_variable_dp + subroutine lammps_extract_variable_dpa (variable, ptr, name, group) + real (C_double), dimension(:), allocatable, intent(out) :: variable + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + character (len=*), intent(in), optional :: group + type (C_ptr) :: Cptr + real (C_double), dimension(:), pointer :: Fptr + integer :: natoms + if ( present(group) ) then + Cptr = lammps_extract_variable_Cptr (ptr, name, group) + else + Cptr = lammps_extract_variable_Cptr (ptr, name) + end if + natoms = lammps_get_natoms (ptr) + allocate (variable(natoms)) + call C_F_pointer (Cptr, Fptr, (/natoms/)) + variable = Fptr + nullify (Fptr) + call lammps_free (Cptr) + end subroutine lammps_extract_variable_dpa + +!-------------------------------------------------------------------------2}}} + + subroutine lammps_gather_atoms_ia (ptr, name, count, data) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + integer, intent(in) :: count + integer, dimension(:), allocatable, intent(out) :: data + type (C_ptr) :: Cdata + integer (C_int), dimension(:), pointer :: Fdata + integer (C_int) :: natoms + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + integer (C_int), parameter :: Ctype = 0_C_int + integer (C_int) :: Ccount + natoms = lammps_get_natoms (ptr) + Cname = string2Cstring (name) + if ( count /= 1 .and. count /= 3 ) then + call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + & count to be either 1 or 3') + else + Ccount = count + end if + allocate ( Fdata(count*natoms) ) + allocate ( data(count*natoms) ) + Cdata = C_loc (Fdata(1)) + call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata) + data = Fdata + deallocate (Fdata) + end subroutine lammps_gather_atoms_ia + subroutine lammps_gather_atoms_dpa (ptr, name, count, data) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + integer, intent(in) :: count + double precision, dimension(:), allocatable, intent(out) :: data + type (C_ptr) :: Cdata + real (C_double), dimension(:), pointer :: Fdata + integer (C_int) :: natoms + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + integer (C_int), parameter :: Ctype = 1_C_int + integer (C_int) :: Ccount + natoms = lammps_get_natoms (ptr) + Cname = string2Cstring (name) + if ( count /= 1 .and. count /= 3 ) then + call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + & count to be either 1 or 3') + else + Ccount = count + end if + allocate ( Fdata(count*natoms) ) + allocate ( data(count*natoms) ) + Cdata = C_loc (Fdata(1)) + call lammps_actual_gather_atoms (ptr, Cname, Ctype, Ccount, Cdata) + data = Fdata(:) + deallocate (Fdata) + end subroutine lammps_gather_atoms_dpa + +!----------------------------------------------------------------------------- + + subroutine lammps_scatter_atoms_ia (ptr, name, data) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + integer, dimension(:), intent(in) :: data + integer (kind=C_int) :: natoms, Ccount + integer (kind=C_int), parameter :: Ctype = 0_C_int + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + integer (C_int), dimension(size(data)), target :: Fdata + type (C_ptr) :: Cdata + natoms = lammps_get_natoms (ptr) + Cname = string2Cstring (name) + Ccount = size(data) / natoms + if ( Ccount /= 1 .and. Ccount /= 3 ) & + call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + & count to be either 1 or 3') + Fdata = data + Cdata = C_loc (Fdata(1)) + call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata) + end subroutine lammps_scatter_atoms_ia + subroutine lammps_scatter_atoms_dpa (ptr, name, data) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: name + double precision, dimension(:), intent(in) :: data + integer (kind=C_int) :: natoms, Ccount + integer (kind=C_int), parameter :: Ctype = 1_C_int + character (kind=C_char), dimension(len_trim(name)+1) :: Cname + real (C_double), dimension(size(data)), target :: Fdata + type (C_ptr) :: Cdata + natoms = lammps_get_natoms (ptr) + Cname = string2Cstring (name) + Ccount = size(data) / natoms + if ( Ccount /= 1 .and. Ccount /= 3 ) & + call lammps_error_all (ptr, FLERR, 'lammps_gather_atoms requires& + & count to be either 1 or 3') + Fdata = data + Cdata = C_loc (Fdata(1)) + call lammps_actual_scatter_atoms (ptr, Cname, Ctype, Ccount, Cdata) + end subroutine lammps_scatter_atoms_dpa + +!----------------------------------------------------------------------------- + + function lammps_extract_compute_vectorsize (ptr, id, style) & + result (vectorsize) + integer :: vectorsize + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style + integer (C_int) :: Cvectorsize, Cstyle + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + Cid = string2Cstring (id) + Cstyle = int(style, C_int) + Cvectorsize = lammps_actual_extract_compute_vectorsize (ptr, Cid, Cstyle) + vectorsize = int(Cvectorsize, kind(vectorsize)) + end function lammps_extract_compute_vectorsize + +!----------------------------------------------------------------------------- + + function lammps_extract_fix_vectorsize (ptr, id, style) & + result (vectorsize) + integer :: vectorsize + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style + integer (C_int) :: Cvectorsize, Cstyle + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + Cid = string2Cstring (id) + Cstyle = int(style, C_int) + Cvectorsize = lammps_actual_extract_fix_vectorsize (ptr, Cid, Cstyle) + vectorsize = int(Cvectorsize, kind(vectorsize)) + end function lammps_extract_fix_vectorsize + +!----------------------------------------------------------------------------- + + subroutine lammps_extract_compute_arraysize (ptr, id, style, nrows, ncols) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style + integer, intent(out) :: nrows, ncols + integer (C_int) :: Cstyle, Cnrows, Cncols + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + Cid = string2Cstring (id) + Cstyle = int (style, C_int) + call lammps_actual_extract_compute_arraysize (ptr, Cid, Cstyle, & + Cnrows, Cncols) + nrows = int (Cnrows, kind(nrows)) + ncols = int (Cncols, kind(ncols)) + end subroutine lammps_extract_compute_arraysize + +!----------------------------------------------------------------------------- + + subroutine lammps_extract_fix_arraysize (ptr, id, style, nrows, ncols) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: id + integer, intent(in) :: style + integer, intent(out) :: nrows, ncols + integer (C_int) :: Cstyle, Cnrows, Cncols + character (kind=C_char), dimension(len_trim(id)+1) :: Cid + Cid = string2Cstring (id) + Cstyle = int (style, kind(Cstyle)) + call lammps_actual_extract_fix_arraysize (ptr, Cid, Cstyle, & + Cnrows, Cncols) + nrows = int (Cnrows, kind(nrows)) + ncols = int (Cncols, kind(ncols)) + end subroutine lammps_extract_fix_arraysize + +!----------------------------------------------------------------------------- + + subroutine lammps_error_all (ptr, file, line, str) + type (C_ptr), intent(in) :: ptr + character (len=*), intent(in) :: file, str + integer, intent(in) :: line + character (kind=C_char), dimension(len_trim(file)+1) :: Cfile + character (kind=C_char), dimension(len_trim(str)+1) :: Cstr + integer (C_int) :: Cline + Cline = int(line, kind(Cline)) + Cfile = string2Cstring (file) + Cstr = string2Cstring (str) + call lammps_actual_error_all (ptr, Cfile, Cline, Cstr) + end subroutine lammps_error_all + +!----------------------------------------------------------------------------- + +! Locally defined helper functions {{{1 + + pure function string2Cstring (string) result (C_string) + use, intrinsic :: ISO_C_binding, only : C_char, C_NULL_CHAR + character (len=*), intent(in) :: string + character (len=1, kind=C_char) :: C_string (len_trim(string)+1) + integer :: i, n + n = len_trim (string) + forall (i = 1:n) + C_string(i) = string(i:i) + end forall + C_string(n+1) = C_NULL_CHAR + end function string2Cstring + +!----------------------------------------------------------------------------- + + subroutine Cstring2argcargv (Cstring, argc, argv) + !! Converts a C-style string to argc and argv, that is, words in Cstring + !! become C-style strings in argv. IMPORTANT: Cstring is modified by + !! this routine! I would make Cstring local TO this routine and accept + !! a Fortran-style string instead, but we run into scoping and + !! allocation problems that way. This routine assumes the string is + !! null-terminated, as all C-style strings must be. + + character (kind=C_char), dimension(*), target, intent(inout) :: Cstring + integer (C_int), intent(out) :: argc + type (C_ptr), dimension(:), allocatable, intent(out) :: argv + + integer :: StringStart, SpaceIndex, strlen, argnum + + argc = 1_C_int + + ! Find the length of the string + strlen = 1 + do while ( Cstring(strlen) /= C_NULL_CHAR ) + strlen = strlen + 1 + end do + + ! Find the number of non-escaped spaces + SpaceIndex = 2 + do while ( SpaceIndex < strlen ) + if ( Cstring(SpaceIndex) == ' ' .and. & + Cstring(SpaceIndex-1) /= '\' ) then + argc = argc + 1_C_int + ! Find the next non-space character + do while ( Cstring(SpaceIndex+1) == ' ') + SpaceIndex = SpaceIndex + 1 + end do + end if + SpaceIndex = SpaceIndex + 1 + end do + + ! Now allocate memory for argv + allocate (argv(argc)) + + ! Now find the string starting and ending locations + StringStart = 1 + SpaceIndex = 2 + argnum = 1 + do while ( SpaceIndex < strlen ) + if ( Cstring(SpaceIndex) == ' ' .and. & + Cstring(SpaceIndex-1) /= '\' ) then + ! Found a real space => split strings and store this one + Cstring(Spaceindex) = C_NULL_CHAR ! Replaces space with NULL + argv(argnum) = C_loc(Cstring(StringStart)) + argnum = argnum + 1 + ! Find the next non-space character + do while ( Cstring(SpaceIndex+1) == ' ') + SpaceIndex = SpaceIndex + 1 + end do + StringStart = SpaceIndex + 1 + else if ( Cstring(SpaceIndex) == ' ' .and. & + Cstring(SpaceIndex-1) == '\' ) then + ! Escaped space => remove backslash and move rest of array + Cstring(SpaceIndex-1:strlen-1) = Cstring(SpaceIndex:strlen) + strlen = strlen - 1 ! Last character is still C_NULL_CHAR + end if + SpaceIndex = SpaceIndex + 1 + end do + ! Now handle the last argument + argv(argnum) = C_loc(Cstring(StringStart)) + + end subroutine Cstring2argcargv + +! 1}}} + +end module LAMMPS + +! vim: foldmethod=marker tabstop=3 softtabstop=3 shiftwidth=3 expandtab diff --git a/examples/COUPLE/fortran3/README b/examples/COUPLE/fortran3/README new file mode 100644 index 0000000000..9effa35ec4 --- /dev/null +++ b/examples/COUPLE/fortran3/README @@ -0,0 +1,33 @@ +This directory has an example of using a callback function to obtain +forces from a fortran code for a LAMMPS simulation. The reader should +refer to the README file in COUPLE/fortran2 before proceeding. Here, +the LAMMPS.F90 file has been modified slightly and additional files +named LAMMPS-wrapper2.h and LAMMPS-wrapper2.cpp have been included in +order to supply wrapper functions to set the LAMMPS callback function +and total energy. + +In this example, the callback function is set to run the +semi-empirical quantum code DFTB+ in serial and then read in the total +energy, forces, and stress tensor from file. In this case, nlocal = +the total number of atoms in the system, so particle positions can be +read from the pos array directly, and DFTB+ forces can simply be +included via the fext array. The user should take care in the case of +a parallel calculation, where LAMMPS can assign different particules +to each processor. For example, the user should use functions such as +lammps_gather_atoms() and lammps_scatter_atoms() in the case where the +fortran force calculating code requires the positions of all atoms, +etc. + +A few more important notes: + +-The stress tensor from DFTB+ is passed in to LAMMPS via pointer. +-Calling the subroutine lammps_set_callback() is required in order to set + a pointer to the callback function in LAMMPS. +-The subroutine lammps_set_user_energy() passes in the potential energy + from DFTB+ to LAMMPS. + +This example was created by Nir Goldman, whom you can contact with +questions: + +Nir Goldman, LLNL +ngoldman@llnl.gov diff --git a/examples/COUPLE/fortran3/data.diamond b/examples/COUPLE/fortran3/data.diamond new file mode 100644 index 0000000000..b3dd599cf4 --- /dev/null +++ b/examples/COUPLE/fortran3/data.diamond @@ -0,0 +1,148 @@ +# Position data file + +64 atoms +1 atom types + +0 7.134 xlo xhi +0 7.134 ylo yhi +0 7.134 zlo zhi + +0.00000000 0.00000000 0.00000000 xy xz yz + +Masses + +1 12.010000 + +Atoms + + 1 1 0 0 0 0 + 2 1 0 0.89175 0.89175 0.89175 + 3 1 0 1.7835 1.7835 0 + 4 1 0 2.67525 2.67525 0.89175 + 5 1 0 0 1.7835 1.7835 + 6 1 0 0.89175 2.67525 2.67525 + 7 1 0 1.7835 0 1.7835 + 8 1 0 2.67525 0.89175 2.67525 + 9 1 0 0 0 3.567 + 10 1 0 0.89175 0.89175 4.45875 + 11 1 0 1.7835 1.7835 3.567 + 12 1 0 2.67525 2.67525 4.45875 + 13 1 0 0 1.7835 5.3505 + 14 1 0 0.89175 2.67525 6.24225 + 15 1 0 1.7835 0 5.3505 + 16 1 0 2.67525 0.89175 6.24225 + 17 1 0 0 3.567 0 + 18 1 0 0.89175 4.45875 0.89175 + 19 1 0 1.7835 5.3505 0 + 20 1 0 2.67525 6.24225 0.89175 + 21 1 0 0 5.3505 1.7835 + 22 1 0 0.89175 6.24225 2.67525 + 23 1 0 1.7835 3.567 1.7835 + 24 1 0 2.67525 4.45875 2.67525 + 25 1 0 0 3.567 3.567 + 26 1 0 0.89175 4.45875 4.45875 + 27 1 0 1.7835 5.3505 3.567 + 28 1 0 2.67525 6.24225 4.45875 + 29 1 0 0 5.3505 5.3505 + 30 1 0 0.89175 6.24225 6.24225 + 31 1 0 1.7835 3.567 5.3505 + 32 1 0 2.67525 4.45875 6.24225 + 33 1 0 3.567 0 0 + 34 1 0 4.45875 0.89175 0.89175 + 35 1 0 5.3505 1.7835 0 + 36 1 0 6.24225 2.67525 0.89175 + 37 1 0 3.567 1.7835 1.7835 + 38 1 0 4.45875 2.67525 2.67525 + 39 1 0 5.3505 0 1.7835 + 40 1 0 6.24225 0.89175 2.67525 + 41 1 0 3.567 0 3.567 + 42 1 0 4.45875 0.89175 4.45875 + 43 1 0 5.3505 1.7835 3.567 + 44 1 0 6.24225 2.67525 4.45875 + 45 1 0 3.567 1.7835 5.3505 + 46 1 0 4.45875 2.67525 6.24225 + 47 1 0 5.3505 0 5.3505 + 48 1 0 6.24225 0.89175 6.24225 + 49 1 0 3.567 3.567 0 + 50 1 0 4.45875 4.45875 0.89175 + 51 1 0 5.3505 5.3505 0 + 52 1 0 6.24225 6.24225 0.89175 + 53 1 0 3.567 5.3505 1.7835 + 54 1 0 4.45875 6.24225 2.67525 + 55 1 0 5.3505 3.567 1.7835 + 56 1 0 6.24225 4.45875 2.67525 + 57 1 0 3.567 3.567 3.567 + 58 1 0 4.45875 4.45875 4.45875 + 59 1 0 5.3505 5.3505 3.567 + 60 1 0 6.24225 6.24225 4.45875 + 61 1 0 3.567 5.3505 5.3505 + 62 1 0 4.45875 6.24225 6.24225 + 63 1 0 5.3505 3.567 5.3505 + 64 1 0 6.24225 4.45875 6.24225 + +Velocities + +1 -0.00733742 -0.0040297 -0.00315229 +2 -0.00788609 -0.00567535 -0.00199152 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0.00523475 +55 0.00305618 -0.00320094 0.00341297 +56 0.004304 0.000615544 -0.00668787 +57 0.00564532 0.00327373 0.00388611 +58 0.000676899 0.00210326 0.00495295 +59 0.000160781 -0.00744313 -0.00279828 +60 0.00623521 0.00371301 0.00178015 +61 0.00520759 0.000642669 0.00207913 +62 0.00398042 0.0046438 -0.00359978 +63 -0.00478071 -0.00304932 -0.00765125 +64 0.00282671 -0.00548392 -0.00692691 diff --git a/examples/COUPLE/fortran3/in.simple b/examples/COUPLE/fortran3/in.simple new file mode 100644 index 0000000000..894a490cf8 --- /dev/null +++ b/examples/COUPLE/fortran3/in.simple @@ -0,0 +1,16 @@ +units real +atom_style charge +atom_modify map array +atom_modify sort 0 0.0 +read_data data.diamond +neighbor 1.0 bin +neigh_modify delay 0 every 5 check no +fix 1 all nve +fix 2 all external pf/callback 1 1 + +fix_modify 2 energy yes +thermo_style custom step temp etotal ke pe lx ly lz pxx pyy pzz press + +thermo 1 +timestep 0.5 + diff --git a/examples/COUPLE/fortran3/makefile b/examples/COUPLE/fortran3/makefile new file mode 100644 index 0000000000..86dea30850 --- /dev/null +++ b/examples/COUPLE/fortran3/makefile @@ -0,0 +1,45 @@ +SHELL = /bin/sh + +# Path to LAMMPS extraction directory +LAMMPS_ROOT = ../../.. +LAMMPS_SRC = $(LAMMPS_ROOT)/src + +# Uncomment the line below if using the MPI stubs library +MPI_STUBS = #-I$(LAMMPS_SRC)/STUBS + +FC = mpif90 # replace with your Fortran compiler +CXX = mpicc # replace with your C++ compiler + +# Flags for Fortran compiler, C++ compiler, and C preprocessor, respectively +FFLAGS = -O2 -fPIC +CXXFLAGS = -O2 -fPIC +CPPFLAGS = -DOMPI_SKIP_MPICXX=1 -DMPICH_SKIP_MPICXX + +all : liblammps_fortran.a liblammps_fortran.so simpleF.x + +liblammps_fortran.so : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o + $(FC) $(FFLAGS) -shared -o $@ $^ + +simpleF.x: simple.o LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o + $(FC) $(FFLAGS) simple.o -o simpleF.x liblammps_fortran.a $(LAMMPS_SRC)/liblammps_mvapich.a -lstdc++ /usr/local/tools/fftw/lib/libfftw.a + +liblammps_fortran.a : LAMMPS.o LAMMPS-wrapper.o LAMMPS-wrapper2.o + $(AR) rs $@ $^ + +LAMMPS.o lammps.mod : LAMMPS.F90 + $(FC) $(CPPFLAGS) $(FFLAGS) -c $< + +simple.o : simple.f90 + $(FC) $(FFLAGS) -c $< + +LAMMPS-wrapper.o : LAMMPS-wrapper.cpp LAMMPS-wrapper.h + $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS) + +LAMMPS-wrapper2.o : LAMMPS-wrapper2.cpp LAMMPS-wrapper2.h + $(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -I$(LAMMPS_SRC) $(MPI_STUBS) + +clean : + $(RM) *.o *.mod liblammps_fortran.a liblammps_fortran.so + +dist : + tar -czvf fortran-interface-callback.tar.gz LAMMPS-wrapper.h LAMMPS-wrapper.cpp LAMMPS-wrapper2.h LAMMPS-wrapper2.cpp LAMMPS.F90 makefile README simple.f90 diff --git a/examples/COUPLE/fortran3/simple.f90 b/examples/COUPLE/fortran3/simple.f90 new file mode 100644 index 0000000000..40f8bf8b86 --- /dev/null +++ b/examples/COUPLE/fortran3/simple.f90 @@ -0,0 +1,114 @@ + module callback + implicit none + contains + subroutine fortran_callback(lmp, timestep, nlocal, ids, c_pos, c_fext) & + & bind(C, name='f_callback') + use, intrinsic :: ISO_C_binding + use LAMMPS + implicit none + type (C_ptr), value :: lmp + integer(C_int64_t), intent(in), value :: timestep + integer(C_int), intent(in), value :: nlocal + real (C_double), dimension(:,:), pointer :: x + type(c_ptr) :: c_pos, c_fext, c_ids + double precision, pointer :: fext(:,:), pos(:,:) + integer, intent(in) :: ids(nlocal) + real (C_double), dimension(:), pointer :: virial => NULL() + real (C_double) :: etot + real(C_double), pointer :: ts_lmp + double precision :: stress(3,3), ts_dftb + integer :: natom , i + real (C_double), parameter :: econv = 627.4947284155114 ! converts from Ha to + double precision, parameter :: fconv = 1185.793095983065 ! converts from Ha/bohr to + double precision, parameter :: autoatm = 2.9037166638E8 + double precision lx, ly, lz + real (C_double), pointer :: boxxlo, boxxhi + real (C_double), pointer :: boxylo, boxyhi + real (C_double), pointer :: boxzlo, boxzhi + double precision, parameter :: nktv2p = 68568.4149999999935972 + double precision :: volume + type (C_ptr) :: Cptr + type (C_ptr), pointer, dimension(:) :: Catom + + call c_f_pointer(c_pos, pos, [3,nlocal]) + call c_f_pointer(c_fext, fext, [3,nlocal]) + call lammps_extract_global(boxxlo, lmp, 'boxxlo') + call lammps_extract_global(boxxhi, lmp, 'boxxhi') + call lammps_extract_global(boxylo, lmp, 'boxylo') + call lammps_extract_global(boxyhi, lmp, 'boxyhi') + call lammps_extract_global(boxzlo, lmp, 'boxzlo') + call lammps_extract_global(boxzhi, lmp, 'boxzhi') + lx = boxxhi - boxxlo + ly = boxyhi - boxylo + lz = boxzhi - boxzlo + volume = lx*ly*lz + open (unit = 10, status = 'replace', action = 'write', file='lammps.gen') + write(10,*)nlocal,"S" + write(10,*) "C" + do i = 1, nlocal + write(10,'(2I,3F15.6)')i,1,pos(:,ids(i)) + enddo + write(10,*)"0.0 0.0 0.0" + write(10,*)lx,0,0 + write(10,*)0,ly,0 + write(10,*)0,0,lz + close(10) + call system("./dftb+ > dftb.out") + open (unit = 10, status = 'old', file = 'results.out') + read(10,*)etot + read(10,*)ts_dftb + do i = 1, 3 + read(10,*)stress(i,:) + enddo + stress (:,:) = stress(:,:)*autoatm + etot = etot*econv + call lammps_extract_global(ts_lmp, lmp, 'TS_dftb') + ts_lmp = ts_dftb + do i = 1, nlocal + read(10,*)fext(:,ids(i)) + fext(:,ids(i)) = fext(:,ids(i))*fconv + enddo + close(10) + call lammps_set_user_energy (lmp, etot) + call lammps_extract_atom (virial, lmp, 'virial') + if (.not. associated(virial)) then + print*,'virial pointer not associated.' + STOP + endif + virial(1) = stress(1,1)/(nktv2p/volume) + virial(2) = stress(2,2)/(nktv2p/volume) + virial(3) = stress(3,3)/(nktv2p/volume) + virial(4) = stress(1,2)/(nktv2p/volume) + virial(5) = stress(1,3)/(nktv2p/volume) + virial(6) = stress(2,3)/(nktv2p/volume) + + end subroutine + end module callback + + +program simple_fortran_callback + + use MPI + use LAMMPS + use callback + use, intrinsic :: ISO_C_binding, only : C_double, C_ptr, C_int, C_FUNPTR + implicit none + type (C_ptr) :: lmp + integer :: error, narg, me, nprocs + + call MPI_Init (error) + call MPI_Comm_rank (MPI_COMM_WORLD, me, error) + call MPI_Comm_size (MPI_COMM_WORLD, nprocs, error) + + call lammps_open_no_mpi ('lmp -log log.simple', lmp) + call lammps_file (lmp, 'in.simple') + call lammps_set_callback(lmp) + + call lammps_command (lmp, 'run 10') + call lammps_close (lmp) + call MPI_Finalize (error) + + +end program simple_fortran_callback + + diff --git a/examples/COUPLE/simple/simple.cpp b/examples/COUPLE/simple/simple.cpp index b279ae704c..894c708978 100644 --- a/examples/COUPLE/simple/simple.cpp +++ b/examples/COUPLE/simple/simple.cpp @@ -153,7 +153,7 @@ int main(int narg, char **arg) for (int i = 0; i < natoms; i++) type[i] = 1; lmp->input->one("delete_atoms group all"); - lammps_create_atoms(lmp,natoms,NULL,type,x,v); + lammps_create_atoms(lmp,natoms,NULL,type,x,v,NULL,0); lmp->input->one("run 10"); } diff --git a/examples/USER/cgdna/util/generate.py b/examples/USER/cgdna/util/generate.py index d5a74e9bf7..eb97f482cc 100644 --- a/examples/USER/cgdna/util/generate.py +++ b/examples/USER/cgdna/util/generate.py @@ -14,7 +14,7 @@ ------------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- - Contributing author: Oliver Henrich (EPCC, University of Edinburgh) + Contributing author: Oliver Henrich (University of Strathclyde, Glasgow) ------------------------------------------------------------------------- */ """ diff --git a/examples/USER/misc/cnp/Cu_Mishin1.eam b/examples/USER/misc/cnp/Cu_Mishin1.eam new file mode 100644 index 0000000000..8ea788b16d --- /dev/null +++ b/examples/USER/misc/cnp/Cu_Mishin1.eam @@ -0,0 +1,30009 @@ +#-> LAMMPS Potential File in DYNAMO 86 setfl Format <-# +# Mishin Cu EAM1 PRB(2001)63:224106 +# Implemented by G. Ziegenhain (2007) gerolf@ziegenhain.com +1 Cu +10001 0.00016401626143851118 10001 0.00089991000899910004 5.50678999999999962967 +1 63.54999999999999715783 3.61500000000000021316 FCC +0.00000499999999981071 +-0.00174266214468410396 +-0.00348892099090747365 +-0.00523377758263166015 +-0.00697723296321983710 +-0.00871928817543166090 +-0.01045994426141616529 +-0.01219920226272552810 +-0.01393706322030219269 +-0.01567352817448997016 +-0.01740859816502871027 +-0.01914227423105074877 +-0.02087455741109200957 +-0.02260544874308356711 +-0.02433494926435164629 +-0.02606306001162250752 +-0.02778978202102377892 +-0.02951511632807468644 +-0.03123906396769937643 +-0.03296162597421536944 +-0.03468280338134377416 +-0.03640259722220395844 +-0.03812100852931310513 +-0.03983803833458932075 +-0.04155368766935163549 +-0.04326795756431689455 +-0.04498084904960464314 +-0.04669236315473579424 +-0.04840250090862818766 +-0.05011126333960413959 +-0.05181865147538822214 +-0.05352466634310193427 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system +lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 +region mdbox block 0 3 0.0 14.0 0 84 units lattice +region system block 0 3 1.1 13.1 0 84 units lattice +create_box 2 mdbox +create_atoms 1 region system + +# Define atoms mass and force field +mass * 63.54 +pair_style eam/alloy +pair_coeff * * Cu_Mishin1.eam Cu Cu + +# Delete a plane of atoms along the z direction to generate a partial dislocation +region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice +delete_atoms region dislocation_atoms +region quarter_up block 0 3 7 11 0 84 units lattice +group middle region quarter_up + +# specify simulation parameters +timestep 0.004 + +# Relax configuration using conjugate gradient +#min_style cg +#minimize 1.0e-4 1.0e-6 100 1000 + +# Setup calculations +compute 1 all cnp/atom 3.086 +compute 2 all cna/atom 3.086 +compute 3 all centro/atom fcc +compute 4 all coord/atom cutoff 3.086 +dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 + +### Set up thermo display +thermo 10 +thermo_style custom step atoms temp press pe ke etotal + +# Relax the system performing a langevin dynamics (freeze motion along y 111 direction) +fix 1 all nve +fix 2 all langevin 50 1 0.1 699483 +fix 3 all setforce NULL 0.0 NULL +fix 4 middle setforce 0.0 0.0 0.0 +run 100 +unfix 4 +run 200 diff --git a/examples/USER/misc/cnp/log.31May17.cnp.g++.4 b/examples/USER/misc/cnp/log.31May17.cnp.g++.4 new file mode 100644 index 0000000000..d86d0b5600 --- /dev/null +++ b/examples/USER/misc/cnp/log.31May17.cnp.g++.4 @@ -0,0 +1,185 @@ +LAMMPS (19 May 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Generation and relaxation of a partial dislocation in Cu perfect FCC crystal + +# Initialization +units metal +boundary p p p +atom_style atomic + +# create simulation box and system +lattice fcc 3.615 origin 0.01 0.01 0.01 orient x -1 -1 2 orient y 1 1 1 orient z -1 1 0 +Lattice spacing in x,y,z = 5.90327 6.26136 5.11238 +region mdbox block 0 3 0.0 14.0 0 84 units lattice +region system block 0 3 1.1 13.1 0 84 units lattice +create_box 2 mdbox +Created orthogonal box = (0 0 0) to (17.7098 87.6591 429.44) + 1 by 1 by 4 MPI processor grid +create_atoms 1 region system +Created 48384 atoms + +# Define atoms mass and force field +mass * 63.54 +pair_style eam/alloy +pair_coeff * * Cu_Mishin1.eam Cu Cu + +# Delete a plane of atoms along the z direction to generate a partial dislocation +region dislocation_atoms block 0 3 7 14 41.9 42.1 units lattice +delete_atoms region dislocation_atoms +Deleted 76 atoms, new total = 48308 +region quarter_up block 0 3 7 11 0 84 units lattice +group middle region quarter_up +16080 atoms in group middle + +# specify simulation parameters +timestep 0.004 + +# Relax configuration using conjugate gradient +#min_style cg +#minimize 1.0e-4 1.0e-6 100 1000 + +# Setup calculations +compute 1 all cnp/atom 3.086 +compute 2 all cna/atom 3.086 +compute 3 all centro/atom fcc +compute 4 all coord/atom cutoff 3.086 +dump 1 all custom 100 dump.lammpstrj id type xu yu zu c_1 c_2 c_3 c_4 + +### Set up thermo display +thermo 10 +thermo_style custom step atoms temp press pe ke etotal + +# Relax the system performing a langevin dynamics (freeze motion along y 111 direction) +fix 1 all nve +fix 2 all langevin 50 1 0.1 699483 +fix 3 all setforce NULL 0.0 NULL +fix 4 middle setforce 0.0 0.0 0.0 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 7.50679 + ghost atom cutoff = 7.50679 + binsize = 3.75339, bins = 5 24 115 + 5 neighbor lists, perpetual/occasional/extra = 1 4 0 + (1) pair eam/alloy, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute cnp/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (3) compute cna/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (4) compute centro/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (5) compute coord/atom, occasional + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes +Step Atoms Temp Press PotEng KinEng TotEng + 0 48308 0 -3388.0911 -169746.07 0 -169746.07 + 10 48308 7.35092 -3091.0864 -169715.96 45.900393 -169670.05 + 20 48308 9.9162268 -2822.7045 -169678.51 61.918604 -169616.59 + 30 48308 12.351316 -2726.7195 -169666.35 77.123716 -169589.23 + 40 48308 13.302856 -2703.586 -169662.9 83.06529 -169579.83 + 50 48308 12.782228 -2706.8662 -169662.36 79.814401 -169582.55 + 60 48308 12.198179 -2772.4206 -169670.02 76.167503 -169593.86 + 70 48308 10.663322 -2841.3384 -169677.48 66.583595 -169610.9 + 80 48308 9.1169804 -2932.3896 -169687.85 56.927974 -169630.92 + 90 48308 7.2905076 -3029.9433 -169699.09 45.523167 -169653.56 + 100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89 +Loop time of 10.9003 on 4 procs for 100 steps with 48308 atoms + +Performance: 3.171 ns/day, 7.570 hours/ns, 9.174 timesteps/s +31.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.8764 | 9.9587 | 10.021 | 1.6 | 91.36 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.1232 | 0.18385 | 0.26683 | 12.1 | 1.69 +Output | 0.45385 | 0.45451 | 0.45634 | 0.2 | 4.17 +Modify | 0.25026 | 0.2537 | 0.25744 | 0.5 | 2.33 +Other | | 0.04949 | | | 0.45 + +Nlocal: 12077 ave 12096 max 12020 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 14204 ave 14261 max 14109 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 814050 ave 818584 max 809212 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 1.6281e+06 ave 1.63296e+06 max 1.61808e+06 min +Histogram: 1 0 0 0 0 0 1 0 0 2 + +Total # of neighbors = 6512400 +Ave neighs/atom = 134.81 +Neighbor list builds = 0 +Dangerous builds = 0 +unfix 4 +run 200 +Per MPI rank memory allocation (min/avg/max) = 45.41 | 45.41 | 45.41 Mbytes +Step Atoms Temp Press PotEng KinEng TotEng + 100 48308 5.4063635 -3139.4496 -169711.65 33.758252 -169677.89 + 110 48308 15.260795 -2793.119 -169677.24 95.290993 -169581.95 + 120 48308 18.548656 -2433.1584 -169624.79 115.82096 -169508.97 + 130 48308 22.15831 -2276.626 -169604.28 138.36025 -169465.92 + 140 48308 24.393841 -2208.1771 -169596.16 152.31929 -169443.84 + 150 48308 24.797558 -2173.3145 -169591.43 154.84016 -169436.59 + 160 48308 24.73371 -2188.909 -169593.08 154.44148 -169438.64 + 170 48308 24.128467 -2220.3404 -169596.96 150.66225 -169446.29 + 180 48308 22.975708 -2275.1244 -169602.72 143.46422 -169459.26 + 190 48308 21.936324 -2348.3762 -169610.59 136.97413 -169473.61 + 200 48308 20.516249 -2432.8447 -169619.98 128.10694 -169491.87 + 210 48308 19.000566 -2510.2915 -169628.58 118.64276 -169509.93 + 220 48308 17.490407 -2597.299 -169638.24 109.21307 -169529.03 + 230 48308 16.062482 -2684.1203 -169648.31 100.29687 -169548.01 + 240 48308 14.360342 -2768.2313 -169657.7 89.668411 -169568.03 + 250 48308 12.802315 -2852.6965 -169666.99 79.939831 -169587.05 + 260 48308 11.258205 -2944.4533 -169677.52 70.298142 -169607.23 + 270 48308 9.6159129 -3038.6304 -169688.06 60.043393 -169628.02 + 280 48308 7.972425 -3129.0826 -169698.03 49.781176 -169648.25 + 290 48308 6.3752377 -3219.2054 -169708.23 39.808067 -169668.42 + 300 48308 4.7374688 -3306.1468 -169718.27 29.58156 -169688.69 +Loop time of 23.0164 on 4 procs for 200 steps with 48308 atoms + +Performance: 3.003 ns/day, 7.992 hours/ns, 8.689 timesteps/s +31.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.221 | 20.423 | 20.57 | 3.1 | 88.73 +Neigh | 0 | 0 | 0 | 0.0 | 0.00 +Comm | 0.27748 | 0.42603 | 0.62832 | 21.4 | 1.85 +Output | 1.5454 | 1.5473 | 1.5529 | 0.3 | 6.72 +Modify | 0.48886 | 0.49773 | 0.50842 | 1.1 | 2.16 +Other | | 0.1221 | | | 0.53 + +Nlocal: 12077 ave 12096 max 12020 min +Histogram: 1 0 0 0 0 0 0 0 0 3 +Nghost: 14204 ave 14261 max 14109 min +Histogram: 1 0 0 0 0 1 0 0 0 2 +Neighs: 814094 ave 818584 max 809212 min +Histogram: 1 0 0 0 0 2 0 0 0 1 +FullNghs: 1.62852e+06 ave 1.63296e+06 max 1.61892e+06 min +Histogram: 1 0 0 0 0 0 0 1 0 2 + +Total # of neighbors = 6514094 +Ave neighs/atom = 134.845 +Neighbor list builds = 0 +Dangerous builds = 0 +Total wall time: 0:00:35 diff --git a/examples/USER/misc/edip/Si.edip b/examples/USER/misc/edip/Si.edip new file mode 100644 index 0000000000..b3b960e738 --- /dev/null +++ b/examples/USER/misc/edip/Si.edip @@ -0,0 +1,26 @@ +# DATE: 2011-09-15 CONTRIBUTOR: Unknown CITATION: Justo, Bazant, Kaxiras, Bulatov and Yip, Phys Rev B, 58, 2539 (1998) + +# EDIP parameters for various elements and mixtures +# multiple entries can be added to this file, LAMMPS reads the ones it needs +# these entries are in LAMMPS "metal" units + +# format of a single entry (one or more lines) +# +# element 1, element 2, element 3, +# A B cutoffA cutoffC alpha beta eta +# gamma lambda mu rho sigma Q0 +# u1 u2 u3 u4 +# +# units for each parameters: +# A , lambda are in eV +# B, cutoffA, cutoffC, gamma, sigma are in Angstrom +# alpha, beta, eta, mu, rho, Q0, u1-u4 are pure numbers + +# Here are the original parameters in metal units, for Silicon from: +# J. F. Justo, M. Z. Bazant, E. Kaxiras, V. V. Bulatov, S. Yip +# Phys. Rev. B 58, 2539 (1998) +# + +Si Si Si 7.9821730 1.5075463 3.1213820 2.5609104 3.1083847 0.0070975 0.2523244 + 1.1247945 1.4533108 0.6966326 1.2085196 0.5774108 312.1341346 + -0.165799 32.557 0.286198 0.66 diff --git a/examples/USER/misc/edip/SiC.edip b/examples/USER/misc/edip/SiC.edip new file mode 100644 index 0000000000..0485d345bb --- /dev/null +++ b/examples/USER/misc/edip/SiC.edip @@ -0,0 +1,38 @@ +# DATE: 2017-05-16 CONTRIBUTOR: Laurent Pizzagalli CITATION: G. Lucas, M. Bertolus, and L. Pizzagalli, J. Phys. : Condens. Matter 22, 035802 (2010) +# element 1, element 2, element 3, +# A B cutoffA cutoffC alpha beta eta +# gamma lambda mu rho sigma Q0 +# u1 u2 u3 u4 +# +Si Si Si 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.589390 + 1.135256 2.417497 0.629131 1.343679 0.298443 208.924548 + -0.165799 32.557 0.286198 0.66 + +C C C 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.275605 + 1.084183 3.633621 0.594236 2.827634 0.536561 289.305617 + -0.165799 32.557 0.286198 0.66 + +C Si Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497 + 1.191567 3.025559 0.611684 2.061835 0.423863 249.115082 + -0.165799 32.557000 0.286198 0.660000 + +Si C C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.432497 + 1.191567 3.025559 0.611684 2.061835 0.423863 249.115082 + -0.165799 32.557000 0.286198 0.660000 + +Si Si C 5.488043 1.446435 2.941586 2.540193 3.066580 0.008593 0.510944 + 1.135256 2.721528 0.620407 1.343679 0.298443 229.019815 + -0.165799 32.557000 0.286198 0.660000 + +Si C Si 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.510944 + 1.191567 2.721528 0.620407 2.061835 0.423863 229.019815 + -0.165799 32.557000 0.286198 0.660000 + +C C Si 10.222599 0.959814 2.212263 1.741598 1.962090 0.025661 0.354051 + 1.084183 3.329590 0.602960 2.827634 0.536561 269.210350 + -0.165799 32.557000 0.286198 0.660000 + +C Si C 7.535967 1.177019 2.534972 1.973974 2.507738 0.015347 0.354051 + 1.191567 3.329590 0.602960 2.061835 0.423863 269.210350 + -0.165799 32.557000 0.286198 0.660000 + diff --git a/examples/USER/misc/edip/data.SiC b/examples/USER/misc/edip/data.SiC new file mode 100644 index 0000000000..fa50c14803 --- /dev/null +++ b/examples/USER/misc/edip/data.SiC @@ -0,0 +1,138 @@ +Position data for Silicon-Carbon system + + 128 atoms + 2 atom types + -6.00 5.97232152 xlo xhi + -6.00 5.97232152 ylo yhi + -6.00 5.97232152 zlo zhi + + Atoms + +1 2 -2.9378454 -4.4592615 -4.8109196 +2 2 5.6222143 -2.7335026 -1.7157569 +3 2 -2.6614623 -5.5431059 1.6353686 +4 2 -5.4326838 -4.6174577 5.9452279 +5 2 5.8679239 -0.1120535 -3.5839373 +6 2 -3.7174621 -0.6623311 -0.3714789 +7 2 -5.0724728 -2.5671623 4.4103461 +8 2 -3.3951436 0.9341126 4.9310702 +9 2 -5.4347593 1.9523767 -5.6180938 +10 2 -4.5884719 2.2904528 -1.0597739 +11 2 -5.9058662 0.6212406 2.0127574 +12 2 -4.7680660 0.1965740 4.3267764 +13 2 -5.4228882 5.2569673 -4.5162920 +14 2 -5.2683965 -5.9193658 -2.8648668 +15 2 -2.8610884 1.0484664 2.0299077 +16 2 -4.0711084 5.3133026 3.8009514 +17 2 -0.1947147 -4.1677696 -5.6950931 +18 2 -2.9892710 -3.1647368 -1.6173910 +19 2 -0.9129311 -4.3819066 -0.1601859 +20 2 -2.4513693 -5.2466501 4.8882912 +21 2 -2.8879952 -0.1633446 -3.3401150 +22 1 -4.6738762 -1.3807254 -2.2946777 +23 2 -0.6973948 -1.4885343 0.6005156 +24 1 -2.7392164 -2.4774843 0.2387186 +25 2 -2.6551254 -2.7229952 2.6350264 +26 1 -3.4644263 -4.6028144 3.3817786 +27 2 0.7227614 -2.0709446 2.9214737 +28 1 -2.1000577 -3.2131296 5.7273437 +29 2 -3.1057649 2.3204819 -2.2725622 +30 1 -2.2298751 0.7168389 -1.3107201 +31 2 -1.8698261 1.4006751 0.7265108 +32 1 -4.1103409 -0.7093340 1.9341753 +33 2 -0.3505581 3.2707182 -0.2880656 +34 1 -3.4045407 -1.4383961 4.3903527 +35 2 -3.0940529 1.4132478 -5.3635505 +36 1 -4.4560663 1.2072875 -3.7310176 +37 2 -2.6061002 4.6373499 -4.6903941 +38 1 -3.3477444 4.6768137 -2.6284678 +39 2 0.8121697 4.8602418 -4.6710946 +40 1 -2.5756922 3.3740738 -0.2136350 +41 2 -0.3867976 5.8745611 -2.1119905 +42 1 -1.6766249 1.3374292 3.8741477 +43 2 -0.8770613 3.3735941 4.3846975 +44 1 -1.8609254 3.3158245 -5.9786556 +45 1 -5.2732321 -4.6073253 -0.9581754 +46 1 -2.7888697 -5.6910152 -0.7922023 +47 1 -2.4717165 4.5801880 2.5083210 +48 1 -3.8819950 5.8456589 -5.7563384 +49 2 2.2314782 -2.7729214 -5.2356862 +50 2 0.2981976 -3.1385279 -3.1608167 +51 2 2.8810785 -3.4658695 -0.5823196 +52 2 0.2509625 -5.7595229 2.7389761 +53 2 -0.2934120 -0.8029431 -3.3698507 +54 1 -1.0075690 -2.0481922 -1.9419298 +55 2 2.0729069 1.4922441 -2.3898096 +56 1 1.1110944 -3.2004208 0.9491078 +57 2 1.6774298 -0.7901860 2.5158773 +58 1 -0.8342297 -4.3342518 2.0971458 +59 2 3.2747406 -1.3107897 4.7884706 +60 1 1.7126246 -3.3691471 4.5581012 +61 2 0.4770605 1.7769008 -5.3339915 +62 1 0.2944391 0.5892781 -2.2030106 +63 2 2.2039275 3.1557557 -2.0276796 +64 1 -0.0404494 0.4767818 1.0396418 +65 2 1.1395867 2.3763443 2.3481007 +66 1 -0.9738374 -1.6325161 3.7538567 +67 2 -0.3291998 0.2996990 5.2770809 +68 1 -1.6185604 -0.3964274 -5.1771220 +69 2 2.5999949 -5.1977715 5.8230717 +70 1 -1.6270675 2.3210900 -3.6299941 +71 2 3.6532700 4.9282597 -5.4319276 +72 1 0.0788934 4.0241037 -2.5011530 +73 2 2.8556507 2.6168653 2.1125546 +74 1 0.9738989 2.6255364 4.3412121 +75 2 3.7452938 3.4521356 4.5946426 +76 1 2.0805182 4.7039015 5.3280260 +77 1 -1.0324174 -5.8155041 -4.3265820 +78 1 0.7622442 -4.3631629 -1.3156572 +79 1 0.3263684 3.9937357 1.6172321 +80 1 -0.4350105 -5.7997058 4.5959134 +81 2 3.9161132 -4.6052788 -3.3191717 +82 2 1.9240657 5.7345079 -1.9754251 +83 2 -5.9794488 -4.2369359 1.8646522 +84 2 4.3339975 -4.4845227 5.3737440 +85 2 2.2755456 -0.6327737 -5.7931837 +86 1 1.8728190 -1.5504906 -3.4560010 +87 2 3.4558100 -1.1054068 -1.8333071 +88 1 4.3788172 -1.9466494 -0.3284637 +89 2 2.5999235 -3.7548996 2.5740569 +90 1 3.9983910 -4.4856603 1.1968663 +91 2 -5.7295580 -2.1475672 -5.9963645 +92 1 4.2664051 -2.6988975 -5.8005478 +93 2 4.5254685 2.2906832 -3.4765798 +94 1 2.3603088 1.3416442 -4.4173836 +95 2 4.7767057 1.4061217 -0.7524620 +96 1 1.8072666 -0.7835973 -0.4581995 +97 2 4.4745018 0.3736224 2.1068274 +98 1 3.6081170 -1.7315713 2.4019053 +99 2 4.6281423 -0.2865409 4.4756524 +100 1 1.7975239 0.2893530 4.2330830 +101 2 5.8341452 4.4986472 -5.9664541 +102 1 3.2401308 4.1655227 -3.5070029 +103 2 4.8720339 4.8709982 -2.3364366 +104 1 3.5526476 1.2262752 0.6926826 +105 2 -5.8173342 4.5420479 1.5578881 +106 1 3.9683224 1.5441137 3.8284375 +107 2 -5.5349308 1.9067049 3.7504113 +108 1 4.4728615 2.6415574 -5.5952809 +109 1 1.7000950 -4.8115440 -4.1953920 +110 1 1.7221527 4.1878404 -0.3712681 +111 1 3.9218156 4.5935583 1.3263407 +112 1 3.1310195 -5.8922481 3.6001155 +113 1 4.7558719 -2.2877771 -3.4742052 +114 1 -5.5050300 -2.7027381 0.8748867 +115 1 5.8418594 -4.6064370 3.8714113 +116 1 -4.7516868 -3.1691984 -4.4099768 +117 1 3.9404971 0.7188702 -2.2898786 +118 1 -5.6869740 0.2042380 -0.1916738 +119 1 5.8949589 -1.2422560 3.1201292 +120 1 5.9675804 -0.0712572 5.8964022 +121 1 -5.6208517 3.3600036 -2.9493510 +122 1 5.2065263 3.4517912 -0.3800894 +123 1 -4.6994522 2.5489583 1.8297431 +124 1 -4.0758407 3.0726196 5.0647973 +125 1 4.1587591 -5.0896820 -1.1443498 +126 1 -4.6963753 -5.7429833 1.1357818 +127 1 5.5994192 4.6887008 3.5948264 +128 1 5.0988369 -5.3774409 -4.9051267 diff --git a/examples/USER/misc/edip/in.edip-Si b/examples/USER/misc/edip/in.edip-Si new file mode 100644 index 0000000000..b4c6669621 --- /dev/null +++ b/examples/USER/misc/edip/in.edip-Si @@ -0,0 +1,72 @@ + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create $t 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del + +pair_style edip +pair_coeff * * Si.edip Si + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 + diff --git a/examples/USER/misc/edip/in.edip-Si-multi b/examples/USER/misc/edip/in.edip-Si-multi new file mode 100644 index 0000000000..73a2e09143 --- /dev/null +++ b/examples/USER/misc/edip/in.edip-Si-multi @@ -0,0 +1,72 @@ + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a & + a1 1.0 0.0 0.0 & + a2 0.0 1.0 0.0 & + a3 0.0 0.0 1.0 & + basis 0.0 0.0 0.0 & + basis 0.0 0.5 0.5 & + basis 0.5 0.0 0.5 & + basis 0.5 0.5 0.0 & + basis 0.25 0.25 0.25 & + basis 0.25 0.75 0.75 & + basis 0.75 0.25 0.75 & + basis 0.75 0.75 0.25 + +region myreg block 0 4 & + 0 4 & + 0 4 +create_box 1 myreg +create_atoms 1 region myreg + +mass 1 28.06 + +group Si type 1 + +velocity all create $t 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +delete_atoms group del + +pair_style edip/multi +pair_coeff * * Si.edip Si + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 + diff --git a/examples/USER/misc/edip/in.edip-SiC b/examples/USER/misc/edip/in.edip-SiC new file mode 100644 index 0000000000..ac95f6c4d1 --- /dev/null +++ b/examples/USER/misc/edip/in.edip-SiC @@ -0,0 +1,33 @@ +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.SiC + +pair_style edip/multi +pair_coeff * * SiC.edip Si C + +mass 1 28.085 +mass 2 12.001 + +neighbor 1.0 bin +neigh_modify delay 1 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 new file mode 100644 index 0000000000..ab7d339023 --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.1 @@ -0,0 +1,167 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 + +pair_style edip/multi +pair_coeff * * Si.edip Si +Reading potential file Si.edip with DATE: 2011-09-15 + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.12138 + ghost atom cutoff = 4.12138 + binsize = 2.06069, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip/multi, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1802.5039 -2372.6618 0 -2253.8359 12261.807 + 10 952.62744 -2316.428 0 -2253.6283 723.08194 + 20 549.13801 -2289.442 0 -2253.2413 -2444.5204 + 30 1047.0106 -2321.1523 0 -2252.1305 9013.201 + 40 663.46141 -2294.2083 0 -2250.4711 2942.5348 + 50 504.74535 -2282.849 0 -2249.5748 -461.44909 + 60 1019.2173 -2315.5639 0 -2248.3744 7706.4286 + 70 844.51195 -2302.5251 0 -2246.8526 3116.8302 + 80 814.90407 -2299.3372 0 -2245.6166 794.77455 + 90 1269.5636 -2327.4775 0 -2243.7845 7729.3968 + 100 977.61563 -2306.1118 0 -2241.6647 2969.9939 + 110 843.08539 -2295.6547 0 -2240.0763 1393.4039 + 120 1161.6968 -2314.6587 0 -2238.0766 7398.3492 + 130 918.19451 -2296.4321 0 -2235.9022 2537.3997 + 140 881.42548 -2292.2768 0 -2234.1709 1550.3339 + 150 1231.1005 -2313.1054 0 -2231.9479 8112.7566 + 160 967.01862 -2293.332 0 -2229.5836 3422.9627 + 170 833.51248 -2282.7489 0 -2227.8015 43.991459 + 180 1240.8488 -2307.3633 0 -2225.5632 6557.8651 + 190 1126.4621 -2297.1922 0 -2222.9328 4289.0067 + 200 947.59571 -2283.29 0 -2220.822 586.2811 + 210 1228.153 -2299.4702 0 -2218.5071 5315.0425 + 220 1215.4104 -2295.9408 0 -2215.8176 4870.3417 + 230 1112.436 -2286.7552 0 -2213.4204 2527.1879 + 240 1300.081 -2296.6013 0 -2210.8965 5738.3708 + 250 1192.5738 -2286.8463 0 -2208.2286 4076.49 + 260 1004.7055 -2272.1753 0 -2205.9424 359.37589 + 270 1241.2018 -2285.3632 0 -2203.5399 4160.5763 + 280 1360.1974 -2290.325 0 -2200.6572 5802.3902 + 290 1151.9365 -2273.9467 0 -2198.008 1418.8887 + 300 1174.3518 -2273.0089 0 -2195.5925 1998.229 + 310 1329.2727 -2280.5049 0 -2192.8757 4721.7297 + 320 1284.4414 -2274.7519 0 -2190.0781 2985.4674 + 330 1328.3761 -2274.9545 0 -2187.3844 4543.2109 + 340 1446.3847 -2279.8693 0 -2184.5198 6254.4059 + 350 1366.2165 -2271.7475 0 -2181.6828 3637.8335 + 360 1358.9609 -2268.5982 0 -2179.0118 3049.5798 + 370 1552.208 -2278.4802 0 -2176.1545 6334.0058 + 380 1562.5295 -2276.1793 0 -2173.1732 5787.5547 + 390 1415.5498 -2263.7824 0 -2170.4655 3438.5766 + 400 1323.1568 -2255.1641 0 -2167.938 2427.2294 + 410 1260.7186 -2248.5373 0 -2165.4273 1208.6299 + 420 1282.1118 -2247.3718 0 -2162.8516 462.65374 + 430 1451.944 -2255.7551 0 -2160.0391 2037.8025 + 440 1568.9415 -2260.417 0 -2156.9882 3531.1602 + 450 1565.8262 -2257.2396 0 -2154.0162 2586.7886 + 460 1677.7143 -2261.7214 0 -2151.122 4112.9756 + 470 1762.9071 -2264.4244 0 -2148.2089 5053.2139 + 480 1704.5898 -2257.8678 0 -2145.4967 4077.4626 + 490 1731.2619 -2257.1048 0 -2142.9753 4710.5263 + 500 1723.9777 -2254.161 0 -2140.5118 4760.7295 +Loop time of 0.679564 on 1 procs for 500 steps with 511 atoms + +Performance: 63.570 ns/day, 0.378 hours/ns, 735.765 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.65181 | 0.65181 | 0.65181 | 0.0 | 95.92 +Neigh | 0.013857 | 0.013857 | 0.013857 | 0.0 | 2.04 +Comm | 0.0033884 | 0.0033884 | 0.0033884 | 0.0 | 0.50 +Output | 0.00070739 | 0.00070739 | 0.00070739 | 0.0 | 0.10 +Modify | 0.0083694 | 0.0083694 | 0.0083694 | 0.0 | 1.23 +Other | | 0.001432 | | | 0.21 + +Nlocal: 511 ave 511 max 511 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 845 ave 845 max 845 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7902 ave 7902 max 7902 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7902 +Ave neighs/atom = 15.4638 +Neighbor list builds = 19 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 new file mode 100644 index 0000000000..91be601fa8 --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si-multi.4 @@ -0,0 +1,167 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 + +pair_style edip/multi +pair_coeff * * Si.edip Si +Reading potential file Si.edip with DATE: 2011-09-15 + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.12138 + ghost atom cutoff = 4.12138 + binsize = 2.06069, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip/multi, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1802.3816 -2372.6618 0 -2253.844 12260.967 + 10 938.75954 -2315.5185 0 -2253.6329 558.21646 + 20 534.27233 -2288.4721 0 -2253.2514 -2710.768 + 30 1043.7796 -2320.9485 0 -2252.1398 8679.4381 + 40 658.0916 -2293.8597 0 -2250.4765 2165.3742 + 50 517.93009 -2283.7238 0 -2249.5805 -1124.9373 + 60 1063.3594 -2318.4409 0 -2248.3414 7277.8526 + 70 868.14006 -2304.0134 0 -2246.7832 2050.2848 + 80 826.37805 -2300.0187 0 -2245.5416 91.099408 + 90 1289.6772 -2328.7151 0 -2243.6961 8180.7423 + 100 976.36208 -2305.9371 0 -2241.5727 3614.0499 + 110 810.81713 -2293.4705 0 -2240.0193 1359.368 + 120 1165.707 -2314.9026 0 -2238.056 7336.45 + 130 929.81245 -2297.139 0 -2235.8432 2793.8451 + 140 804.47874 -2287.2074 0 -2234.174 704.92455 + 150 1182.4141 -2310.0266 0 -2232.0787 7822.2337 + 160 979.92391 -2294.2969 0 -2229.6977 3206.7458 + 170 830.14748 -2282.6079 0 -2227.8824 -296.87377 + 180 1271.1133 -2309.4274 0 -2225.6322 7199.614 + 190 1209.6006 -2302.6407 0 -2222.9006 5528.3784 + 200 954.67693 -2283.6621 0 -2220.7273 47.02795 + 210 1260.814 -2301.5582 0 -2218.442 4829.788 + 220 1274.9954 -2299.7285 0 -2215.6774 5518.0597 + 230 1048.0074 -2282.398 0 -2213.3106 1754.4144 + 240 1261.7072 -2294.1108 0 -2210.9356 5233.2712 + 250 1272.6178 -2292.0793 0 -2208.1849 4795.9325 + 260 989.14205 -2271.0278 0 -2205.8209 -820.1828 + 270 1212.0445 -2283.4212 0 -2203.52 3395.8634 + 280 1391.9572 -2292.3809 0 -2200.6194 6666.2451 + 290 1093.1204 -2270.0421 0 -2197.9807 206.94523 + 300 1159.4831 -2272.102 0 -2195.6657 778.53806 + 310 1407.3528 -2285.6228 0 -2192.8463 5223.048 + 320 1236.7163 -2271.5389 0 -2190.0113 1865.3943 + 330 1258.8275 -2270.4611 0 -2187.4758 2333.3209 + 340 1507.9519 -2283.9906 0 -2184.5824 6775.5456 + 350 1366.5116 -2271.7287 0 -2181.6446 3432.115 + 360 1305.2829 -2265.1092 0 -2179.0614 1498.4073 + 370 1581.4335 -2280.4645 0 -2176.2122 6518.5597 + 380 1589.5319 -2277.9428 0 -2173.1567 6334.6506 + 390 1402.6781 -2262.9323 0 -2170.464 3278.3038 + 400 1374.9587 -2258.5717 0 -2167.9307 3608.7284 + 410 1295.7416 -2250.7752 0 -2165.3565 1877.5222 + 420 1278.6727 -2247.1099 0 -2162.8164 1599.4181 + 430 1508.1328 -2259.4245 0 -2160.0044 4300.2224 + 440 1624.2957 -2263.9806 0 -2156.9026 4432.625 + 450 1597.3356 -2259.263 0 -2153.9624 3370.3816 + 460 1772.0922 -2267.9106 0 -2151.0895 5788.3214 + 470 1806.4047 -2267.304 0 -2148.221 5950.1166 + 480 1593.0406 -2250.7469 0 -2145.7294 2518.0576 + 490 1660.9767 -2252.894 0 -2143.398 4282.1643 + 500 1714.283 -2253.9295 0 -2140.9194 5740.0247 +Loop time of 0.205398 on 4 procs for 500 steps with 511 atoms + +Performance: 210.324 ns/day, 0.114 hours/ns, 2434.304 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.16285 | 0.1688 | 0.17446 | 1.1 | 82.18 +Neigh | 0.0035172 | 0.0036234 | 0.0038214 | 0.2 | 1.76 +Comm | 0.018727 | 0.024851 | 0.030996 | 2.9 | 12.10 +Output | 0.0013061 | 0.0014012 | 0.0015635 | 0.3 | 0.68 +Modify | 0.0046582 | 0.0048603 | 0.0050988 | 0.2 | 2.37 +Other | | 0.001861 | | | 0.91 + +Nlocal: 127.75 ave 131 max 124 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 433.75 ave 441 max 426 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1979.5 ave 2040 max 1895 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 7918 +Ave neighs/atom = 15.4951 +Neighbor list builds = 19 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 new file mode 100644 index 0000000000..f7ce00371f --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.1 @@ -0,0 +1,167 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 1 by 1 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 + +pair_style edip +pair_coeff * * Si.edip Si +Reading potential file Si.edip with DATE: 2011-09-15 + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.12138 + ghost atom cutoff = 4.12138 + binsize = 2.06069, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.979 | 2.979 | 2.979 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1802.5039 -2372.6618 0 -2253.8359 12261.807 + 10 952.62744 -2316.428 0 -2253.6283 723.08283 + 20 549.138 -2289.442 0 -2253.2413 -2444.5194 + 30 1047.0106 -2321.1522 0 -2252.1305 9013.2015 + 40 663.46143 -2294.2083 0 -2250.4711 2942.5358 + 50 504.74533 -2282.849 0 -2249.5748 -461.44817 + 60 1019.2173 -2315.5639 0 -2248.3744 7706.429 + 70 844.51197 -2302.5251 0 -2246.8526 3116.8313 + 80 814.90406 -2299.3372 0 -2245.6165 794.77536 + 90 1269.5635 -2327.4775 0 -2243.7845 7729.3971 + 100 977.61566 -2306.1118 0 -2241.6647 2969.9952 + 110 843.08538 -2295.6547 0 -2240.0763 1393.4046 + 120 1161.6968 -2314.6587 0 -2238.0766 7398.3495 + 130 918.19453 -2296.4321 0 -2235.9022 2537.4011 + 140 881.42546 -2292.2768 0 -2234.1709 1550.3345 + 150 1231.1005 -2313.1054 0 -2231.9479 8112.7568 + 160 967.01865 -2293.332 0 -2229.5836 3422.964 + 170 833.51246 -2282.7489 0 -2227.8015 43.99251 + 180 1240.8487 -2307.3633 0 -2225.5632 6557.8652 + 190 1126.4621 -2297.1922 0 -2222.9328 4289.0083 + 200 947.5957 -2283.29 0 -2220.8219 586.28203 + 210 1228.153 -2299.4702 0 -2218.5071 5315.0427 + 220 1215.4104 -2295.9407 0 -2215.8176 4870.343 + 230 1112.436 -2286.7552 0 -2213.4204 2527.1887 + 240 1300.081 -2296.6013 0 -2210.8965 5738.3711 + 250 1192.5739 -2286.8463 0 -2208.2286 4076.4913 + 260 1004.7055 -2272.1753 0 -2205.9424 359.3769 + 270 1241.2018 -2285.3632 0 -2203.5399 4160.5764 + 280 1360.1974 -2290.325 0 -2200.6572 5802.3912 + 290 1151.9366 -2273.9467 0 -2198.008 1418.8905 + 300 1174.3518 -2273.0089 0 -2195.5925 1998.2297 + 310 1329.2726 -2280.5049 0 -2192.8757 4721.7304 + 320 1284.4414 -2274.7519 0 -2190.0781 2985.4687 + 330 1328.3761 -2274.9545 0 -2187.3844 4543.2115 + 340 1446.3847 -2279.8693 0 -2184.5198 6254.4071 + 350 1366.2165 -2271.7475 0 -2181.6828 3637.8351 + 360 1358.9609 -2268.5982 0 -2179.0118 3049.5811 + 370 1552.2079 -2278.4802 0 -2176.1545 6334.0061 + 380 1562.5295 -2276.1793 0 -2173.1731 5787.5565 + 390 1415.5498 -2263.7823 0 -2170.4655 3438.5782 + 400 1323.1568 -2255.1641 0 -2167.938 2427.2311 + 410 1260.7186 -2248.5373 0 -2165.4273 1208.6316 + 420 1282.1118 -2247.3718 0 -2162.8516 462.65508 + 430 1451.9439 -2255.7551 0 -2160.0391 2037.8027 + 440 1568.9415 -2260.417 0 -2156.9882 3531.1613 + 450 1565.8261 -2257.2396 0 -2154.0161 2586.7896 + 460 1677.7143 -2261.7214 0 -2151.122 4112.976 + 470 1762.9071 -2264.4244 0 -2148.2089 5053.2148 + 480 1704.5898 -2257.8678 0 -2145.4966 4077.4649 + 490 1731.2619 -2257.1048 0 -2142.9753 4710.5276 + 500 1723.9777 -2254.161 0 -2140.5118 4760.7316 +Loop time of 0.312472 on 1 procs for 500 steps with 511 atoms + +Performance: 138.252 ns/day, 0.174 hours/ns, 1600.143 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.28525 | 0.28525 | 0.28525 | 0.0 | 91.29 +Neigh | 0.013753 | 0.013753 | 0.013753 | 0.0 | 4.40 +Comm | 0.0033333 | 0.0033333 | 0.0033333 | 0.0 | 1.07 +Output | 0.00071096 | 0.00071096 | 0.00071096 | 0.0 | 0.23 +Modify | 0.008044 | 0.008044 | 0.008044 | 0.0 | 2.57 +Other | | 0.001385 | | | 0.44 + +Nlocal: 511 ave 511 max 511 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 845 ave 845 max 845 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 7902 ave 7902 max 7902 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 7902 +Ave neighs/atom = 15.4638 +Neighbor list builds = 19 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 new file mode 100644 index 0000000000..e33f0116f4 --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-Si.4 @@ -0,0 +1,167 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task + +units metal + +atom_style atomic +atom_modify map array +boundary p p p +atom_modify sort 0 0.0 + +# temperature + +variable t equal 1800.0 + +# coordination number cutoff + +variable r equal 2.835 + +# minimization parameters + +variable etol equal 1.0e-5 +variable ftol equal 1.0e-5 +variable maxiter equal 100 +variable maxeval equal 100 +variable dmax equal 1.0e-1 + +# diamond unit cell + +variable a equal 5.431 +lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25 +Lattice spacing in x,y,z = 5.431 5.431 5.431 + +region myreg block 0 4 0 4 0 4 +create_box 1 myreg +Created orthogonal box = (0 0 0) to (21.724 21.724 21.724) + 1 by 2 by 2 MPI processor grid +create_atoms 1 region myreg +Created 512 atoms + +mass 1 28.06 + +group Si type 1 +512 atoms in group Si + +velocity all create $t 5287287 mom yes rot yes dist gaussian +velocity all create 1800 5287287 mom yes rot yes dist gaussian + +# make a vacancy + +group del id 300 +1 atoms in group del +delete_atoms group del +Deleted 1 atoms, new total = 511 + +pair_style edip +pair_coeff * * Si.edip Si +Reading potential file Si.edip with DATE: 2011-09-15 + +thermo 10 + +fix 1 all nvt temp $t $t 0.1 +fix 1 all nvt temp 1800 $t 0.1 +fix 1 all nvt temp 1800 1800 0.1 + +timestep 1.0e-3 +neighbor 1.0 bin +neigh_modify every 1 delay 10 check yes + +# equilibrate + +run 500 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.12138 + ghost atom cutoff = 4.12138 + binsize = 2.06069, bins = 11 11 11 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.955 | 2.955 | 2.955 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1802.3816 -2372.6618 0 -2253.8439 12260.967 + 10 938.75954 -2315.5185 0 -2253.6329 558.21736 + 20 534.27232 -2288.4721 0 -2253.2514 -2710.767 + 30 1043.7796 -2320.9485 0 -2252.1398 8679.4385 + 40 658.09162 -2293.8597 0 -2250.4765 2165.3752 + 50 517.93008 -2283.7238 0 -2249.5805 -1124.9362 + 60 1063.3594 -2318.4409 0 -2248.3414 7277.853 + 70 868.14007 -2304.0133 0 -2246.7832 2050.2859 + 80 826.37803 -2300.0187 0 -2245.5416 91.100098 + 90 1289.6772 -2328.7151 0 -2243.6961 8180.7427 + 100 976.36211 -2305.9371 0 -2241.5727 3614.0511 + 110 810.81711 -2293.4705 0 -2240.0193 1359.3687 + 120 1165.707 -2314.9026 0 -2238.056 7336.4505 + 130 929.81248 -2297.139 0 -2235.8432 2793.8463 + 140 804.47872 -2287.2074 0 -2234.174 704.92524 + 150 1182.414 -2310.0266 0 -2232.0787 7822.2339 + 160 979.92395 -2294.2969 0 -2229.6977 3206.7474 + 170 830.14746 -2282.6079 0 -2227.8824 -296.87288 + 180 1271.1133 -2309.4274 0 -2225.6322 7199.614 + 190 1209.6006 -2302.6407 0 -2222.9006 5528.3799 + 200 954.67692 -2283.6621 0 -2220.7272 47.02925 + 210 1260.814 -2301.5582 0 -2218.442 4829.7879 + 220 1274.9954 -2299.7285 0 -2215.6774 5518.0611 + 230 1048.0074 -2282.398 0 -2213.3106 1754.4157 + 240 1261.7071 -2294.1107 0 -2210.9356 5233.2714 + 250 1272.6179 -2292.0793 0 -2208.1849 4795.934 + 260 989.14207 -2271.0278 0 -2205.8209 -820.18098 + 270 1212.0444 -2283.4212 0 -2203.52 3395.8631 + 280 1391.9572 -2292.3809 0 -2200.6194 6666.2464 + 290 1093.1205 -2270.0421 0 -2197.9807 206.94752 + 300 1159.483 -2272.102 0 -2195.6657 778.53823 + 310 1407.3528 -2285.6227 0 -2192.8463 5223.0487 + 320 1236.7164 -2271.5389 0 -2190.0112 1865.3963 + 330 1258.8275 -2270.4611 0 -2187.4758 2333.321 + 340 1507.9519 -2283.9906 0 -2184.5824 6775.546 + 350 1366.5116 -2271.7287 0 -2181.6446 3432.1175 + 360 1305.2828 -2265.1091 0 -2179.0614 1498.4079 + 370 1581.4334 -2280.4645 0 -2176.2122 6518.5598 + 380 1589.5319 -2277.9428 0 -2173.1566 6334.6527 + 390 1402.6782 -2262.9323 0 -2170.464 3278.3048 + 400 1374.9587 -2258.5717 0 -2167.9307 3608.7293 + 410 1295.7416 -2250.7752 0 -2165.3565 1877.5245 + 420 1278.6727 -2247.1099 0 -2162.8164 1599.4189 + 430 1508.1328 -2259.4245 0 -2160.0044 4300.2235 + 440 1624.2957 -2263.9806 0 -2156.9026 4432.6267 + 450 1597.3356 -2259.263 0 -2153.9623 3370.3829 + 460 1772.0921 -2267.9105 0 -2151.0895 5788.3219 + 470 1806.4047 -2267.304 0 -2148.221 5950.1188 + 480 1593.0406 -2250.7469 0 -2145.7294 2518.0601 + 490 1660.9766 -2252.894 0 -2143.398 4282.1654 + 500 1714.2831 -2253.9295 0 -2140.9194 5740.0268 +Loop time of 0.109584 on 4 procs for 500 steps with 511 atoms + +Performance: 394.220 ns/day, 0.061 hours/ns, 4562.726 timesteps/s +99.0% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.074678 | 0.077817 | 0.084705 | 1.4 | 71.01 +Neigh | 0.0036662 | 0.0037943 | 0.0039661 | 0.2 | 3.46 +Comm | 0.013665 | 0.020312 | 0.023178 | 2.7 | 18.54 +Output | 0.0010247 | 0.0010931 | 0.0012922 | 0.3 | 1.00 +Modify | 0.0043213 | 0.0047521 | 0.0051889 | 0.6 | 4.34 +Other | | 0.001814 | | | 1.66 + +Nlocal: 127.75 ave 131 max 124 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Nghost: 433.75 ave 441 max 426 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 1979.5 ave 2040 max 1895 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 7918 +Ave neighs/atom = 15.4951 +Neighbor list builds = 19 +Dangerous builds = 0 + +Total wall time: 0:00:00 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 new file mode 100644 index 0000000000..125106c504 --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.1 @@ -0,0 +1,92 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.SiC + orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 128 atoms + +pair_style edip/multi +pair_coeff * * SiC.edip Si C +Reading potential file SiC.edip with DATE: 2017-05-16 + +mass 1 28.085 +mass 2 12.001 + +neighbor 1.0 bin +neigh_modify delay 1 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 +Neighbor list info ... + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.94159 + ghost atom cutoff = 3.94159 + binsize = 1.97079, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip/multi, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.692 | 2.692 | 2.692 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -563.61621 0 -563.61621 -726147.34 + 10 4224.3601 -633.24829 0 -563.90103 -312355.55 + 20 4528.5661 -638.15183 0 -563.81071 -20091.291 + 30 4817.3654 -642.92111 0 -563.83905 106625.5 + 40 4619.4324 -639.6884 0 -563.85562 107180.42 + 50 4783.0025 -642.26961 0 -563.75166 75134.335 + 60 4525.145 -638.06177 0 -563.77681 71591.713 + 70 4685.2578 -640.72377 0 -563.8104 63956.042 + 80 4621.8393 -639.75912 0 -563.88682 18177.383 + 90 4834.7702 -643.34582 0 -563.97805 15282.823 + 100 4424.0589 -636.60208 0 -563.97656 47963.501 +Loop time of 0.0552888 on 1 procs for 100 steps with 128 atoms + +Performance: 156.270 ns/day, 0.154 hours/ns, 1808.685 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.051872 | 0.051872 | 0.051872 | 0.0 | 93.82 +Neigh | 0.0023525 | 0.0023525 | 0.0023525 | 0.0 | 4.25 +Comm | 0.0004518 | 0.0004518 | 0.0004518 | 0.0 | 0.82 +Output | 0.00014806 | 0.00014806 | 0.00014806 | 0.0 | 0.27 +Modify | 0.00024796 | 0.00024796 | 0.00024796 | 0.0 | 0.45 +Other | | 0.0002165 | | | 0.39 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 473 ave 473 max 473 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 0 ave 0 max 0 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 2376 ave 2376 max 2376 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2376 +Ave neighs/atom = 18.5625 +Neighbor list builds = 11 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 new file mode 100644 index 0000000000..eb6955703e --- /dev/null +++ b/examples/USER/misc/edip/log.4May2017.g++.edip-SiC.4 @@ -0,0 +1,92 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.SiC + orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 128 atoms + +pair_style edip/multi +pair_coeff * * SiC.edip Si C +Reading potential file SiC.edip with DATE: 2017-05-16 + +mass 1 28.085 +mass 2 12.001 + +neighbor 1.0 bin +neigh_modify delay 1 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 +Neighbor list info ... + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 3.94159 + ghost atom cutoff = 3.94159 + binsize = 1.97079, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair edip/multi, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.686 | 2.686 | 2.686 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -563.61621 0 -563.61621 -726147.34 + 10 4224.3601 -633.24829 0 -563.90103 -312355.55 + 20 4528.5661 -638.15183 0 -563.81071 -20091.291 + 30 4817.3654 -642.92111 0 -563.83905 106625.5 + 40 4619.4324 -639.6884 0 -563.85562 107180.42 + 50 4783.0025 -642.26961 0 -563.75166 75134.335 + 60 4525.145 -638.06177 0 -563.77681 71591.713 + 70 4685.2578 -640.72377 0 -563.8104 63956.042 + 80 4621.8393 -639.75912 0 -563.88682 18177.383 + 90 4834.7702 -643.34582 0 -563.97805 15282.823 + 100 4424.0589 -636.60208 0 -563.97656 47963.501 +Loop time of 0.020755 on 4 procs for 100 steps with 128 atoms + +Performance: 416.285 ns/day, 0.058 hours/ns, 4818.118 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.011816 | 0.013825 | 0.016871 | 1.6 | 66.61 +Neigh | 0.00061321 | 0.00066817 | 0.00074816 | 0.0 | 3.22 +Comm | 0.0023363 | 0.0054012 | 0.0075014 | 2.7 | 26.02 +Output | 0.00020909 | 0.00022268 | 0.00025558 | 0.0 | 1.07 +Modify | 8.3208e-05 | 9.346e-05 | 0.00010395 | 0.0 | 0.45 +Other | | 0.0005446 | | | 2.62 + +Nlocal: 32 ave 36 max 25 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 262.75 ave 273 max 255 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 0 ave 0 max 0 min +Histogram: 4 0 0 0 0 0 0 0 0 0 +FullNghs: 594 ave 687 max 453 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 2376 +Ave neighs/atom = 18.5625 +Neighbor list builds = 11 +Dangerous builds = 0 +Total wall time: 0:00:00 diff --git a/examples/USER/misc/filter_corotate/in.bpti b/examples/USER/misc/filter_corotate/in.bpti index 6507a78704..2e4d8dda6f 100644 --- a/examples/USER/misc/filter_corotate/in.bpti +++ b/examples/USER/misc/filter_corotate/in.bpti @@ -28,7 +28,7 @@ thermo 100 thermo_style multi timestep 8 -run_style respa 3 2 8 bond 1 pair 2 kspace 3 +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 velocity all create 200.0 12345678 dist uniform #dump dump1 all atom 100 4pti.dump diff --git a/examples/USER/misc/filter_corotate/in.peptide b/examples/USER/misc/filter_corotate/in.peptide index 0a17f995b3..e10dc09f0d 100644 --- a/examples/USER/misc/filter_corotate/in.peptide +++ b/examples/USER/misc/filter_corotate/in.peptide @@ -20,7 +20,7 @@ thermo 50 timestep 8 -run_style respa 3 2 8 bond 1 pair 2 kspace 3 +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 fix cor all filter/corotate m 1.0 diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1 b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1 deleted file mode 100644 index 5253b47b2d..0000000000 --- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.1 +++ /dev/null @@ -1,240 +0,0 @@ -LAMMPS (10 Mar 2017) - using 1 OpenMP thread(s) per MPI task - -units real - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic - -pair_style lj/charmm/coul/long 8 10 -pair_modify mix arithmetic -kspace_style pppm 1e-4 - -read_data data.bpti - orthogonal box = (-10 -10 -30) to (50 50 30) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 892 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 18 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 906 bonds - reading angles ... - 1626 angles - reading dihedrals ... - 2501 dihedrals - reading impropers ... - 137 impropers - 4 = max # of 1-2 neighbors - 9 = max # of 1-3 neighbors - 19 = max # of 1-4 neighbors - 21 = max # of special neighbors - -special_bonds charmm -neigh_modify delay 2 every 1 - - -# ------------- MINIMIZE ---------- - -minimize 1e-4 1e-6 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -PPPM initialization ... -WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302) -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.203272 - grid = 16 16 16 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0316399 - estimated relative force accuracy = 9.52826e-05 - using double precision FFTs - 3d grid and FFT values/proc = 9261 4096 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmm/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory usage (min/avg/max) = 17.8596/1/0 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 - 241 0 -4503.313 749.58662 -3753.7264 -29.045104 -Loop time of 3.35722 on 1 procs for 241 steps with 892 atoms - -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -2131.73812515 -3753.43984087 -3753.72636847 - Force two-norm initial, final = 1086.21 26.3688 - Force max component initial, final = 310.811 3.92748 - Final line search alpha, max atom move = 0.00596649 0.0234333 - Iterations, force evaluations = 241 463 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 2.5003 | 2.5003 | 2.5003 | 0.0 | 74.48 -Bond | 0.24287 | 0.24287 | 0.24287 | 0.0 | 7.23 -Kspace | 0.53428 | 0.53428 | 0.53428 | 0.0 | 15.91 -Neigh | 0.069765 | 0.069765 | 0.069765 | 0.0 | 2.08 -Comm | 0.00065374 | 0.00065374 | 0.00065374 | 0.0 | 0.02 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.009358 | | | 0.28 - -Nlocal: 892 ave 892 max 892 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 31 ave 31 max 31 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 148891 ave 148891 max 148891 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 148891 -Ave neighs/atom = 166.918 -Ave special neighs/atom = 10.9395 -Neighbor list builds = 15 -Dangerous builds = 0 -reset_timestep 0 - -# ------------- RUN --------------- - -thermo 100 -thermo_style multi -timestep 8 - -run_style respa 3 2 8 bond 1 pair 2 kspace 3 -Respa levels: - 1 = bond angle dihedral improper - 2 = pair - 3 = kspace - -velocity all create 200.0 12345678 dist uniform -#dump dump1 all atom 100 4pti.dump - -fix 1 all nvt temp 200 300 25 -fix cor all filter/corotate m 1.0 - 163 = # of size 2 clusters - 0 = # of size 3 clusters - 25 = # of size 4 clusters - 0 = # of size 5 clusters - 100 = # of frozen angles - -run 1000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.203272 - grid = 16 16 16 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0316399 - estimated relative force accuracy = 9.52826e-05 - using double precision FFTs - 3d grid and FFT values/proc = 9261 4096 -Per MPI rank memory usage (min/avg/max) = 19.5425/1/0 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 -PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592 -E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 -E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283 ----------------- Step 100 ----- CPU = 3.9414 (sec) ---------------- -TotEng = -2718.8970 KinEng = 538.6206 Temp = 202.8014 -PotEng = -3257.5176 E_bond = 203.3367 E_angle = 566.5317 -E_dihed = 397.6202 E_impro = 34.6623 E_vdwl = -248.7451 -E_coul = -874.5122 E_long = -3336.4111 Press = 135.8662 ----------------- Step 200 ----- CPU = 7.9028 (sec) ---------------- -TotEng = -2660.1406 KinEng = 626.3319 Temp = 235.8265 -PotEng = -3286.4725 E_bond = 209.5147 E_angle = 591.7773 -E_dihed = 388.9591 E_impro = 29.4992 E_vdwl = -243.5808 -E_coul = -923.5115 E_long = -3339.1306 Press = 88.9000 ----------------- Step 300 ----- CPU = 11.8246 (sec) ---------------- -TotEng = -2673.8090 KinEng = 616.7924 Temp = 232.2346 -PotEng = -3290.6014 E_bond = 202.8254 E_angle = 568.6860 -E_dihed = 378.4182 E_impro = 38.2399 E_vdwl = -221.3236 -E_coul = -915.3004 E_long = -3342.1468 Press = 78.8527 ----------------- Step 400 ----- CPU = 15.7990 (sec) ---------------- -TotEng = -2614.9416 KinEng = 649.3474 Temp = 244.4922 -PotEng = -3264.2890 E_bond = 211.6116 E_angle = 617.2026 -E_dihed = 399.8744 E_impro = 40.2678 E_vdwl = -211.7790 -E_coul = -978.1624 E_long = -3343.3041 Press = -4.1958 ----------------- Step 500 ----- CPU = 19.8146 (sec) ---------------- -TotEng = -2588.6772 KinEng = 660.1424 Temp = 248.5568 -PotEng = -3248.8196 E_bond = 218.4786 E_angle = 620.8605 -E_dihed = 390.3220 E_impro = 41.6794 E_vdwl = -226.3657 -E_coul = -953.1676 E_long = -3340.6269 Press = 99.3200 ----------------- Step 600 ----- CPU = 23.8587 (sec) ---------------- -TotEng = -2550.4618 KinEng = 693.3384 Temp = 261.0557 -PotEng = -3243.8002 E_bond = 232.3563 E_angle = 606.2922 -E_dihed = 396.2469 E_impro = 37.1980 E_vdwl = -235.8425 -E_coul = -937.1208 E_long = -3342.9303 Press = -21.7737 ----------------- Step 700 ----- CPU = 27.8381 (sec) ---------------- -TotEng = -2554.4355 KinEng = 692.8951 Temp = 260.8888 -PotEng = -3247.3306 E_bond = 216.3395 E_angle = 637.7785 -E_dihed = 391.5940 E_impro = 43.1426 E_vdwl = -187.6159 -E_coul = -1008.1694 E_long = -3340.3998 Press = 75.1484 ----------------- Step 800 ----- CPU = 31.8039 (sec) ---------------- -TotEng = -2508.3551 KinEng = 699.0766 Temp = 263.2163 -PotEng = -3207.4317 E_bond = 241.9936 E_angle = 641.3631 -E_dihed = 386.2198 E_impro = 43.7793 E_vdwl = -217.7523 -E_coul = -964.6070 E_long = -3338.4282 Press = -127.7337 ----------------- Step 900 ----- CPU = 35.7700 (sec) ---------------- -TotEng = -2452.7644 KinEng = 762.1842 Temp = 286.9776 -PotEng = -3214.9485 E_bond = 243.9191 E_angle = 649.8664 -E_dihed = 382.4351 E_impro = 39.0029 E_vdwl = -221.3389 -E_coul = -970.8965 E_long = -3337.9366 Press = 122.7720 ----------------- Step 1000 ----- CPU = 39.7695 (sec) ---------------- -TotEng = -2386.6805 KinEng = 799.0253 Temp = 300.8490 -PotEng = -3185.7058 E_bond = 265.3649 E_angle = 661.7543 -E_dihed = 374.6843 E_impro = 38.6877 E_vdwl = -229.2030 -E_coul = -960.7041 E_long = -3336.2899 Press = -17.9910 -Loop time of 39.7695 on 1 procs for 1000 steps with 892 atoms - -Performance: 17.380 ns/day, 1.381 hours/ns, 25.145 timesteps/s -99.6% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 29.169 | 29.169 | 29.169 | 0.0 | 73.34 -Bond | 7.6249 | 7.6249 | 7.6249 | 0.0 | 19.17 -Kspace | 1.1525 | 1.1525 | 1.1525 | 0.0 | 2.90 -Neigh | 0.87606 | 0.87606 | 0.87606 | 0.0 | 2.20 -Comm | 0.01563 | 0.01563 | 0.01563 | 0.0 | 0.04 -Output | 0.00048423 | 0.00048423 | 0.00048423 | 0.0 | 0.00 -Modify | 0.80446 | 0.80446 | 0.80446 | 0.0 | 2.02 -Other | | 0.1266 | | | 0.32 - -Nlocal: 892 ave 892 max 892 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 27 ave 27 max 27 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 146206 ave 146206 max 146206 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 146206 -Ave neighs/atom = 163.908 -Ave special neighs/atom = 10.9395 -Neighbor list builds = 186 -Dangerous builds = 0 - -unfix cor -unfix 1 - - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:43 diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4 b/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4 deleted file mode 100644 index 4300c1caf5..0000000000 --- a/examples/USER/misc/filter_corotate/log.10Mar2017.bpti.g++.4 +++ /dev/null @@ -1,240 +0,0 @@ -LAMMPS (10 Mar 2017) - using 1 OpenMP thread(s) per MPI task - -units real - -atom_style full -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic - -pair_style lj/charmm/coul/long 8 10 -pair_modify mix arithmetic -kspace_style pppm 1e-4 - -read_data data.bpti - orthogonal box = (-10 -10 -30) to (50 50 30) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 892 atoms - scanning bonds ... - 4 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 18 = max dihedrals/atom - scanning impropers ... - 2 = max impropers/atom - reading bonds ... - 906 bonds - reading angles ... - 1626 angles - reading dihedrals ... - 2501 dihedrals - reading impropers ... - 137 impropers - 4 = max # of 1-2 neighbors - 9 = max # of 1-3 neighbors - 19 = max # of 1-4 neighbors - 21 = max # of special neighbors - -special_bonds charmm -neigh_modify delay 2 every 1 - - -# ------------- MINIMIZE ---------- - -minimize 1e-4 1e-6 1000 10000 -WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) -PPPM initialization ... -WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302) -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.203272 - grid = 16 16 16 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0316399 - estimated relative force accuracy = 9.52826e-05 - using double precision FFTs - 3d grid and FFT values/proc = 3549 1024 -Neighbor list info ... - update every 1 steps, delay 0 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6, bins = 10 10 10 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmm/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory usage (min/avg/max) = 16.9693/0.981879/0 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 - 241 0 -4503.3131 749.58666 -3753.7264 -29.045153 -Loop time of 1.26594 on 4 procs for 241 steps with 892 atoms - -99.0% CPU use with 4 MPI tasks x 1 OpenMP threads - -Minimization stats: - Stopping criterion = energy tolerance - Energy initial, next-to-last, final = - -2131.73812515 -3753.43983927 -3753.72640137 - Force two-norm initial, final = 1086.21 26.3688 - Force max component initial, final = 310.811 3.92751 - Final line search alpha, max atom move = 0.00596649 0.0234334 - Iterations, force evaluations = 241 463 - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.34267 | 0.63792 | 0.90268 | 25.2 | 50.39 -Bond | 0.025776 | 0.063318 | 0.095631 | 10.8 | 5.00 -Kspace | 0.21904 | 0.51601 | 0.84895 | 31.3 | 40.76 -Neigh | 0.023185 | 0.023363 | 0.023538 | 0.1 | 1.85 -Comm | 0.012025 | 0.014189 | 0.016335 | 1.4 | 1.12 -Output | 0 | 0 | 0 | 0.0 | 0.00 -Modify | 0 | 0 | 0 | 0.0 | 0.00 -Other | | 0.01114 | | | 0.88 - -Nlocal: 223 ave 323 max 89 min -Histogram: 1 0 0 0 1 0 0 0 1 1 -Nghost: 613 ave 675 max 557 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 37222.8 ave 50005 max 20830 min -Histogram: 1 0 0 0 1 0 0 1 0 1 - -Total # of neighbors = 148891 -Ave neighs/atom = 166.918 -Ave special neighs/atom = 10.9395 -Neighbor list builds = 15 -Dangerous builds = 0 -reset_timestep 0 - -# ------------- RUN --------------- - -thermo 100 -thermo_style multi -timestep 8 - -run_style respa 3 2 8 bond 1 pair 2 kspace 3 -Respa levels: - 1 = bond angle dihedral improper - 2 = pair - 3 = kspace - -velocity all create 200.0 12345678 dist uniform -#dump dump1 all atom 100 4pti.dump - -fix 1 all nvt temp 200 300 25 -fix cor all filter/corotate m 1.0 - 163 = # of size 2 clusters - 0 = # of size 3 clusters - 25 = # of size 4 clusters - 0 = # of size 5 clusters - 100 = # of frozen angles - -run 1000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.203272 - grid = 16 16 16 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0316399 - estimated relative force accuracy = 9.52826e-05 - using double precision FFTs - 3d grid and FFT values/proc = 3549 1024 -Per MPI rank memory usage (min/avg/max) = 17.142/0.97212/0 Mbytes ----------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- -TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 -PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2592 -E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 -E_coul = -886.3622 E_long = -3326.2088 Press = 83.2282 ----------------- Step 100 ----- CPU = 1.5457 (sec) ---------------- -TotEng = -2718.9184 KinEng = 538.6205 Temp = 202.8014 -PotEng = -3257.5389 E_bond = 203.3365 E_angle = 566.5311 -E_dihed = 397.6202 E_impro = 34.6621 E_vdwl = -248.7451 -E_coul = -874.5326 E_long = -3336.4111 Press = 135.8435 ----------------- Step 200 ----- CPU = 3.0720 (sec) ---------------- -TotEng = -2660.1146 KinEng = 626.3474 Temp = 235.8323 -PotEng = -3286.4620 E_bond = 209.5168 E_angle = 591.7735 -E_dihed = 388.9615 E_impro = 29.5000 E_vdwl = -243.5840 -E_coul = -923.4998 E_long = -3339.1299 Press = 88.8857 ----------------- Step 300 ----- CPU = 4.5597 (sec) ---------------- -TotEng = -2669.7442 KinEng = 619.3625 Temp = 233.2023 -PotEng = -3289.1067 E_bond = 203.4405 E_angle = 569.5281 -E_dihed = 378.3314 E_impro = 38.2880 E_vdwl = -221.1904 -E_coul = -915.3396 E_long = -3342.1646 Press = 79.3780 ----------------- Step 400 ----- CPU = 5.9808 (sec) ---------------- -TotEng = -2618.9975 KinEng = 644.6145 Temp = 242.7102 -PotEng = -3263.6119 E_bond = 209.5864 E_angle = 618.8954 -E_dihed = 401.3798 E_impro = 39.9064 E_vdwl = -212.1271 -E_coul = -977.1589 E_long = -3344.0940 Press = -7.8938 ----------------- Step 500 ----- CPU = 7.4159 (sec) ---------------- -TotEng = -2579.7486 KinEng = 666.4643 Temp = 250.9371 -PotEng = -3246.2129 E_bond = 219.2549 E_angle = 620.3474 -E_dihed = 388.4395 E_impro = 41.4499 E_vdwl = -225.9686 -E_coul = -949.3689 E_long = -3340.3672 Press = 113.2543 ----------------- Step 600 ----- CPU = 8.9252 (sec) ---------------- -TotEng = -2535.8235 KinEng = 708.5919 Temp = 266.7990 -PotEng = -3244.4154 E_bond = 243.9451 E_angle = 606.0866 -E_dihed = 400.0562 E_impro = 33.9708 E_vdwl = -223.1319 -E_coul = -964.9940 E_long = -3340.3482 Press = -102.4475 ----------------- Step 700 ----- CPU = 10.4022 (sec) ---------------- -TotEng = -2552.6681 KinEng = 702.3080 Temp = 264.4330 -PotEng = -3254.9761 E_bond = 250.8834 E_angle = 639.0977 -E_dihed = 386.4014 E_impro = 42.3004 E_vdwl = -224.4816 -E_coul = -1011.8551 E_long = -3337.3222 Press = 10.6424 ----------------- Step 800 ----- CPU = 11.8699 (sec) ---------------- -TotEng = -2423.5415 KinEng = 772.1254 Temp = 290.7206 -PotEng = -3195.6670 E_bond = 238.5831 E_angle = 640.9180 -E_dihed = 377.7994 E_impro = 40.3135 E_vdwl = -216.5705 -E_coul = -935.1087 E_long = -3341.6019 Press = -38.2479 ----------------- Step 900 ----- CPU = 13.3548 (sec) ---------------- -TotEng = -2394.4779 KinEng = 766.6895 Temp = 288.6739 -PotEng = -3161.1673 E_bond = 284.8428 E_angle = 671.0959 -E_dihed = 380.3406 E_impro = 51.2975 E_vdwl = -219.5211 -E_coul = -990.6305 E_long = -3338.5925 Press = -15.2279 ----------------- Step 1000 ----- CPU = 14.7908 (sec) ---------------- -TotEng = -2340.1471 KinEng = 799.0198 Temp = 300.8469 -PotEng = -3139.1669 E_bond = 271.0389 E_angle = 683.8278 -E_dihed = 407.0795 E_impro = 39.6209 E_vdwl = -230.5355 -E_coul = -974.2981 E_long = -3335.9003 Press = -94.3420 -Loop time of 14.7909 on 4 procs for 1000 steps with 892 atoms - -Performance: 46.732 ns/day, 0.514 hours/ns, 67.609 timesteps/s -99.1% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 4.4184 | 7.5543 | 10.133 | 74.2 | 51.07 -Bond | 0.94027 | 1.9781 | 2.7492 | 54.4 | 13.37 -Kspace | 0.45487 | 0.45887 | 0.46343 | 0.4 | 3.10 -Neigh | 0.28145 | 0.28339 | 0.28539 | 0.3 | 1.92 -Comm | 0.7515 | 4.1484 | 8.3861 | 135.5 | 28.05 -Output | 0.00049973 | 0.00055474 | 0.00066924 | 0.0 | 0.00 -Modify | 0.26165 | 0.31142 | 0.35023 | 6.7 | 2.11 -Other | | 0.05572 | | | 0.38 - -Nlocal: 223 ave 313 max 122 min -Histogram: 1 0 0 1 0 0 0 1 0 1 -Nghost: 584.5 ave 605 max 553 min -Histogram: 1 0 0 0 0 1 0 0 0 2 -Neighs: 35448 ave 42093 max 25175 min -Histogram: 1 0 0 0 0 0 1 1 0 1 - -Total # of neighbors = 141792 -Ave neighs/atom = 158.96 -Ave special neighs/atom = 10.9395 -Neighbor list builds = 186 -Dangerous builds = 0 - -unfix cor -unfix 1 - - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:16 diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1 b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1 deleted file mode 100644 index 23dd4c8a89..0000000000 --- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.1 +++ /dev/null @@ -1,146 +0,0 @@ -LAMMPS (10 Mar 2017) - using 1 OpenMP thread(s) per MPI task -# Solvated 5-mer peptide, run for 8ps in NVT - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 2004 atoms - reading velocities ... - 2004 velocities - scanning bonds ... - 3 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 14 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -thermo 50 -#dump dump1 all atom 100 peptide.dump - -timestep 8 - -run_style respa 3 2 8 bond 1 pair 2 kspace 3 -Respa levels: - 1 = bond angle dihedral improper - 2 = pair - 3 = kspace - -fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 -fix cor all filter/corotate m 1.0 - 19 = # of size 2 clusters - 0 = # of size 3 clusters - 3 = # of size 4 clusters - 0 = # of size 5 clusters - 646 = # of frozen angles -run 1000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.268725 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0228209 - estimated relative force accuracy = 6.87243e-05 - using double precision FFTs - 3d grid and FFT values/proc = 10648 3375 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmm/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory usage (min/avg/max) = 22.6706/1/0 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821 - 50 239.46028 -7546.5667 1092.8874 -5023.9668 -24643.891 - 100 242.81799 -7125.5527 416.0788 -5259.7139 15525.465 - 150 235.97108 -7531.9334 932.35464 -5190.6987 -14838.489 - 200 252.06415 -7195.6011 568.02993 -5122.6064 8841.332 - 250 249.99431 -7586.5092 881.83491 -5212.0676 -9330.345 - 300 240.3382 -7333.0933 633.29951 -5264.8395 5137.9757 - 350 255.34529 -7568.2413 856.46371 -5187.2226 -6206.063 - 400 242.99276 -7419.9031 713.23943 -5255.8602 2447.0091 - 450 251.10653 -7622.061 844.20584 -5278.6079 -4906.6559 - 500 255.59314 -7439.253 710.84907 -5202.3691 1571.0032 - 550 253.2025 -7660.5101 823.05373 -5325.695 -4551.399 - 600 249.05313 -7509.6729 741.48104 -5281.2046 992.87 - 650 251.75984 -7593.6589 847.08244 -5243.4286 -3510.1176 - 700 249.25027 -7601.9112 794.0912 -5319.6557 305.76021 - 750 255.415 -7602.2674 822.98524 -5254.3109 -2333.421 - 800 241.99621 -7643.8878 796.53352 -5402.5008 -298.66565 - 850 253.6428 -7598.3764 816.45457 -5267.5316 -1905.3478 - 900 247.20231 -7690.2806 789.75999 -5424.5838 -1331.7228 - 950 255.92583 -7634.7505 831.18272 -5275.5466 -2186.5117 - 1000 253.2126 -7647.9526 823.93602 -5312.195 -1189.9659 -Loop time of 150.664 on 1 procs for 1000 steps with 2004 atoms - -Performance: 4.588 ns/day, 5.231 hours/ns, 6.637 timesteps/s -99.7% CPU use with 1 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 135.81 | 135.81 | 135.81 | 0.0 | 90.14 -Bond | 2.5889 | 2.5889 | 2.5889 | 0.0 | 1.72 -Kspace | 2.0379 | 2.0379 | 2.0379 | 0.0 | 1.35 -Neigh | 5.893 | 5.893 | 5.893 | 0.0 | 3.91 -Comm | 1.6998 | 1.6998 | 1.6998 | 0.0 | 1.13 -Output | 0.00077915 | 0.00077915 | 0.00077915 | 0.0 | 0.00 -Modify | 2 | 2 | 2 | 0.0 | 1.33 -Other | | 0.6352 | | | 0.42 - -Nlocal: 2004 ave 2004 max 2004 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 11197 ave 11197 max 11197 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 707779 ave 707779 max 707779 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 707779 -Ave neighs/atom = 353.183 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 200 -Dangerous builds = 200 -unfix cor -unfix 1 - - - - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:02:30 diff --git a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4 b/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4 deleted file mode 100644 index 2cdd645fe3..0000000000 --- a/examples/USER/misc/filter_corotate/log.10Mar2017.peptide.g++.4 +++ /dev/null @@ -1,146 +0,0 @@ -LAMMPS (10 Mar 2017) - using 1 OpenMP thread(s) per MPI task -# Solvated 5-mer peptide, run for 8ps in NVT - -units real -atom_style full - -pair_style lj/charmm/coul/long 8.0 10.0 10.0 -bond_style harmonic -angle_style charmm -dihedral_style charmm -improper_style harmonic -kspace_style pppm 0.0001 - -read_data data.peptide - orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) - 1 by 2 by 2 MPI processor grid - reading atoms ... - 2004 atoms - reading velocities ... - 2004 velocities - scanning bonds ... - 3 = max bonds/atom - scanning angles ... - 6 = max angles/atom - scanning dihedrals ... - 14 = max dihedrals/atom - scanning impropers ... - 1 = max impropers/atom - reading bonds ... - 1365 bonds - reading angles ... - 786 angles - reading dihedrals ... - 207 dihedrals - reading impropers ... - 12 impropers - 4 = max # of 1-2 neighbors - 7 = max # of 1-3 neighbors - 14 = max # of 1-4 neighbors - 18 = max # of special neighbors - -neighbor 2.0 bin -neigh_modify delay 5 - -thermo 50 -#dump dump1 all atom 100 peptide.dump - -timestep 8 - -run_style respa 3 2 8 bond 1 pair 2 kspace 3 -Respa levels: - 1 = bond angle dihedral improper - 2 = pair - 3 = kspace - -fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 -fix cor all filter/corotate m 1.0 - 19 = # of size 2 clusters - 0 = # of size 3 clusters - 3 = # of size 4 clusters - 0 = # of size 5 clusters - 646 = # of frozen angles -run 1000 -PPPM initialization ... -WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) - G vector (1/distance) = 0.268725 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0228209 - estimated relative force accuracy = 6.87243e-05 - using double precision FFTs - 3d grid and FFT values/proc = 4312 960 -Neighbor list info ... - update every 1 steps, delay 5 steps, check yes - max neighbors/atom: 2000, page size: 100000 - master list distance cutoff = 12 - ghost atom cutoff = 12 - binsize = 6, bins = 5 5 5 - 1 neighbor lists, perpetual/occasional/extra = 1 0 0 - (1) pair lj/charmm/coul/long, perpetual - attributes: half, newton on - pair build: half/bin/newton - stencil: half/bin/3d/newton - bin: standard -Per MPI rank memory usage (min/avg/max) = 16.8394/0.98826/0 Mbytes -Step Temp E_pair E_mol TotEng Press - 0 190.0857 -6785.6785 70.391457 -5580.3684 19434.821 - 50 239.46028 -7546.5668 1092.8874 -5023.9668 -24643.891 - 100 242.81819 -7125.5629 416.08082 -5259.7209 15525.244 - 150 235.94928 -7531.9186 932.50658 -5190.6621 -14842.431 - 200 255.85551 -7254.4065 568.8803 -5157.9249 8936.8651 - 250 247.8705 -7607.4583 858.06087 -5269.4711 -9926.0442 - 300 257.64176 -7267.424 618.5573 -5110.6004 5173.3307 - 350 251.65439 -7572.3806 821.15745 -5248.7049 -7092.327 - 400 256.87927 -7414.2145 655.33178 -5225.169 4119.4095 - 450 257.12393 -7576.5541 853.39773 -5187.9819 -5224.8823 - 500 242.42371 -7524.705 705.75357 -5371.5455 2111.3878 - 550 248.97188 -7541.076 792.86994 -5261.7038 -2278.4185 - 600 249.81862 -7592.0499 767.17722 -5333.3149 -1149.4759 - 650 253.31349 -7578.2665 813.75975 -5252.0827 -2915.5706 - 700 256.61152 -7588.1475 761.03356 -5294.9988 -747.88089 - 750 248.3606 -7660.457 837.71615 -5339.8883 -3072.8311 - 800 253.81464 -7638.6089 782.4229 -5340.7698 -1025.909 - 850 245.69185 -7660.9036 795.66792 -5398.3172 -2717.5851 - 900 249.13156 -7589.4769 806.43464 -5295.5867 -761.63361 - 950 251.11482 -7691.4981 869.34937 -5322.852 -3282.3031 - 1000 241.9195 -7630.9899 828.59107 -5358.0033 -95.962685 -Loop time of 45.5507 on 4 procs for 1000 steps with 2004 atoms - -Performance: 15.174 ns/day, 1.582 hours/ns, 21.954 timesteps/s -99.4% CPU use with 4 MPI tasks x 1 OpenMP threads - -MPI task timing breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 35.545 | 36.674 | 38.004 | 15.8 | 80.51 -Bond | 0.51302 | 0.67796 | 0.86345 | 18.6 | 1.49 -Kspace | 0.66031 | 0.68459 | 0.70506 | 2.1 | 1.50 -Neigh | 1.5605 | 1.5627 | 1.5649 | 0.1 | 3.43 -Comm | 3.4611 | 4.9841 | 6.294 | 47.2 | 10.94 -Output | 0.00079799 | 0.00086641 | 0.0010369 | 0.0 | 0.00 -Modify | 0.67341 | 0.69059 | 0.71186 | 1.7 | 1.52 -Other | | 0.2762 | | | 0.61 - -Nlocal: 501 ave 523 max 473 min -Histogram: 1 0 0 0 0 0 2 0 0 1 -Nghost: 6643.25 ave 6708 max 6566 min -Histogram: 1 1 0 0 0 0 0 0 0 2 -Neighs: 176977 ave 185765 max 164931 min -Histogram: 1 0 0 0 1 0 0 0 1 1 - -Total # of neighbors = 707908 -Ave neighs/atom = 353.248 -Ave special neighs/atom = 2.34032 -Neighbor list builds = 200 -Dangerous builds = 200 -unfix cor -unfix 1 - - - - -Please see the log.cite file for references relevant to this simulation - -Total wall time: 0:00:45 diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 new file mode 100644 index 0000000000..1e708a9d39 --- /dev/null +++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.1 @@ -0,0 +1,241 @@ +LAMMPS (20 Jun 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task + +units real + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 8 10 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data data.bpti + orthogonal box = (-10 -10 -30) to (50 50 30) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 892 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 906 bonds + reading angles ... + 1626 angles + reading dihedrals ... + 2501 dihedrals + reading impropers ... + 137 impropers + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 21 = max # of special neighbors + +special_bonds charmm +neigh_modify delay 2 every 1 + + +# ------------- MINIMIZE ---------- + +minimize 1e-4 1e-6 1000 10000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +PPPM initialization ... +WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302) +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.203272 + grid = 16 16 16 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0316399 + estimated relative force accuracy = 9.52826e-05 + using double precision FFTs + 3d grid and FFT values/proc = 9261 4096 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 17.86 | 17.86 | 17.86 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 + 241 0 -4503.313 749.58662 -3753.7264 -29.045104 +Loop time of 7.63279 on 1 procs for 241 steps with 892 atoms + +32.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -2131.73812515 -3753.43984087 -3753.72636847 + Force two-norm initial, final = 1086.21 26.3688 + Force max component initial, final = 310.811 3.92748 + Final line search alpha, max atom move = 0.00596649 0.0234333 + Iterations, force evaluations = 241 463 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.8395 | 5.8395 | 5.8395 | 0.0 | 76.51 +Bond | 0.46414 | 0.46414 | 0.46414 | 0.0 | 6.08 +Kspace | 1.1535 | 1.1535 | 1.1535 | 0.0 | 15.11 +Neigh | 0.14908 | 0.14908 | 0.14908 | 0.0 | 1.95 +Comm | 0.001932 | 0.001932 | 0.001932 | 0.0 | 0.03 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02465 | | | 0.32 + +Nlocal: 892 ave 892 max 892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 31 ave 31 max 31 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 148891 ave 148891 max 148891 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 148891 +Ave neighs/atom = 166.918 +Ave special neighs/atom = 10.9395 +Neighbor list builds = 15 +Dangerous builds = 0 +reset_timestep 0 + +# ------------- RUN --------------- + +thermo 100 +thermo_style multi +timestep 8 + +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 +Respa levels: + 1 = bond angle + 2 = dihedral improper pair + 3 = kspace + +velocity all create 200.0 12345678 dist uniform +#dump dump1 all atom 100 4pti.dump + +fix 1 all nvt temp 200 300 25 +fix cor all filter/corotate m 1.0 + 163 = # of size 2 clusters + 0 = # of size 3 clusters + 25 = # of size 4 clusters + 0 = # of size 5 clusters + 100 = # of frozen angles + +run 1000 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.203272 + grid = 16 16 16 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0316399 + estimated relative force accuracy = 9.52826e-05 + using double precision FFTs + 3d grid and FFT values/proc = 9261 4096 +Per MPI rank memory allocation (min/avg/max) = 19.55 | 19.55 | 19.55 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 +PotEng = -3751.5181 E_bond = 42.2810 E_angle = 345.2592 +E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 +E_coul = -886.3622 E_long = -3326.2088 Press = 83.2283 +---------------- Step 100 ----- CPU = 8.4380 (sec) ---------------- +TotEng = -2718.4258 KinEng = 539.6265 Temp = 203.1802 +PotEng = -3258.0524 E_bond = 203.2307 E_angle = 566.1893 +E_dihed = 397.6759 E_impro = 34.7696 E_vdwl = -248.6577 +E_coul = -874.8466 E_long = -3336.4135 Press = 135.8640 +---------------- Step 200 ----- CPU = 16.9012 (sec) ---------------- +TotEng = -2661.9611 KinEng = 625.0674 Temp = 235.3503 +PotEng = -3287.0285 E_bond = 208.1804 E_angle = 590.8462 +E_dihed = 389.1482 E_impro = 30.5882 E_vdwl = -240.5448 +E_coul = -926.3091 E_long = -3338.9378 Press = 103.4738 +---------------- Step 300 ----- CPU = 25.3046 (sec) ---------------- +TotEng = -2662.4139 KinEng = 622.2647 Temp = 234.2951 +PotEng = -3284.6785 E_bond = 202.4210 E_angle = 573.6793 +E_dihed = 382.8919 E_impro = 41.8973 E_vdwl = -218.9895 +E_coul = -924.8414 E_long = -3341.7372 Press = 40.6746 +---------------- Step 400 ----- CPU = 33.8063 (sec) ---------------- +TotEng = -2604.9431 KinEng = 662.9890 Temp = 249.6286 +PotEng = -3267.9321 E_bond = 195.9116 E_angle = 616.1383 +E_dihed = 407.8502 E_impro = 43.3560 E_vdwl = -219.0377 +E_coul = -966.3118 E_long = -3345.8387 Press = -91.8856 +---------------- Step 500 ----- CPU = 42.3470 (sec) ---------------- +TotEng = -2609.3867 KinEng = 657.0939 Temp = 247.4090 +PotEng = -3266.4806 E_bond = 236.4955 E_angle = 570.6256 +E_dihed = 390.5111 E_impro = 41.9250 E_vdwl = -223.9927 +E_coul = -939.5249 E_long = -3342.5201 Press = 236.7471 +---------------- Step 600 ----- CPU = 50.9590 (sec) ---------------- +TotEng = -2564.7161 KinEng = 701.8494 Temp = 264.2603 +PotEng = -3266.5655 E_bond = 223.5820 E_angle = 582.7722 +E_dihed = 394.6196 E_impro = 43.8581 E_vdwl = -201.7759 +E_coul = -967.4136 E_long = -3342.2079 Press = 26.6595 +---------------- Step 700 ----- CPU = 59.4791 (sec) ---------------- +TotEng = -2510.1142 KinEng = 689.5931 Temp = 259.6455 +PotEng = -3199.7072 E_bond = 254.6476 E_angle = 611.9715 +E_dihed = 403.0624 E_impro = 44.1360 E_vdwl = -205.6377 +E_coul = -964.7455 E_long = -3343.1416 Press = 60.5789 +---------------- Step 800 ----- CPU = 67.9330 (sec) ---------------- +TotEng = -2452.7408 KinEng = 777.5962 Temp = 292.7805 +PotEng = -3230.3370 E_bond = 250.4950 E_angle = 656.6738 +E_dihed = 382.4702 E_impro = 39.5378 E_vdwl = -225.0375 +E_coul = -994.4519 E_long = -3340.0244 Press = -19.6463 +---------------- Step 900 ----- CPU = 76.3690 (sec) ---------------- +TotEng = -2339.9766 KinEng = 808.7116 Temp = 304.4961 +PotEng = -3148.6883 E_bond = 247.7657 E_angle = 679.0658 +E_dihed = 398.2984 E_impro = 43.7890 E_vdwl = -230.2498 +E_coul = -945.8152 E_long = -3341.5422 Press = -64.4343 +---------------- Step 1000 ----- CPU = 84.8757 (sec) ---------------- +TotEng = -2329.1819 KinEng = 822.9820 Temp = 309.8691 +PotEng = -3152.1639 E_bond = 264.9609 E_angle = 691.7104 +E_dihed = 385.9914 E_impro = 40.5525 E_vdwl = -230.5182 +E_coul = -954.6203 E_long = -3350.2405 Press = -146.6649 +Loop time of 84.8758 on 1 procs for 1000 steps with 892 atoms + +Performance: 8.144 ns/day, 2.947 hours/ns, 11.782 timesteps/s +32.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 68.548 | 68.548 | 68.548 | 0.0 | 80.76 +Bond | 10.263 | 10.263 | 10.263 | 0.0 | 12.09 +Kspace | 2.4528 | 2.4528 | 2.4528 | 0.0 | 2.89 +Neigh | 1.9041 | 1.9041 | 1.9041 | 0.0 | 2.24 +Comm | 0.044126 | 0.044126 | 0.044126 | 0.0 | 0.05 +Output | 0.000983 | 0.000983 | 0.000983 | 0.0 | 0.00 +Modify | 1.4113 | 1.4113 | 1.4113 | 0.0 | 1.66 +Other | | 0.2516 | | | 0.30 + +Nlocal: 892 ave 892 max 892 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 38 ave 38 max 38 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 144068 ave 144068 max 144068 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 144068 +Ave neighs/atom = 161.511 +Ave special neighs/atom = 10.9395 +Neighbor list builds = 190 +Dangerous builds = 0 + +unfix cor +unfix 1 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:32 diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 new file mode 100644 index 0000000000..5367f0e624 --- /dev/null +++ b/examples/USER/misc/filter_corotate/log.22Jun2017.bpti.g++.4 @@ -0,0 +1,241 @@ +LAMMPS (20 Jun 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task + +units real + +atom_style full +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic + +pair_style lj/charmm/coul/long 8 10 +pair_modify mix arithmetic +kspace_style pppm 1e-4 + +read_data data.bpti + orthogonal box = (-10 -10 -30) to (50 50 30) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 892 atoms + scanning bonds ... + 4 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 18 = max dihedrals/atom + scanning impropers ... + 2 = max impropers/atom + reading bonds ... + 906 bonds + reading angles ... + 1626 angles + reading dihedrals ... + 2501 dihedrals + reading impropers ... + 137 impropers + 4 = max # of 1-2 neighbors + 9 = max # of 1-3 neighbors + 19 = max # of 1-4 neighbors + 21 = max # of special neighbors + +special_bonds charmm +neigh_modify delay 2 every 1 + + +# ------------- MINIMIZE ---------- + +minimize 1e-4 1e-6 1000 10000 +WARNING: Resetting reneighboring criteria during minimization (../min.cpp:168) +PPPM initialization ... +WARNING: System is not charge neutral, net charge = 6 (../kspace.cpp:302) +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.203272 + grid = 16 16 16 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0316399 + estimated relative force accuracy = 9.52826e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3549 1024 +Neighbor list info ... + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 10 10 10 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.97 | 17.2 | 17.52 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -3075.6498 943.91164 -2131.7381 -380.67776 + 241 0 -4503.3131 749.58665 -3753.7264 -29.044989 +Loop time of 3.06327 on 4 procs for 241 steps with 892 atoms + +31.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +Minimization stats: + Stopping criterion = energy tolerance + Energy initial, next-to-last, final = + -2131.73812515 -3753.4398752 -3753.72640446 + Force two-norm initial, final = 1086.21 26.3687 + Force max component initial, final = 310.811 3.92765 + Final line search alpha, max atom move = 0.0059665 0.0234343 + Iterations, force evaluations = 241 463 + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.91458 | 1.6235 | 2.2701 | 38.2 | 53.00 +Bond | 0.055164 | 0.13173 | 0.19487 | 15.1 | 4.30 +Kspace | 0.48966 | 1.1993 | 1.9847 | 48.7 | 39.15 +Neigh | 0.053297 | 0.053442 | 0.053576 | 0.0 | 1.74 +Comm | 0.031677 | 0.035006 | 0.038061 | 1.5 | 1.14 +Output | 0 | 0 | 0 | 0.0 | 0.00 +Modify | 0 | 0 | 0 | 0.0 | 0.00 +Other | | 0.02021 | | | 0.66 + +Nlocal: 223 ave 323 max 89 min +Histogram: 1 0 0 0 1 0 0 0 1 1 +Nghost: 613 ave 675 max 557 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 37222.8 ave 50005 max 20830 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 148891 +Ave neighs/atom = 166.918 +Ave special neighs/atom = 10.9395 +Neighbor list builds = 15 +Dangerous builds = 0 +reset_timestep 0 + +# ------------- RUN --------------- + +thermo 100 +thermo_style multi +timestep 8 + +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 +Respa levels: + 1 = bond angle + 2 = dihedral improper pair + 3 = kspace + +velocity all create 200.0 12345678 dist uniform +#dump dump1 all atom 100 4pti.dump + +fix 1 all nvt temp 200 300 25 +fix cor all filter/corotate m 1.0 + 163 = # of size 2 clusters + 0 = # of size 3 clusters + 25 = # of size 4 clusters + 0 = # of size 5 clusters + 100 = # of frozen angles + +run 1000 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.203272 + grid = 16 16 16 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0316399 + estimated relative force accuracy = 9.52826e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3549 1024 +Per MPI rank memory allocation (min/avg/max) = 17.14 | 17.63 | 18.14 Mbytes +---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- +TotEng = -3220.3378 KinEng = 531.1804 Temp = 200.0000 +PotEng = -3751.5182 E_bond = 42.2810 E_angle = 345.2593 +E_dihed = 337.8361 E_impro = 24.2103 E_vdwl = -288.5339 +E_coul = -886.3622 E_long = -3326.2088 Press = 83.2284 +---------------- Step 100 ----- CPU = 3.4639 (sec) ---------------- +TotEng = -2718.4266 KinEng = 539.6246 Temp = 203.1794 +PotEng = -3258.0513 E_bond = 203.2306 E_angle = 566.1887 +E_dihed = 397.6756 E_impro = 34.7695 E_vdwl = -248.6577 +E_coul = -874.8446 E_long = -3336.4135 Press = 135.8653 +---------------- Step 200 ----- CPU = 6.8898 (sec) ---------------- +TotEng = -2662.0450 KinEng = 625.0178 Temp = 235.3317 +PotEng = -3287.0628 E_bond = 208.1691 E_angle = 590.8259 +E_dihed = 389.1424 E_impro = 30.5879 E_vdwl = -240.5397 +E_coul = -926.3110 E_long = -3338.9375 Press = 103.4843 +---------------- Step 300 ----- CPU = 10.2791 (sec) ---------------- +TotEng = -2661.8829 KinEng = 623.0352 Temp = 234.5852 +PotEng = -3284.9181 E_bond = 203.0274 E_angle = 573.6583 +E_dihed = 383.0124 E_impro = 41.9015 E_vdwl = -218.0696 +E_coul = -926.5806 E_long = -3341.8675 Press = 45.6868 +---------------- Step 400 ----- CPU = 13.5874 (sec) ---------------- +TotEng = -2594.5220 KinEng = 672.8693 Temp = 253.3487 +PotEng = -3267.3914 E_bond = 201.3378 E_angle = 612.7099 +E_dihed = 410.1920 E_impro = 44.0201 E_vdwl = -217.9714 +E_coul = -971.6203 E_long = -3346.0595 Press = -121.1015 +---------------- Step 500 ----- CPU = 16.9047 (sec) ---------------- +TotEng = -2603.9306 KinEng = 668.2122 Temp = 251.5952 +PotEng = -3272.1428 E_bond = 238.1081 E_angle = 578.3310 +E_dihed = 399.1305 E_impro = 41.4314 E_vdwl = -216.9664 +E_coul = -969.4047 E_long = -3342.7729 Press = 156.7851 +---------------- Step 600 ----- CPU = 20.1970 (sec) ---------------- +TotEng = -2531.1096 KinEng = 728.1698 Temp = 274.1705 +PotEng = -3259.2794 E_bond = 232.8396 E_angle = 621.3323 +E_dihed = 398.1952 E_impro = 37.0914 E_vdwl = -241.6350 +E_coul = -963.1540 E_long = -3343.9488 Press = 58.6784 +---------------- Step 700 ----- CPU = 23.4360 (sec) ---------------- +TotEng = -2499.9495 KinEng = 742.1211 Temp = 279.4234 +PotEng = -3242.0705 E_bond = 240.5622 E_angle = 582.9270 +E_dihed = 396.6246 E_impro = 36.6510 E_vdwl = -228.4925 +E_coul = -926.8734 E_long = -3343.4695 Press = -60.7458 +---------------- Step 800 ----- CPU = 26.6709 (sec) ---------------- +TotEng = -2426.0217 KinEng = 760.1083 Temp = 286.1959 +PotEng = -3186.1300 E_bond = 266.5863 E_angle = 652.3401 +E_dihed = 380.7407 E_impro = 34.6861 E_vdwl = -225.3729 +E_coul = -953.2382 E_long = -3341.8721 Press = -57.9824 +---------------- Step 900 ----- CPU = 29.8152 (sec) ---------------- +TotEng = -2419.4636 KinEng = 780.8361 Temp = 294.0004 +PotEng = -3200.2996 E_bond = 269.3237 E_angle = 665.7171 +E_dihed = 408.3527 E_impro = 43.7811 E_vdwl = -254.0696 +E_coul = -1002.0694 E_long = -3331.3352 Press = -52.0169 +---------------- Step 1000 ----- CPU = 32.8748 (sec) ---------------- +TotEng = -2398.7244 KinEng = 811.9856 Temp = 305.7288 +PotEng = -3210.7099 E_bond = 258.2207 E_angle = 639.3671 +E_dihed = 379.3353 E_impro = 41.7602 E_vdwl = -207.2654 +E_coul = -983.9330 E_long = -3338.1948 Press = 89.4870 +Loop time of 32.8751 on 4 procs for 1000 steps with 892 atoms + +Performance: 21.025 ns/day, 1.141 hours/ns, 30.418 timesteps/s +31.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.449 | 19.023 | 24.612 | 99.6 | 57.86 +Bond | 1.4547 | 2.8768 | 3.9098 | 61.4 | 8.75 +Kspace | 1.0537 | 1.0778 | 1.0992 | 2.1 | 3.28 +Neigh | 0.67542 | 0.67994 | 0.68323 | 0.3 | 2.07 +Comm | 1.8602 | 8.4515 | 16.516 | 182.9 | 25.71 +Output | 0.000839 | 0.00147 | 0.003293 | 2.7 | 0.00 +Modify | 0.56658 | 0.63186 | 0.69304 | 6.8 | 1.92 +Other | | 0.133 | | | 0.40 + +Nlocal: 223 ave 339 max 136 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 590 ave 626 max 552 min +Histogram: 1 0 0 0 1 0 1 0 0 1 +Neighs: 36488.2 ave 41965 max 29054 min +Histogram: 1 0 0 0 1 0 0 0 1 1 + +Total # of neighbors = 145953 +Ave neighs/atom = 163.624 +Ave special neighs/atom = 10.9395 +Neighbor list builds = 189 +Dangerous builds = 0 + +unfix cor +unfix 1 + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:00:36 diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 new file mode 100644 index 0000000000..22c5483c9e --- /dev/null +++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.1 @@ -0,0 +1,147 @@ +LAMMPS (20 Jun 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide, run for 8ps in NVT + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +thermo 50 +#dump dump1 all atom 100 peptide.dump + +timestep 8 + +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 +Respa levels: + 1 = bond angle + 2 = dihedral improper pair + 3 = kspace + +fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 +fix cor all filter/corotate m 1.0 + 19 = # of size 2 clusters + 0 = # of size 3 clusters + 3 = # of size 4 clusters + 0 = # of size 5 clusters + 646 = # of frozen angles +run 1000 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 10648 3375 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 22.72 | 22.72 | 22.72 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984 + 50 239.47667 -7205.1006 1092.7664 -4682.5237 -23733.122 + 100 244.63086 -6788.0793 422.97204 -4904.5234 16458.011 + 150 240.79042 -7267.0791 966.31411 -4863.1107 -13554.894 + 200 254.77122 -6868.5713 591.00071 -4756.4431 10532.563 + 250 241.87417 -7264.9349 856.9357 -4963.8743 -9043.4359 + 300 251.37775 -6976.8 650.55612 -4825.3773 6986.2021 + 350 250.81494 -7286.7011 880.11184 -4909.0829 -6392.4665 + 400 247.55673 -7104.4036 701.89555 -4924.4551 4720.7811 + 450 258.54988 -7215.3011 832.23692 -4839.3759 -3446.3859 + 500 246.80928 -7151.2468 715.61007 -4962.0464 2637.5769 + 550 246.20721 -7159.0464 805.24974 -4883.8011 -2725.227 + 600 250.62483 -7201.7688 806.10076 -4899.2968 770.22352 + 650 247.59777 -7260.1607 802.97277 -4978.8899 -430.42309 + 700 246.86951 -7286.2971 825.99865 -4986.3486 -427.88651 + 750 252.79268 -7307.8572 833.4822 -4965.0605 -614.74372 + 800 251.73191 -7315.2457 839.59859 -4972.666 952.56448 + 850 246.75844 -7303.6221 816.67112 -5013.6642 -2055.2823 + 900 251.00123 -7317.4219 825.12165 -4993.6817 -356.53166 + 950 259.20822 -7252.3466 854.62611 -4850.1016 -1719.5267 + 1000 245.72486 -7347.5547 811.48146 -5068.9576 -717.6136 +Loop time of 357.523 on 1 procs for 1000 steps with 2004 atoms + +Performance: 1.933 ns/day, 12.414 hours/ns, 2.797 timesteps/s +32.0% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 328.2 | 328.2 | 328.2 | 0.0 | 91.80 +Bond | 4.4815 | 4.4815 | 4.4815 | 0.0 | 1.25 +Kspace | 3.9448 | 3.9448 | 3.9448 | 0.0 | 1.10 +Neigh | 12.457 | 12.457 | 12.457 | 0.0 | 3.48 +Comm | 3.2147 | 3.2147 | 3.2147 | 0.0 | 0.90 +Output | 0.001689 | 0.001689 | 0.001689 | 0.0 | 0.00 +Modify | 3.937 | 3.937 | 3.937 | 0.0 | 1.10 +Other | | 1.289 | | | 0.36 + +Nlocal: 2004 ave 2004 max 2004 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 11191 ave 11191 max 11191 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 708610 ave 708610 max 708610 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 708610 +Ave neighs/atom = 353.598 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 200 +Dangerous builds = 200 +unfix cor +unfix 1 + + + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:05:57 diff --git a/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4 b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4 new file mode 100644 index 0000000000..eec3843bd0 --- /dev/null +++ b/examples/USER/misc/filter_corotate/log.22Jun2017.peptide.g++.4 @@ -0,0 +1,147 @@ +LAMMPS (20 Jun 2017) +OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90) + using 1 OpenMP thread(s) per MPI task +# Solvated 5-mer peptide, run for 8ps in NVT + +units real +atom_style full + +pair_style lj/charmm/coul/long 8.0 10.0 10.0 +bond_style harmonic +angle_style charmm +dihedral_style charmm +improper_style harmonic +kspace_style pppm 0.0001 + +read_data data.peptide + orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 2004 atoms + reading velocities ... + 2004 velocities + scanning bonds ... + 3 = max bonds/atom + scanning angles ... + 6 = max angles/atom + scanning dihedrals ... + 14 = max dihedrals/atom + scanning impropers ... + 1 = max impropers/atom + reading bonds ... + 1365 bonds + reading angles ... + 786 angles + reading dihedrals ... + 207 dihedrals + reading impropers ... + 12 impropers + 4 = max # of 1-2 neighbors + 7 = max # of 1-3 neighbors + 14 = max # of 1-4 neighbors + 18 = max # of special neighbors + +neighbor 2.0 bin +neigh_modify delay 5 + +thermo 50 +#dump dump1 all atom 100 peptide.dump + +timestep 8 + +run_style respa 3 2 8 bond 1 dihedral 2 pair 2 kspace 3 +Respa levels: + 1 = bond angle + 2 = dihedral improper pair + 3 = kspace + +fix 1 all nvt temp 250.0 250.0 100.0 tchain 1 +fix cor all filter/corotate m 1.0 + 19 = # of size 2 clusters + 0 = # of size 3 clusters + 3 = # of size 4 clusters + 0 = # of size 5 clusters + 646 = # of frozen angles +run 1000 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.268725 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0228209 + estimated relative force accuracy = 6.87243e-05 + using double precision FFTs + 3d grid and FFT values/proc = 4312 960 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6, bins = 5 5 5 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/charmm/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 16.87 | 17.05 | 17.26 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 190.0857 -6442.7438 70.391457 -5237.4338 20361.984 + 50 239.47667 -7205.1005 1092.7664 -4682.5237 -23733.122 + 100 244.63889 -6788.1152 422.96733 -4904.5161 16457.756 + 150 239.36917 -7258.7053 967.87775 -4861.6589 -13526.261 + 200 255.14702 -6864.0525 604.58036 -4736.1009 11013.1 + 250 252.72919 -7303.0966 898.11178 -4896.0494 -8480.8766 + 300 250.66477 -6989.2603 652.83649 -4839.8141 6209.3375 + 350 243.30794 -7218.8575 838.31977 -4927.8525 -5180.4928 + 400 256.3573 -7090.677 706.24197 -4853.8377 3302.577 + 450 246.15776 -7274.574 834.31676 -4970.557 -3427.971 + 500 256.28473 -7082.1447 735.42828 -4816.5524 2846.086 + 550 251.32327 -7341.739 812.64934 -5028.5484 -1786.9277 + 600 254.57737 -7152.3448 740.52534 -4891.8494 825.91675 + 650 244.95305 -7207.1136 790.67659 -4953.9295 -520.79769 + 700 249.4984 -7204.2699 779.06969 -4935.5544 -940.75384 + 750 248.46962 -7232.1037 791.6642 -4956.9361 -548.12171 + 800 260.2974 -7293.1982 793.23282 -4945.8435 -1171.26 + 850 249.79023 -7258.3759 823.56789 -4943.4198 -499.76275 + 900 249.97237 -7267.0584 784.57992 -4990.0028 -271.33531 + 950 251.29018 -7261.0642 823.467 -4937.2534 -538.7168 + 1000 246.05777 -7285.0948 847.90892 -4968.0826 -2613.1854 +Loop time of 94.6835 on 4 procs for 1000 steps with 2004 atoms + +Performance: 7.300 ns/day, 3.288 hours/ns, 10.562 timesteps/s +37.9% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 33.389 | 78.508 | 94.639 | 294.1 | 82.92 +Bond | 0.39957 | 1.104 | 1.4443 | 40.6 | 1.17 +Kspace | 0.53324 | 1.2631 | 1.5137 | 37.5 | 1.33 +Neigh | 1.2668 | 3.011 | 3.5942 | 58.0 | 3.18 +Comm | 3.4563 | 8.8707 | 11.494 | 107.9 | 9.37 +Output | 0.000435 | 0.0017425 | 0.004136 | 3.4 | 0.00 +Modify | 0.59335 | 1.4123 | 1.6921 | 39.8 | 1.49 +Other | | 0.5129 | | | 0.54 + +Nlocal: 501 ave 515 max 476 min +Histogram: 1 0 0 0 0 0 0 1 1 1 +Nghost: 6681.5 ave 6740 max 6634 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 176872 ave 182642 max 168464 min +Histogram: 1 0 0 0 0 0 1 1 0 1 + +Total # of neighbors = 707486 +Ave neighs/atom = 353.037 +Ave special neighs/atom = 2.34032 +Neighbor list builds = 200 +Dangerous builds = 200 +unfix cor +unfix 1 + + + + +Please see the log.cite file for references relevant to this simulation + +Total wall time: 0:01:53 diff --git a/examples/USER/misc/grem/lj-temper/0/log.lammps.0 b/examples/USER/misc/grem/lj-temper/0/log.lammps.0 index 22998f8893..1c1aaaf042 100644 --- a/examples/USER/misc/grem/lj-temper/0/log.lammps.0 +++ b/examples/USER/misc/grem/lj-temper/0/log.lammps.0 @@ -16,10 +16,6 @@ read_data 0/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 900 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 900 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38195 Mbytes -Step Temp PotEng TotEng Press Volume - 0 299.42262 -3416.9 -2971.5315 134.01052 11328.967 - 100 294.63941 -3417.2566 -2979.0028 164.62038 11328.996 - 200 302.86941 -3421.7405 -2971.2452 116.35909 11329.199 - 300 297.43413 -3417.6882 -2975.2774 143.60143 11329.666 - 400 300.1465 -3421.466 -2975.0208 108.02406 11330.366 - 500 300.2847 -3419.7205 -2973.0698 51.93802 11331.264 - 600 297.98642 -3416.0758 -2972.8436 102.67264 11332.303 - 700 308.88819 -3423.7386 -2964.2908 -84.991092 11333.461 - 800 300.03002 -3418.2447 -2971.9728 61.530839 11334.623 - 900 294.38296 -3416.7286 -2978.8563 59.4512 11336.02 - 1000 301.55478 -3419.3685 -2970.8287 -70.828164 11337.415 - 1100 304.76191 -3420.01 -2966.6997 -46.02246 11338.757 - 1200 300.87935 -3418.357 -2970.8218 -27.557375 11340.179 - 1300 297.90925 -3416.7586 -2973.6412 27.202549 11341.647 - 1400 304.0426 -3421.0828 -2968.8425 -150.93733 11343.177 - 1500 293.50425 -3416.0019 -2979.4366 -32.703088 11344.538 - 1600 298.70817 -3416.4247 -2972.1189 -111.16189 11345.702 - 1700 293.12426 -3415.1528 -2979.1527 -12.438698 11346.701 - 1800 289.23529 -3413.4211 -2983.2055 -27.234713 11347.494 - 1900 292.62679 -3415.5324 -2980.2722 -121.80014 11347.911 - 2000 295.3705 -3415.4594 -2976.1182 -118.35918 11347.97 - 2100 288.3131 -3411.9071 -2983.0632 11.471141 11347.887 - 2200 312.55009 -3422.4761 -2957.5815 -294.72858 11347.644 - 2300 285.92437 -3414.5956 -2989.3047 -43.986075 11346.986 - 2400 300.19294 -3419.6619 -2973.1476 -153.30034 11346.114 - 2500 295.61459 -3415.1159 -2975.4116 20.33969 11344.962 - 2600 297.71268 -3415.7827 -2972.9577 -52.926913 11343.679 - 2700 298.56462 -3417.9995 -2973.9072 -131.29953 11342.271 - 2800 286.03931 -3410.6373 -2985.1754 164.72078 11340.629 - 2900 290.70577 -3411.5311 -2979.1283 143.13209 11338.97 - 3000 303.332 -3415.7792 -2964.5958 -49.330701 11337.303 - 3100 301.73339 -3417.0188 -2968.2132 -8.5041565 11335.568 - 3200 313.04988 -3423.077 -2957.439 -122.70098 11333.927 - 3300 286.09745 -3408.4061 -2982.8579 353.68123 11332.253 - 3400 303.00349 -3413.2328 -2962.5381 231.93254 11330.816 - 3500 308.79241 -3417.4556 -2958.1503 91.741468 11329.674 - 3600 287.41302 -3407.5431 -2980.038 543.23683 11329.043 - 3700 294.17479 -3407.5416 -2969.9788 449.07447 11329.318 - 3800 289.81831 -3405.492 -2974.4092 576.60121 11330.443 - 3900 295.40157 -3408.4609 -2969.0734 451.50877 11332.572 - 4000 287.71309 -3402.6497 -2974.6982 573.42617 11335.583 - 4100 290.02657 -3403.0786 -2971.686 527.71502 11339.534 - 4200 297.74424 -3409.8018 -2966.9298 277.40905 11344.404 - 4300 292.06583 -3402.1684 -2967.7426 444.89069 11349.944 - 4400 300.74402 -3406.2366 -2958.9027 139.09782 11356.223 - 4500 295.14988 -3402.5929 -2963.5798 173.91619 11362.896 - 4600 299.82229 -3402.1676 -2956.2047 114.51482 11369.919 - 4700 299.72789 -3400.7608 -2954.9383 83.204669 11377.21 - 4800 292.34822 -3393.2268 -2958.3809 161.50646 11384.622 - 4900 298.32652 -3395.3712 -2951.6331 29.917068 11392.178 - 5000 293.0855 -3395.7079 -2959.7654 -67.018003 11399.715 - 5100 302.58088 -3398.1836 -2948.1175 -214.79018 11407.054 - 5200 302.00186 -3395.3231 -2946.1182 -305.62771 11413.967 - 5300 308.44521 -3396.6926 -2937.9037 -455.80177 11420.397 - 5400 305.55347 -3392.9576 -2938.4699 -464.74116 11426.162 - 5500 306.15731 -3393.3834 -2937.9976 -453.93342 11431.122 - 5600 300.86617 -3390.7578 -2943.2421 -413.36436 11435.339 - 5700 311.4673 -3395.9418 -2932.6578 -637.62795 11438.796 - 5800 302.31851 -3388.9636 -2939.2877 -501.87858 11441.318 - 5900 315.93456 -3400.2717 -2930.343 -753.56358 11443.043 - 6000 304.69067 -3391.9711 -2938.7668 -477.72322 11443.646 - 6100 311.80005 -3393.0048 -2929.2259 -633.56098 11443.351 - 6200 307.36579 -3391.6406 -2934.4573 -532.82298 11442.106 - 6300 302.7084 -3389.8455 -2939.5897 -490.38666 11439.901 - 6400 306.78573 -3392.1276 -2935.807 -547.43007 11436.8 - 6500 304.23179 -3388.17 -2935.6483 -348.52993 11432.753 - 6600 296.7094 -3385.8464 -2944.5136 -201.5605 11428.01 - 6700 313.3959 -3395.26 -2929.1073 -415.82786 11422.724 - 6800 316.4072 -3399.1224 -2928.4906 -496.33753 11416.786 - 6900 302.56547 -3389.7698 -2939.7266 -80.175542 11410.218 - 7000 299.36836 -3387.708 -2942.4203 128.86864 11403.334 - 7100 309.39575 -3396.2826 -2936.0798 -53.969342 11396.555 - 7200 324.25215 -3405.3158 -2923.0153 -227.25827 11389.761 - 7300 305.99737 -3393.6219 -2938.474 235.46369 11382.905 - 7400 317.73948 -3402.1318 -2929.5184 21.699572 11376.471 - 7500 315.75908 -3400.7608 -2931.0931 148.23486 11370.37 - 7600 311.46203 -3401.9952 -2938.7191 182.85745 11364.81 - 7700 309.3606 -3403.1221 -2942.9717 257.80591 11359.711 - 7800 300.78232 -3397.6295 -2950.2386 440.63834 11355.144 - 7900 306.59047 -3402.2326 -2946.2025 287.86462 11351.377 - 8000 311.28944 -3406.6966 -2943.6772 268.88617 11348.336 - 8100 299.93421 -3405.6032 -2959.4738 356.79664 11346.007 - 8200 302.26336 -3406.5846 -2956.9908 246.8694 11344.383 - 8300 294.27353 -3406.1343 -2968.4247 428.02411 11343.38 - 8400 273.01304 -3396.291 -2990.2048 712.6039 11343.239 - 8500 294.90301 -3407.461 -2968.8151 259.18716 11344.147 - 8600 295.43347 -3410.2779 -2970.8431 127.32619 11345.636 - 8700 285.2568 -3407.4342 -2983.1364 223.78377 11347.458 - 8800 296.45048 -3413.1605 -2972.2128 61.542232 11349.754 - 8900 306.82798 -3417.5232 -2961.1398 -170.00394 11352.317 - 9000 287.0527 -3408.5483 -2981.5791 46.683648 11354.612 - 9100 296.30539 -3414.6325 -2973.9007 -222.07876 11356.77 - 9200 300.16761 -3415.9641 -2969.4875 -218.94764 11358.601 - 9300 310.01596 -3418.7396 -2957.6143 -409.04518 11360.094 - 9400 293.6059 -3411.4846 -2974.768 -112.34303 11361.015 - 9500 306.2565 -3416.0499 -2960.5165 -230.75414 11361.667 - 9600 298.77172 -3410.0086 -2965.6083 -160.9185 11361.994 - 9700 287.60936 -3408.4236 -2980.6264 -50.45167 11361.936 - 9800 298.13818 -3413.9967 -2970.5387 -252.57086 11361.537 - 9900 292.93826 -3411.9851 -2976.2616 -152.45548 11360.629 - 10000 286.02579 -3405.9303 -2980.4887 67.188883 11359.503 -Loop time of 3.25987 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.728 | 5.728 | 5.728 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 299.42262 102.507 -3416.9 -2971.5315 134.01052 11328.967 + 10 305.01315 102.57259 -3419.0863 -2965.4023 52.103984 11328.968 + 20 309.92197 102.64755 -3421.585 -2960.5996 -26.370593 11328.97 + 30 311.99962 102.71885 -3423.9618 -2959.886 -76.248163 11328.972 + 40 310.18839 102.69518 -3423.1727 -2961.791 -52.274449 11328.972 + 50 305.15121 102.6302 -3421.0067 -2967.1174 16.259045 11328.972 + 60 299.39836 102.5938 -3419.7932 -2974.4609 80.723613 11328.972 + 70 295.2947 102.55104 -3418.3682 -2979.1397 134.53808 11328.974 + 80 293.51832 102.50438 -3416.8126 -2980.2263 170.69406 11328.978 + 90 293.4313 102.51498 -3417.1659 -2980.7091 170.93297 11328.985 + 100 294.63941 102.5177 -3417.2566 -2979.0028 164.62038 11328.996 + 110 297.25348 102.56555 -3418.8518 -2976.7098 131.78524 11329.01 + 120 300.50388 102.60344 -3420.1147 -2973.138 98.057487 11329.026 + 130 302.95328 102.6409 -3421.3632 -2970.7432 69.182017 11329.044 + 140 304.05933 102.70523 -3423.5076 -2971.2424 38.480693 11329.064 + 150 304.21872 102.71956 -3423.9853 -2971.483 33.117628 11329.084 + 160 304.38371 102.70642 -3423.5475 -2970.7998 39.859883 11329.105 + 170 304.80117 102.70106 -3423.3687 -2970.0001 43.810288 11329.127 + 180 305.13983 102.71028 -3423.6759 -2969.8035 46.007676 11329.15 + 190 304.94578 102.68774 -3422.9246 -2969.3408 69.449779 11329.173 + 200 302.86941 102.65221 -3421.7405 -2971.2452 116.35909 11329.199 + 210 297.662 102.5571 -3418.57 -2975.8203 210.54052 11329.226 + 220 290.84972 102.4888 -3416.2934 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201.91582 11343.916 + 8490 297.17189 112.26233 -3408.7442 -2966.7235 226.26406 11344.03 + 8500 294.90301 112.22383 -3407.461 -2968.8151 259.18716 11344.147 + 8510 292.39286 112.18913 -3406.3042 -2971.392 296.96289 11344.27 + 8520 291.14853 112.17538 -3405.846 -2972.7846 317.20394 11344.398 + 8530 291.91158 112.22667 -3407.5555 -2973.3592 296.58708 11344.533 + 8540 292.91813 112.20303 -3406.7678 -2971.0743 300.20133 11344.673 + 8550 292.41103 112.21716 -3407.2388 -2972.2995 296.55479 11344.819 + 8560 290.68114 112.17923 -3405.9744 -2973.6082 315.31139 11344.971 + 8570 289.55071 112.13935 -3404.6451 -2973.9604 319.78648 11345.129 + 8580 290.6424 112.19571 -3406.5237 -2974.2152 262.81263 11345.294 + 8590 293.21275 112.22539 -3407.5131 -2971.3814 202.44971 11345.463 + 8600 295.43347 112.30834 -3410.2779 -2970.8431 127.32619 11345.636 + 8610 296.92031 112.35132 -3411.7105 -2970.0641 79.917896 11345.813 + 8620 298.80424 112.35356 -3411.7855 -2967.3368 55.019334 11345.991 + 8630 301.09269 112.47699 -3415.8997 -2968.0471 -8.9530463 11346.17 + 8640 302.0151 112.47499 -3415.8331 -2966.6086 -7.2783877 11346.349 + 8650 300.48551 112.47536 -3415.8453 -2968.8959 14.896825 11346.529 + 8660 297.18394 112.39077 -3413.0258 -2970.9872 83.855865 11346.709 + 8670 293.06895 112.33588 -3411.1961 -2975.2782 143.368 11346.891 + 8680 289.20075 112.28907 -3409.6357 -2979.4715 190.45842 11347.076 + 8690 286.48191 112.27321 -3409.107 -2982.9869 208.66022 11347.265 + 8700 285.2568 112.22303 -3407.4342 -2983.1364 223.78377 11347.458 + 8710 284.66091 112.21085 -3407.0284 -2983.6169 221.89784 11347.655 + 8720 282.71291 112.18784 -3406.2612 -2985.7472 244.16641 11347.857 + 8730 277.88776 112.09313 -3403.1044 -2989.7675 327.27761 11348.064 + 8740 271.06737 111.98882 -3399.6275 -2996.4353 437.0719 11348.277 + 8750 265.18763 111.90797 -3396.9322 -3002.4857 531.24712 11348.499 + 8760 263.21239 111.84863 -3394.9545 -3003.446 579.13885 11348.731 + 8770 266.98443 111.86908 -3395.6361 -2998.517 540.52799 11348.974 + 8780 276.00421 112.05186 -3401.7288 -2991.1934 388.42612 11349.227 + 8790 287.04901 112.2291 -3407.6367 -2980.6731 215.77508 11349.489 + 8800 296.45048 112.39481 -3413.1605 -2972.2128 61.542232 11349.754 + 8810 303.84332 102.5009 -3416.6966 -2964.7527 -102.60393 11350.021 + 8820 308.35593 102.54287 -3418.0955 -2959.4395 -156.26397 11350.286 + 8830 309.34553 102.56267 -3418.7555 -2958.6275 -169.44279 11350.548 + 8840 307.92936 102.57728 -3419.2427 -2961.2211 -159.36337 11350.808 + 8850 306.49168 102.51666 -3417.2219 -2961.3388 -120.8613 11351.065 + 8860 307.02003 102.50577 -3416.8591 -2960.19 -118.8501 11351.32 + 8870 308.78244 102.51765 -3417.255 -2957.9645 -139.87882 11351.573 + 8880 309.4166 102.52413 -3417.471 -2957.2372 -156.54316 11351.824 + 8890 308.17218 102.52172 -3417.3905 -2959.0077 -161.32511 11352.072 + 8900 306.82798 102.52569 -3417.5232 -2961.1398 -170.00394 11352.317 + 8910 306.92686 102.52414 -3417.4712 -2960.9407 -186.21426 11352.56 + 8920 308.0801 102.54255 -3418.0851 -2959.8393 -215.35285 11352.799 + 8930 309.07511 102.53491 -3417.8303 -2958.1045 -229.29742 11353.034 + 8940 308.83435 102.54793 -3418.2644 -2958.8967 -236.83009 11353.266 + 8950 306.20013 102.50473 -3416.8242 -2961.3747 -198.18845 11353.493 + 8960 299.78229 102.45513 -3415.1708 -2969.2674 -124.11711 11353.717 + 8970 290.40609 102.32891 -3410.9636 -2979.0066 1.3665885 11353.939 + 8980 282.5525 102.23389 -3407.7963 -2987.5209 99.179915 11354.161 + 8990 281.20504 102.18256 -3406.0854 -2987.8142 125.84255 11354.385 + 9000 287.0527 102.25645 -3408.5483 -2981.5791 46.683648 11354.612 + 9010 295.6651 102.36854 -3412.2846 -2972.5052 -70.693581 11354.84 + 9020 302.05074 102.44673 -3414.8911 -2965.6136 -159.48967 11355.067 + 9030 304.50107 102.50445 -3416.8148 -2963.8926 -211.01569 11355.291 + 9040 304.28774 102.51765 -3417.255 -2964.6501 -223.85983 11355.511 + 9050 302.28659 102.46413 -3415.471 -2965.8426 -196.35161 11355.728 + 9060 298.64342 102.41317 -3413.7725 -2969.563 -159.56094 11355.942 + 9070 294.89692 102.3567 -3411.8898 -2973.253 -123.95652 11356.152 + 9080 292.89751 102.31892 -3410.6307 -2974.9679 -113.05552 11356.36 + 9090 293.44894 102.39098 -3413.0327 -2976.5497 -164.79219 11356.567 + 9100 296.30539 102.43897 -3414.6325 -2973.9007 -222.07876 11356.77 + 9110 300.45266 102.4672 -3415.5735 -2968.6729 -273.82557 11356.97 + 9120 303.24645 102.47481 -3415.8271 -2964.771 -295.97287 11357.165 + 9130 302.0034 102.50375 -3416.7918 -2967.5846 -285.82159 11357.354 + 9140 297.22892 102.43941 -3414.6469 -2972.5414 -207.07355 11357.538 + 9150 291.80756 102.39282 -3413.0939 -2979.0523 -128.58195 11357.719 + 9160 288.25245 102.34705 -3411.5685 -2982.8148 -67.13035 11357.898 + 9170 287.47436 102.34359 -3411.4531 -2983.8568 -50.741803 11358.076 + 9180 289.65745 102.36539 -3412.1798 -2981.3363 -76.008823 11358.253 + 9190 294.40993 102.43028 -3414.3425 -2976.4301 -145.63657 11358.428 + 9200 300.16761 102.47892 -3415.9641 -2969.4875 -218.94764 11358.601 + 9210 304.03105 102.53822 -3417.9405 -2965.7174 -279.64516 11358.771 + 9220 304.45288 102.53714 -3417.9046 -2965.054 -285.20667 11358.935 + 9230 302.34912 102.45421 -3415.1404 -2965.419 -234.46962 11359.094 + 9240 299.9859 102.40287 -3413.429 -2967.2227 -191.14447 11359.249 + 9250 299.26036 102.40403 -3413.4677 -2968.3406 -182.52388 11359.401 + 9260 300.61341 102.41715 -3413.905 -2966.7654 -201.16731 11359.549 + 9270 303.15524 102.4879 -3416.2632 -2965.3428 -259.88954 11359.693 + 9280 305.7968 102.55222 -3418.4075 -2963.5579 -324.73273 11359.833 + 9290 308.13692 102.54889 -3418.2962 -2959.9659 -365.60648 11359.967 + 9300 310.01596 102.56219 -3418.7396 -2957.6143 -409.04518 11360.094 + 9310 310.51245 102.5781 -3419.27 -2957.4063 -438.84588 11360.214 + 9320 308.74264 102.52394 -3417.4648 -2958.2335 -415.60354 11360.325 + 9330 304.79422 102.4761 -3415.8701 -2962.5118 -367.20347 11360.429 + 9340 299.98192 102.39538 -3413.1793 -2966.9789 -290.51501 11360.526 + 9350 296.40204 102.34525 -3411.5082 -2970.6326 -230.13543 11360.618 + 9360 295.69416 102.34673 -3411.5575 -2971.7349 -209.91046 11360.705 + 9370 297.70643 102.38972 -3412.9908 -2970.1751 -224.99069 11360.789 + 9380 299.82096 102.43428 -3414.4761 -2968.5151 -239.37907 11360.868 + 9390 298.72337 102.42593 -3414.1978 -2969.8694 -206.21757 11360.943 + 9400 293.6059 102.34454 -3411.4846 -2974.768 -112.34303 11361.015 + 9410 287.13801 102.25842 -3408.614 -2981.5179 -5.7729342 11361.084 + 9420 282.8911 102.1548 -3405.1599 -2984.3808 87.012111 11361.153 + 9430 283.42692 102.17512 -3405.8373 -2984.2613 87.107479 11361.224 + 9440 289.72806 102.25543 -3408.5142 -2977.5657 10.6752 11361.297 + 9450 299.9244 102.41878 -3413.9592 -2967.8444 -133.86835 11361.37 + 9460 309.66009 102.532 -3417.7333 -2957.1374 -259.63954 11361.441 + 9470 315.28802 102.61817 -3420.6055 -2951.6385 -343.43136 11361.507 + 9480 315.52197 102.64969 -3421.6563 -2952.3412 -362.61942 11361.567 + 9490 311.57319 102.59769 -3419.923 -2956.4815 -315.2172 11361.62 + 9500 306.2565 102.4815 -3416.0499 -2960.5165 -230.75414 11361.667 + 9510 301.77507 102.40965 -3413.655 -2964.7874 -168.80118 11361.711 + 9520 298.06371 102.36942 -3412.3141 -2968.9669 -127.60351 11361.75 + 9530 294.76822 102.34731 -3411.5771 -2973.1317 -102.52302 11361.788 + 9540 292.90584 102.28385 -3409.4618 -2973.7865 -77.156962 11361.824 + 9550 293.16449 102.2921 -3409.7367 -2973.6767 -95.839672 11361.858 + 9560 294.55295 102.32549 -3410.8498 -2972.7246 -130.00817 11361.89 + 9570 295.8006 102.34483 -3411.4945 -2971.5135 -152.72227 11361.921 + 9580 296.56754 102.34105 -3411.3684 -2970.2466 -158.45379 11361.948 + 9590 297.31038 102.32507 -3410.8355 -2968.6089 -157.7167 11361.972 + 9600 298.77172 102.30026 -3410.0086 -2965.6083 -160.9185 11361.994 + 9610 301.97013 102.34529 -3411.5097 -2962.352 -206.50568 11362.013 + 9620 306.75609 102.42638 -3414.2128 -2957.9364 -278.49373 11362.027 + 9630 310.90991 102.52954 -3417.6512 -2955.1963 -353.7554 11362.037 + 9640 312.31799 102.61062 -3420.354 -2955.8047 -397.46392 11362.04 + 9650 310.56146 102.5724 -3419.0801 -2957.1435 -366.33137 11362.036 + 9660 306.52496 102.52312 -3417.4373 -2961.5047 -309.52269 11362.025 + 9670 301.5321 102.45538 -3415.1793 -2966.6732 -237.6061 11362.008 + 9680 296.45601 102.39829 -3413.2764 -2972.3206 -171.66047 11361.986 + 9690 291.72252 102.30306 -3410.1021 -2976.187 -97.600507 11361.962 + 9700 287.60936 102.25271 -3408.4236 -2980.6264 -50.45167 11361.936 + 9710 284.48914 102.20566 -3406.8552 -2983.6992 -17.860652 11361.908 + 9720 283.50169 102.17913 -3405.971 -2984.2837 -14.443294 11361.881 + 9730 286.7196 102.21649 -3407.2163 -2980.7426 -68.48769 11361.852 + 9740 294.47386 102.35054 -3411.6845 -2973.677 -189.93928 11361.823 + 9750 303.04659 102.46162 -3415.3875 -2964.6286 -302.19943 11361.79 + 9760 307.57479 102.51124 -3417.0413 -2959.5471 -355.30344 11361.752 + 9770 306.33697 102.48869 -3416.2898 -2960.6367 -335.18312 11361.707 + 9780 301.59673 102.4207 -3414.0233 -2965.421 -271.49738 11361.655 + 9790 297.79054 102.41425 -3413.8083 -2970.8674 -241.91326 11361.599 + 9800 298.13818 102.4199 -3413.9967 -2970.5387 -252.57086 11361.537 + 9810 302.00013 102.47911 -3415.9702 -2966.7679 -313.68954 11361.471 + 9820 306.02146 102.5605 -3418.6833 -2963.4996 -383.20843 11361.399 + 9830 306.37399 102.56224 -3418.7413 -2963.0332 -388.56733 11361.32 + 9840 301.99104 102.49174 -3416.3914 -2967.2027 -323.29197 11361.234 + 9850 296.02715 102.3854 -3412.8467 -2972.5287 -226.75584 11361.141 + 9860 292.42188 102.30722 -3410.2407 -2975.2854 -155.99935 11361.044 + 9870 291.8673 102.30306 -3410.1021 -2975.9716 -137.71183 11360.944 + 9880 292.47183 102.29279 -3409.7597 -2974.73 -129.16333 11360.842 + 9890 292.67046 102.31184 -3410.3947 -2975.0696 -133.25336 11360.737 + 9900 292.93826 102.35955 -3411.9851 -2976.2616 -152.45548 11360.629 + 9910 292.98738 112.38031 -3412.677 -2976.8805 -98.388723 11360.519 + 9920 291.50325 112.33603 -3411.2009 -2977.612 -60.193026 11360.407 + 9930 289.16 112.27732 -3409.2439 -2979.1403 -8.3725785 11360.294 + 9940 287.58579 112.26303 -3408.7678 -2981.0057 18.664629 11360.18 + 9950 287.74855 112.25799 -3408.5998 -2980.5956 25.021437 11360.067 + 9960 289.38626 112.25385 -3408.4617 -2978.0215 15.413572 11359.954 + 9970 291.31111 112.27816 -3409.2721 -2975.9689 -9.6707803 11359.842 + 9980 291.60283 112.29087 -3409.6956 -2975.9585 -17.695205 11359.729 + 9990 289.34786 112.2374 -3407.9134 -2977.5304 19.599433 11359.616 + 10000 286.02579 112.17791 -3405.9303 -2980.4887 67.188883 11359.503 +Loop time of 2.50279 on 1 procs for 10000 steps with 500 atoms -Performance: 265.041 ns/day, 0.091 hours/ns, 3067.606 timesteps/s -100.1% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.215 ns/day, 0.070 hours/ns, 3995.539 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5777 | 2.5777 | 2.5777 | 0.0 | 79.07 -Bond | 0.0006814 | 0.0006814 | 0.0006814 | 0.0 | 0.02 -Neigh | 0.019258 | 0.019258 | 0.019258 | 0.0 | 0.59 -Comm | 0.088224 | 0.088224 | 0.088224 | 0.0 | 2.71 -Output | 0.0010309 | 0.0010309 | 0.0010309 | 0.0 | 0.03 -Modify | 0.33808 | 0.33808 | 0.33808 | 0.0 | 10.37 -Other | | 0.2349 | | | 7.20 +Pair | 2.0544 | 2.0544 | 2.0544 | 0.0 | 82.08 +Bond | 0.00075364 | 0.00075364 | 0.00075364 | 0.0 | 0.03 +Neigh | 0.015478 | 0.015478 | 0.015478 | 0.0 | 0.62 +Comm | 0.07215 | 0.07215 | 0.07215 | 0.0 | 2.88 +Output | 0.0074148 | 0.0074148 | 0.0074148 | 0.0 | 0.30 +Modify | 0.23494 | 0.23494 | 0.23494 | 0.0 | 9.39 +Other | | 0.1177 | | | 4.70 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 20 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/1/log.lammps.1 b/examples/USER/misc/grem/lj-temper/1/log.lammps.1 index 8b12a2c318..3241f17a5c 100644 --- a/examples/USER/misc/grem/lj-temper/1/log.lammps.1 +++ b/examples/USER/misc/grem/lj-temper/1/log.lammps.1 @@ -16,10 +16,6 @@ read_data 1/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 910 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 910 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38334 Mbytes -Step Temp PotEng TotEng Press Volume - 0 288.55656 -3406.7669 -2977.5609 178.123 11354.789 - 100 292.15244 -3406.6138 -2972.0592 101.11822 11354.9 - 200 284.76856 -3403.8146 -2980.243 229.78409 11355.232 - 300 292.70849 -3408.8867 -2973.505 148.33374 11355.918 - 400 300.34739 -3407.488 -2960.744 182.63695 11357.028 - 500 285.96923 -3401.9081 -2976.5506 276.3915 11358.563 - 600 307.70286 -3413.8121 -2956.1274 -99.74504 11360.502 - 700 282.68114 -3402.3696 -2981.9028 215.37371 11362.639 - 800 296.16373 -3406.3812 -2965.8601 17.480161 11365.099 - 900 295.1242 -3403.489 -2964.5141 139.94644 11367.775 - 1000 298.65751 -3404.9437 -2960.7133 43.569751 11370.721 - 1100 299.9828 -3403.2527 -2957.051 1.5561287 11373.784 - 1200 283.05677 -3393.2885 -2972.263 279.02297 11376.992 - 1300 301.24616 -3401.9018 -2953.821 -61.001277 11380.464 - 1400 289.04947 -3395.7975 -2965.8583 92.997624 11383.831 - 1500 274.01283 -3384.3607 -2976.7874 455.32787 11387.235 - 1600 302.26525 -3397.7531 -2948.1564 12.134543 11391.218 - 1700 293.79228 -3393.1889 -2956.1952 57.363507 11395.294 - 1800 306.98845 -3396.1039 -2939.4818 -135.9312 11399.326 - 1900 293.15719 -3386.5828 -2950.5337 132.42643 11403.179 - 2000 307.19197 -3395.5097 -2938.585 -161.2466 11406.936 - 2100 307.45189 -3392.5861 -2935.2747 -157.46524 11410.403 - 2200 300.88603 -3388.4914 -2940.9462 -28.501997 11413.598 - 2300 289.88236 -3384.6698 -2953.4918 122.58753 11416.723 - 2400 296.43305 -3388.0129 -2947.0912 -25.774318 11420.076 - 2500 317.23755 -3397.1902 -2925.3234 -459.4925 11423.59 - 2600 287.60187 -3378.3654 -2950.5794 184.57759 11426.853 - 2700 303.64909 -3386.2885 -2934.6335 -135.08152 11430.242 - 2800 302.47742 -3388.9859 -2939.0737 -323.13721 11433.517 - 2900 291.98004 -3377.25 -2942.9518 -47.677493 11436.421 - 3000 307.8161 -3390.9845 -2933.1314 -381.60025 11439.119 - 3100 279.57067 -3372.6802 -2956.8401 112.35716 11441.316 - 3200 288.77945 -3377.9064 -2948.3688 -56.270381 11443.418 - 3300 304.79453 -3385.7254 -2932.3667 -445.46244 11445.179 - 3400 292.93209 -3377.8456 -2942.1313 -194.7257 11446.284 - 3500 306.76065 -3386.1118 -2929.8286 -428.54219 11447.116 - 3600 309.27383 -3386.5092 -2926.4878 -396.29387 11447.442 - 3700 295.73613 -3380.6566 -2940.7715 -224.46949 11447.298 - 3800 286.51576 -3373.1466 -2946.9762 -38.200592 11446.876 - 3900 297.11081 -3379.8253 -2937.8955 -209.71089 11446.168 - 4000 298.6827 -3378.5589 -2934.291 -161.67235 11445.075 - 4100 296.79632 -3375.8545 -2934.3925 -3.2770185 11443.642 - 4200 293.39337 -3373.8298 -2937.4294 61.151041 11442.097 - 4300 305.32078 -3376.9036 -2922.7621 -35.097493 11440.456 - 4400 288.33476 -3367.9377 -2939.0616 323.25684 11438.693 - 4500 301.83114 -3379.5242 -2930.5732 44.950393 11437.061 - 4600 296.53718 -3370.7936 -2929.717 247.99542 11435.523 - 4700 313.14834 -3380.7524 -2914.9679 24.50122 11434.29 - 4800 316.57471 -3385.4942 -2914.6133 -89.103894 11433.295 - 4900 295.8169 -3373.4805 -2933.4753 186.45389 11432.498 - 5000 302.82001 -3376.4769 -2926.0551 126.1166 11431.848 - 5100 293.31592 -3369.1186 -2932.8334 398.18962 11431.273 - 5200 300.8404 -3371.9981 -2924.5208 325.82663 11431.294 - 5300 288.65507 -3366.8598 -2937.5072 560.98385 11432.053 - 5400 300.15414 -3370.3662 -2923.9097 331.21385 11433.792 - 5500 293.62342 -3364.1197 -2927.3771 510.06055 11436.251 - 5600 293.52337 -3365.0972 -2928.5034 443.00006 11439.517 - 5700 314.46913 -3373.0792 -2905.3302 116.1735 11443.39 - 5800 316.07035 -3371.7131 -2901.5824 59.579025 11447.527 - 5900 302.07546 -3364.3048 -2914.9904 292.07764 11452.145 - 6000 298.16549 -3363.0572 -2919.5586 322.85603 11457.452 - 6100 299.62417 -3361.8594 -2916.1912 270.01732 11463.408 - 6200 307.26123 -3366.6924 -2909.6646 33.334477 11469.872 - 6300 301.85984 -3360.01 -2911.0164 152.48267 11476.656 - 6400 304.04037 -3359.0287 -2906.7917 85.558236 11483.787 - 6500 315.39938 -3361.3137 -2892.181 -27.949849 11491.188 - 6600 312.50182 -3354.0774 -2889.2547 14.380903 11498.754 - 6700 312.24745 -3354.727 -2890.2826 -11.564949 11506.565 - 6800 299.5486 -3344.6674 -2899.1115 140.00843 11514.587 - 6900 319.34442 -3353.0254 -2878.0248 -369.57931 11522.809 - 7000 312.5114 -3351.5646 -2886.7275 -338.9529 11530.444 - 7100 301.83696 -3339.7552 -2890.7956 -59.056671 11537.499 - 7200 317.79602 -3352.0354 -2879.3379 -476.34779 11544.273 - 7300 305.24957 -3341.8025 -2887.7669 -284.85596 11550.312 - 7400 327.39994 -3353.74 -2866.7574 -694.54924 11555.826 - 7500 320.25094 -3351.0448 -2874.6958 -667.61837 11560.396 - 7600 298.07438 -3332.5105 -2889.1475 -256.85225 11564.025 - 7700 310.50497 -3344.7831 -2882.9305 -657.61332 11566.855 - 7800 314.16294 -3347.8412 -2880.5476 -688.03112 11568.446 - 7900 300.40053 -3338.4536 -2891.6306 -476.3332 11568.775 - 8000 316.35903 -3348.7364 -2878.1763 -751.21864 11567.899 - 8100 308.957 -3347.7238 -2888.1737 -689.04336 11565.712 - 8200 296.70594 -3337.3321 -2896.0045 -354.23246 11562.212 - 8300 306.40458 -3348.666 -2892.9124 -647.83868 11557.563 - 8400 314.95559 -3354.0671 -2885.5945 -672.95129 11551.603 - 8500 299.19386 -3343.5909 -2898.5628 -244.49812 11544.459 - 8600 313.97242 -3350.861 -2883.8508 -417.72283 11536.587 - 8700 308.40661 -3348.3697 -2889.6382 -234.46379 11527.955 - 8800 299.75365 -3345.1001 -2899.2392 30.349293 11518.756 - 8900 310.85222 -3354.562 -2892.1929 -112.13993 11509.361 - 9000 307.93603 -3354.4949 -2896.4634 -24.119632 11499.746 - 9100 294.88785 -3349.2164 -2910.593 357.76086 11489.968 - 9200 296.56133 -3350.8626 -2909.7501 415.59418 11480.36 - 9300 304.6863 -3357.1682 -2903.9704 367.05129 11471.041 - 9400 314.87579 -3363.7046 -2895.3507 267.77411 11462.364 - 9500 295.39002 -3353.7081 -2914.3378 677.18586 11454.261 - 9600 310.14825 -3364.8576 -2903.5356 492.49166 11447.14 - 9700 302.90439 -3360.306 -2909.7587 620.88798 11441.001 - 9800 308.43227 -3363.4547 -2904.6851 678.75194 11435.989 - 9900 297.04137 -3358.0021 -2916.1755 801.45219 11432.184 - 10000 306.41271 -3360.5568 -2904.7911 825.76031 11429.68 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.729 | 5.729 | 5.729 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 288.55656 112.20301 -3406.7669 -2977.5609 178.123 11354.789 + 10 288.31142 112.19886 -3406.6287 -2977.7873 169.48583 11354.791 + 20 289.8223 112.2004 -3406.6801 -2975.5914 143.0151 11354.796 + 30 291.70551 112.20808 -3406.9361 -2973.0463 110.8113 11354.804 + 40 292.3991 112.19188 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-3403.7829 -2980.3472 235.97079 11355.183 + 200 284.76856 112.11444 -3403.8146 -2980.243 229.78409 11355.232 + 210 287.30412 112.19165 -3406.3882 -2979.0451 178.2025 11355.285 + 220 290.24387 112.2716 -3409.0532 -2977.3375 128.2392 11355.341 + 230 291.75312 112.26846 -3408.9488 -2974.9881 127.5165 11355.4 + 240 291.56602 112.24089 -3408.0298 -2974.3475 156.54095 11355.461 + 250 289.54014 112.18263 -3406.0876 -2975.4186 212.94237 11355.526 + 260 286.70194 112.15809 -3405.2696 -2978.8222 257.79759 11355.594 + 270 285.294 112.15348 -3405.1159 -2980.7627 275.81206 11355.668 + 280 286.55908 112.15001 -3405.0003 -2978.7654 263.50914 11355.747 + 290 289.68555 112.21705 -3407.235 -2976.3497 203.07914 11355.83 + 300 292.70849 112.2666 -3408.8867 -2973.505 148.33374 11355.918 + 310 294.49815 112.29546 -3409.8488 -2971.8051 116.25484 11356.008 + 320 295.01917 112.26366 -3408.7887 -2969.97 128.97587 11356.101 + 330 293.62796 112.22757 -3407.5857 -2970.8364 172.03075 11356.196 + 340 289.75335 112.17364 -3405.7881 -2974.802 251.12304 11356.295 + 350 284.97643 112.09285 -3403.0949 -2979.214 349.19648 11356.399 + 360 281.8078 112.02317 -3400.7724 -2981.6047 424.30214 11356.509 + 370 281.86417 111.99526 -3399.842 -2980.5904 446.31739 11356.627 + 380 285.76759 112.05907 -3401.969 -2976.9114 388.90905 11356.754 + 390 292.89931 112.11358 -3403.7861 -2968.1206 299.89217 11356.888 + 400 300.34739 112.22464 -3407.488 -2960.744 182.63695 11357.028 + 410 304.41494 112.31486 -3410.4953 -2957.7011 100.39899 11357.171 + 420 303.85492 112.30406 -3410.1355 -2958.1743 95.619711 11357.317 + 430 300.81739 112.25584 -3408.528 -2961.0849 126.6436 11357.464 + 440 298.33667 112.26429 -3408.8098 -2965.0566 131.90634 11357.614 + 450 297.59531 112.2703 -3409.0098 -2966.3594 123.7656 11357.766 + 460 297.63297 112.29317 -3409.7725 -2967.066 102.31468 11357.921 + 470 297.08461 112.30627 -3410.2092 -2968.3183 91.899247 11358.078 + 480 294.93467 112.27288 -3409.096 -2970.403 117.26815 11358.237 + 490 290.85555 112.17178 -3405.726 -2973.1004 189.72375 11358.398 + 500 285.96923 112.05724 -3401.9081 -2976.5506 276.3915 11358.563 + 510 282.89047 111.98875 -3399.6252 -2978.847 332.0296 11358.733 + 520 282.00698 111.95278 -3398.4259 -2978.9619 356.61549 11358.909 + 530 281.59566 111.97984 -3399.3281 -2980.4759 347.9844 11359.092 + 540 282.13143 112.00287 -3400.0957 -2980.4466 327.18332 11359.282 + 550 285.29816 112.05396 -3401.7988 -2977.4394 270.12617 11359.477 + 560 290.61836 112.13691 -3404.5637 -2972.2909 180.78896 11359.678 + 570 296.03555 112.19783 -3406.5945 -2966.264 98.242808 11359.883 + 580 300.53871 112.26318 -3408.7725 -2961.744 23.345649 11360.089 + 590 304.57492 112.35224 -3411.7414 -2958.7093 -51.135366 11360.296 + 600 307.70286 112.41436 -3413.8121 -2956.1274 -99.74504 11360.502 + 610 307.4453 112.41196 -3413.7319 -2956.4303 -89.528722 11360.707 + 620 302.60338 112.36055 -3412.0183 -2961.9187 -20.95705 11360.909 + 630 295.45279 112.24699 -3408.2329 -2968.7692 88.92139 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111.96061 -3398.6872 -2967.8147 228.61897 11368.639 + 940 294.3022 112.0659 -3402.1968 -2964.4446 130.39654 11368.936 + 950 301.51105 112.13134 -3404.378 -2955.9032 25.61018 11369.235 + 960 306.83743 112.27981 -3409.327 -2952.9296 -91.059043 11369.535 + 970 307.4444 112.29416 -3409.8054 -2952.5051 -109.84508 11369.833 + 980 304.50616 112.27686 -3409.2287 -2956.2989 -78.391305 11370.13 + 990 301.06082 112.21176 -3407.0587 -2959.2536 -15.295458 11370.425 + 1000 298.65751 112.14831 -3404.9437 -2960.7133 43.569751 11370.721 + 1010 297.03945 112.14146 -3404.7155 -2962.8918 73.28153 11371.017 + 1020 295.59833 112.09804 -3403.268 -2963.5879 110.62196 11371.314 + 1030 293.93194 112.05872 -3401.9573 -2964.7558 139.816 11371.614 + 1040 292.24705 112.00732 -3400.2439 -2965.5486 164.01425 11371.917 + 1050 291.34252 111.98463 -3399.4876 -2966.1376 163.57877 11372.222 + 1060 291.75453 112.00753 -3400.2511 -2966.2883 132.24681 11372.531 + 1070 293.50063 112.03285 -3401.0949 -2964.535 90.509052 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294.26987 130.50569 -3350.1896 -2912.4855 612.94872 11468.34 + 9340 297.79784 130.55732 -3351.9108 -2908.9591 568.23655 11467.462 + 9350 302.06161 130.67461 -3355.8205 -2906.5267 487.27345 11466.593 + 9360 305.65979 130.75139 -3358.3797 -2903.734 426.52958 11465.733 + 9370 308.13529 130.75508 -3358.5027 -2900.1748 404.16449 11464.881 + 9380 309.79498 130.79821 -3359.9404 -2899.1439 371.59399 11464.036 + 9390 311.83462 130.83297 -3361.0991 -2897.2688 334.00848 11463.197 + 9400 314.87579 130.91114 -3363.7046 -2895.3507 267.77411 11462.364 + 9410 317.77773 130.9827 -3366.09 -2893.4197 202.58548 11461.536 + 9420 319.5121 130.99995 -3366.665 -2891.415 169.30437 11460.711 + 9430 319.78186 131.02436 -3367.4788 -2891.8275 152.44783 11459.888 + 9440 318.0284 131.033 -3367.7667 -2894.7236 168.17497 11459.068 + 9450 314.07956 130.99487 -3366.4958 -2899.3263 230.89701 11458.251 + 9460 308.88675 130.89308 -3363.1027 -2903.6571 337.65267 11457.437 + 9470 303.86886 130.8065 -3360.2168 -2908.2349 442.66844 11456.63 + 9480 300.09247 130.73217 -3357.7389 -2911.374 534.21071 11455.83 + 9490 297.63992 130.67176 -3355.7255 -2913.0086 608.38651 11455.04 + 9500 295.39002 130.61124 -3353.7081 -2914.3378 677.18586 11454.261 + 9510 292.9949 130.5596 -3351.9868 -2916.1791 737.41686 11453.495 + 9520 292.11259 130.51759 -3350.5864 -2916.091 773.3085 11452.742 + 9530 294.4661 130.57388 -3352.4626 -2914.4666 738.24886 11452.003 + 9540 299.38922 130.71571 -3357.1904 -2911.8716 644.91949 11451.278 + 9550 304.61534 130.80826 -3360.2752 -2907.183 567.12796 11450.564 + 9560 308.2118 130.86129 -3362.0431 -2903.6014 519.63194 11449.861 + 9570 309.67974 130.9321 -3364.4033 -2903.7782 485.4507 11449.167 + 9580 309.61632 130.9455 -3364.85 -2904.3192 487.11561 11448.482 + 9590 309.328 130.919 -3363.9668 -2903.8648 505.27085 11447.806 + 9600 310.14825 130.94573 -3364.8576 -2903.5356 492.49166 11447.14 + 9610 311.91025 130.97111 -3365.7037 -2901.7609 472.4479 11446.481 + 9620 312.52224 130.98603 -3366.2011 -2901.348 466.68927 11445.832 + 9630 310.61312 130.9715 -3365.7167 -2903.7032 494.10973 11445.191 + 9640 307.17584 130.94291 -3364.7637 -2907.8629 539.71782 11444.559 + 9650 304.09736 130.88185 -3362.7285 -2910.4067 592.50642 11443.937 + 9660 302.4362 130.79714 -3359.9048 -2910.0539 639.90038 11443.326 + 9670 301.86504 130.76119 -3358.7064 -2909.705 656.77165 11442.727 + 9680 301.77435 130.77397 -3359.1325 -2910.266 650.22315 11442.14 + 9690 301.90553 130.76734 -3358.9114 -2909.8498 648.64441 11441.564 + 9700 302.90439 130.80918 -3360.306 -2909.7587 620.88798 11441.001 + 9710 305.54876 130.85542 -3361.8473 -2907.3667 578.03014 11440.449 + 9720 309.28161 130.91899 -3363.9664 -2903.9334 523.63499 11439.908 + 9730 311.72538 130.97724 -3365.9079 -2902.2401 490.08238 11439.377 + 9740 310.48175 130.94398 -3364.7994 -2902.9814 532.58841 11438.854 + 9750 305.27899 130.86509 -3362.1697 -2908.0903 634.12318 11438.342 + 9760 298.8736 130.7234 -3357.4467 -2912.8949 771.70021 11437.842 + 9770 295.63662 130.65505 -3355.1682 -2915.4311 849.35391 11437.355 + 9780 298.18574 130.69524 -3356.5078 -2912.9792 829.70901 11436.885 + 9790 304.03087 130.84699 -3361.5664 -2909.3435 732.38636 11436.43 + 9800 308.43227 130.90364 -3363.4547 -2904.6851 678.75194 11435.989 + 9810 309.389 130.94449 -3364.8163 -2904.6236 655.73171 11435.56 + 9820 309.20478 130.94735 -3364.9117 -2904.993 650.04196 11435.144 + 9830 311.58621 130.9963 -3366.5432 -2903.0824 597.89887 11434.74 + 9840 316.80613 131.07312 -3369.104 -2897.8789 507.30369 11434.347 + 9850 320.92896 131.18393 -3372.7976 -2895.4401 414.42821 11433.963 + 9860 320.01362 131.12947 -3370.9825 -2894.9865 433.4292 11433.587 + 9870 313.81089 131.05079 -3368.3598 -2901.5899 515.78327 11433.22 + 9880 305.53941 130.90419 -3363.4731 -2909.0064 649.28439 11432.862 + 9890 299.21519 130.7995 -3359.9832 -2914.9233 753.05794 11432.516 + 9900 297.04137 130.74006 -3358.0021 -2916.1755 801.45219 11432.184 + 9910 298.82519 130.76151 -3358.7171 -2914.2373 781.78912 11431.867 + 9920 302.18487 130.79397 -3359.7989 -2910.3219 743.67238 11431.564 + 9930 304.1639 130.83896 -3361.2986 -2908.8779 716.25452 11431.276 + 9940 303.39638 130.86995 -3362.3318 -2911.0527 726.22258 11431.001 + 9950 300.5113 130.78869 -3359.623 -2912.6352 804.30803 11430.741 + 9960 297.71143 130.74853 -3358.2844 -2915.4612 867.5875 11430.495 + 9970 297.2169 130.70973 -3356.991 -2914.9034 908.28216 11430.266 + 9980 299.38293 130.71469 -3357.1564 -2911.847 904.21977 11430.054 + 9990 303.00811 130.7639 -3358.7965 -2908.0949 865.72383 11429.859 + 10000 306.41271 130.8167 -3360.5568 -2904.7911 825.76031 11429.68 +Loop time of 2.50278 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.589 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.216 ns/day, 0.070 hours/ns, 3995.560 timesteps/s +100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.688 | 2.688 | 2.688 | 0.0 | 82.46 -Bond | 0.00086093 | 0.00086093 | 0.00086093 | 0.0 | 0.03 -Neigh | 0.03159 | 0.03159 | 0.03159 | 0.0 | 0.97 -Comm | 0.093323 | 0.093323 | 0.093323 | 0.0 | 2.86 -Output | 0.0014281 | 0.0014281 | 0.0014281 | 0.0 | 0.04 -Modify | 0.35664 | 0.35664 | 0.35664 | 0.0 | 10.94 -Other | | 0.0881 | | | 2.70 +Pair | 2.0969 | 2.0969 | 2.0969 | 0.0 | 83.78 +Bond | 0.0007844 | 0.0007844 | 0.0007844 | 0.0 | 0.03 +Neigh | 0.026091 | 0.026091 | 0.026091 | 0.0 | 1.04 +Comm | 0.076576 | 0.076576 | 0.076576 | 0.0 | 3.06 +Output | 0.0075617 | 0.0075617 | 0.0075617 | 0.0 | 0.30 +Modify | 0.2441 | 0.2441 | 0.2441 | 0.0 | 9.75 +Other | | 0.05081 | | | 2.03 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 32 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/2/log.lammps.2 b/examples/USER/misc/grem/lj-temper/2/log.lammps.2 index cc4fd71a24..4d3076a406 100644 --- a/examples/USER/misc/grem/lj-temper/2/log.lammps.2 +++ b/examples/USER/misc/grem/lj-temper/2/log.lammps.2 @@ -16,10 +16,6 @@ read_data 2/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 920 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 920 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.3797 Mbytes -Step Temp PotEng TotEng Press Volume - 0 303.5147 -3379.1918 -2927.7367 939.06157 11374.376 - 100 318.12855 -3389.1972 -2916.0051 732.24211 11375.313 - 200 300.55209 -3378.8051 -2931.7566 879.17024 11377.778 - 300 303.98225 -3382.1398 -2929.9893 688.68264 11381.592 - 400 315.07191 -3384.8092 -2916.1636 538.20119 11386.698 - 500 309.36576 -3382.7455 -2922.5874 478.65718 11393.035 - 600 310.56557 -3382.7619 -2920.8192 337.42905 11400.274 - 700 304.59438 -3382.4412 -2929.3802 343.41809 11408.201 - 800 307.37357 -3384.554 -2927.3591 165.57164 11416.925 - 900 316.86746 -3390.4013 -2919.085 -181.01119 11426.176 - 1000 299.18538 -3381.9504 -2936.9349 -39.701634 11435.48 - 1100 300.12698 -3382.5392 -2936.1231 -186.50374 11444.773 - 1200 296.14975 -3382.3095 -2941.8092 -328.47519 11453.747 - 1300 290.48513 -3379.3388 -2947.2642 -379.01155 11462.196 - 1400 307.12598 -3390.0083 -2933.1817 -784.07577 11469.94 - 1500 292.27399 -3382.948 -2948.2126 -757.50578 11476.37 - 1600 298.4373 -3386.9034 -2943.0005 -916.53485 11481.206 - 1700 284.99283 -3380.9051 -2956.9999 -761.53168 11484.379 - 1800 296.30929 -3387.9389 -2947.2013 -939.04947 11486.001 - 1900 274.95571 -3376.1525 -2967.1767 -557.57811 11485.93 - 2000 286.6494 -3387.2487 -2960.8795 -874.00502 11484.534 - 2100 301.45624 -3391.8264 -2943.4331 -1081.5931 11481.54 - 2200 294.31641 -3388.9801 -2951.2068 -874.50856 11476.941 - 2300 308.19066 -3397.6354 -2939.2252 -1180.813 11470.81 - 2400 294.64485 -3394.5337 -2956.2718 -968.71497 11462.705 - 2500 298.56162 -3398.2204 -2954.1326 -933.7456 11452.815 - 2600 294.06753 -3394.6475 -2957.2443 -699.18137 11441.168 - 2700 293.43299 -3392.0706 -2955.6113 -469.64296 11428.099 - 2800 294.09756 -3396.3977 -2958.9499 -245.0764 11414.04 - 2900 299.63675 -3400.8857 -2955.1988 -183.76834 11399.474 - 3000 289.06398 -3398.5529 -2968.5921 99.751425 11384.569 - 3100 307.44213 -3408.7747 -2951.4778 -8.3031637 11369.696 - 3200 302.98498 -3406.3856 -2955.7184 182.98744 11355.058 - 3300 291.9362 -3402.8973 -2968.6643 497.72457 11340.867 - 3400 295.54663 -3410.1026 -2970.4993 587.20344 11327.555 - 3500 304.27556 -3418.4127 -2965.8259 574.20245 11315.364 - 3600 303.72416 -3418.133 -2966.3663 573.08992 11304.186 - 3700 309.84914 -3426.5382 -2965.6611 418.30717 11294.016 - 3800 317.00037 -3430.4681 -2958.9541 467.30843 11284.802 - 3900 297.49383 -3424.0999 -2981.6004 779.41312 11276.818 - 4000 299.31354 -3421.8877 -2976.6815 903.93135 11270.237 - 4100 294.42695 -3423.8465 -2985.9087 1006.7998 11265.197 - 4200 300.01777 -3428.3819 -2982.1283 922.16275 11261.965 - 4300 292.77221 -3426.1312 -2990.6547 959.47941 11260.451 - 4400 300.87895 -3431.0308 -2983.4961 790.75992 11260.593 - 4500 290.78158 -3422.5048 -2989.9892 1001.9136 11262.315 - 4600 297.70252 -3430.615 -2987.8051 741.34784 11265.627 - 4700 303.5284 -3430.3888 -2978.9133 665.85341 11270.32 - 4800 291.67229 -3426.7342 -2992.8938 674.67006 11276.471 - 4900 297.00112 -3426.7467 -2984.98 532.96983 11283.928 - 5000 301.01123 -3430.4774 -2982.746 304.12386 11292.466 - 5100 302.29794 -3430.5071 -2980.8618 154.274 11301.776 - 5200 298.81333 -3428.9592 -2984.497 71.617996 11311.612 - 5300 287.74054 -3421.9947 -2994.0024 126.94546 11321.814 - 5400 299.8741 -3430.5222 -2984.4822 -283.50833 11332.317 - 5500 285.30311 -3421.1025 -2996.7357 -152.79946 11342.614 - 5600 293.4497 -3423.1142 -2986.63 -384.69324 11352.571 - 5700 292.90437 -3421.8788 -2986.2057 -385.78559 11361.964 - 5800 295.75086 -3421.8274 -2981.9204 -538.6221 11370.715 - 5900 285.54471 -3417.8008 -2993.0746 -584.6133 11378.554 - 6000 279.42138 -3415.0373 -2999.4192 -496.44729 11385.309 - 6100 292.98635 -3420.2915 -2984.4965 -807.7782 11390.881 - 6200 285.18497 -3413.9471 -2989.7561 -720.47221 11394.96 - 6300 296.76693 -3419.0502 -2977.6318 -883.05972 11397.626 - 6400 288.53322 -3415.8922 -2986.7209 -743.81572 11398.671 - 6500 301.89212 -3418.3134 -2969.2718 -760.06071 11398.197 - 6600 295.43874 -3414.401 -2974.9583 -595.49387 11396.453 - 6700 307.77134 -3414.4111 -2956.6245 -619.65168 11393.607 - 6800 307.77881 -3415.132 -2957.3343 -598.73379 11389.666 - 6900 299.95571 -3411.6113 -2965.4499 -414.64515 11384.775 - 7000 310.48581 -3418.9557 -2957.1316 -554.8734 11379.061 - 7100 297.78265 -3411.5928 -2968.6637 -204.17877 11372.511 - 7200 308.16321 -3414.8796 -2956.5102 -168.32518 11365.403 - 7300 305.49867 -3410.8638 -2956.4577 -63.088242 11357.993 - 7400 302.44796 -3410.8142 -2960.9458 62.696434 11350.522 - 7500 312.15684 -3419.0214 -2954.7118 27.395999 11343.127 - 7600 307.34561 -3414.5741 -2957.4208 257.94209 11335.847 - 7700 304.79016 -3411.896 -2958.5437 470.94979 11328.999 - 7800 311.79257 -3417.7252 -2953.9574 385.82094 11322.846 - 7900 316.24138 -3419.8749 -2949.4899 332.38484 11317.485 - 8000 315.73781 -3421.0721 -2951.436 300.24782 11312.939 - 8100 303.38025 -3416.1142 -2964.8591 623.97214 11309.099 - 8200 313.53945 -3418.4381 -2952.072 462.62665 11306.275 - 8300 312.90183 -3417.7579 -2952.3402 535.34718 11304.458 - 8400 302.89319 -3412.1607 -2961.63 754.08676 11303.725 - 8500 321.89652 -3422.325 -2943.5284 382.37676 11304.219 - 8600 308.02194 -3419.4464 -2961.2871 471.90335 11305.76 - 8700 310.12893 -3419.2625 -2957.9692 389.78683 11308.17 - 8800 306.85617 -3418.0084 -2961.5831 425.37989 11311.375 - 8900 287.92832 -3407.5424 -2979.2708 659.46236 11315.622 - 9000 278.06342 -3403.7402 -2990.142 757.54946 11321.103 - 9100 290.97422 -3412.7395 -2979.9374 406.79415 11327.735 - 9200 285.14294 -3408.7977 -2984.6692 329.51839 11335.252 - 9300 280.67249 -3406.8005 -2989.3214 234.83036 11343.32 - 9400 289.42707 -3416.0941 -2985.5933 -28.179186 11351.699 - 9500 285.62232 -3407.4208 -2982.5793 10.204022 11360.293 - 9600 285.51121 -3409.1935 -2984.5173 -102.42078 11368.884 - 9700 280.01648 -3404.052 -2987.5487 -91.259523 11377.233 - 9800 289.42587 -3410.2875 -2979.7884 -383.72706 11385.424 - 9900 291.01583 -3408.3435 -2975.4795 -514.96551 11393.129 - 10000 290.66211 -3409.5137 -2977.1759 -667.48493 11399.792 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.725 | 5.725 | 5.725 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 303.5147 121.37576 -3379.1918 -2927.7367 939.06157 11374.376 + 10 302.01819 121.39208 -3379.7359 -2930.5067 955.34812 11374.385 + 20 299.66358 121.35742 -3378.5808 -2932.854 998.03963 11374.412 + 30 297.90005 121.29795 -3376.5984 -2933.4946 1044.5312 11374.459 + 40 297.80982 121.28845 -3376.2818 -2933.3122 1054.8591 11374.525 + 50 299.23154 121.29836 -3376.6121 -2931.5279 1041.3766 11374.611 + 60 302.03518 121.3687 -3378.9567 -2929.7023 989.46264 11374.717 + 70 306.89734 121.46445 -3382.1482 -2925.6616 909.21372 11374.842 + 80 312.96036 121.61757 -3387.2525 -2921.7477 798.74753 11374.984 + 90 317.17373 121.67419 -3389.1395 -2917.3676 741.54767 11375.141 + 100 318.12855 121.67592 -3389.1972 -2916.0051 732.24211 11375.313 + 110 317.40874 121.63553 -3387.8509 -2915.7295 752.10626 11375.498 + 120 317.26883 121.64121 -3388.0404 -2916.1271 747.01078 11375.698 + 130 318.44405 121.66687 -3388.8957 -2915.2343 716.45621 11375.912 + 140 320.49327 121.72022 -3390.6741 -2913.9647 662.18511 11376.14 + 150 321.57523 121.72069 -3390.6897 -2912.3709 631.6531 11376.38 + 160 319.8381 121.66628 -3388.8758 -2913.1409 645.43574 11376.633 + 170 314.72914 121.61398 -3387.1325 -2918.9968 690.12596 11376.897 + 180 307.88565 121.47522 -3382.5075 -2924.5509 787.49791 11377.175 + 190 302.4306 121.38539 -3379.5129 -2929.6703 860.06931 11377.468 + 200 300.55209 121.36415 -3378.8051 -2931.7566 879.17024 11377.778 + 210 302.1658 121.35469 -3378.4897 -2929.0409 861.25419 11378.104 + 220 306.03052 121.42929 -3380.9764 -2925.7792 784.32025 11378.447 + 230 311.24302 121.51255 -3383.7517 -2920.8013 683.50702 11378.804 + 240 317.19613 121.63306 -3387.7686 -2915.9634 557.05248 11379.175 + 250 321.84027 121.77732 -3392.5772 -2913.8642 433.86307 11379.556 + 260 322.49145 121.77838 -3392.6128 -2912.9312 405.00168 11379.945 + 270 319.15693 121.73888 -3391.296 -2916.5742 434.93244 11380.343 + 280 313.97609 121.65023 -3388.341 -2921.3254 510.85834 11380.749 + 290 308.48891 121.54438 -3384.8125 -2925.9586 605.15694 11381.164 + 300 303.98225 121.46419 -3382.1398 -2929.9893 688.68264 11381.592 + 310 301.16194 121.35538 -3378.5127 -2930.5572 772.56756 11382.032 + 320 299.57734 121.33603 -3377.8676 -2932.269 811.10407 11382.487 + 330 298.20583 121.29686 -3376.5619 -2933.0033 850.91749 11382.958 + 340 296.68231 121.27869 -3375.9562 -2934.6638 875.27503 11383.445 + 350 296.07804 121.2376 -3374.5866 -2934.193 890.91889 11383.949 + 360 297.85202 121.28674 -3376.2248 -2933.1925 843.92836 11384.469 + 370 302.07191 121.34854 -3378.2848 -2928.9758 765.82512 11385.006 + 380 307.49834 121.42425 -3380.8082 -2923.4278 672.28582 11385.557 + 390 312.23703 121.47974 -3382.6579 -2918.229 595.95834 11386.122 + 400 315.07191 121.54428 -3384.8092 -2916.1636 538.20119 11386.698 + 410 315.94513 121.55364 -3385.1213 -2915.1768 524.5897 11387.284 + 420 315.30599 121.57916 -3385.9721 -2916.9783 521.24858 11387.881 + 430 313.40144 121.54636 -3384.8785 -2918.7176 551.21708 11388.488 + 440 310.63766 121.51 -3383.6667 -2921.6167 585.62129 11389.105 + 450 308.5878 121.47864 -3382.6214 -2923.6204 604.44349 11389.733 + 460 308.95854 121.50288 -3383.4294 -2923.877 573.35315 11390.374 + 470 311.48972 121.52682 -3384.2274 -2920.91 518.66227 11391.025 + 480 313.53991 121.55393 -3385.131 -2918.7641 464.40873 11391.686 + 490 312.7438 121.56121 -3385.3737 -2920.191 442.86257 11392.356 + 500 309.36576 121.48237 -3382.7455 -2922.5874 478.65718 11393.035 + 510 306.02972 121.44378 -3381.4592 -2926.2632 503.73832 11393.723 + 520 304.91443 121.42569 -3380.8562 -2927.3191 503.69667 11394.421 + 530 306.90624 121.44801 -3381.6004 -2925.1006 461.88876 11395.128 + 540 310.95566 121.50359 -3383.453 -2920.93 389.09174 11395.845 + 550 314.97025 121.58624 -3386.2079 -2917.7136 305.58596 11396.569 + 560 317.27856 121.58689 -3386.2296 -2914.3018 271.64243 11397.299 + 570 316.65742 121.58979 -3386.3265 -2915.3226 265.5502 11398.034 + 580 313.57724 121.55613 -3385.2042 -2918.7818 296.4929 11398.775 + 590 310.76616 121.50776 -3383.592 -2921.3508 332.13482 11399.521 + 600 310.56557 121.48286 -3382.7619 -2920.8192 337.42905 11400.274 + 610 312.25189 121.52378 -3384.1259 -2919.6749 301.12723 11401.034 + 620 313.24348 121.52065 -3384.0218 -2918.0959 287.28351 11401.799 + 630 311.62555 121.50992 -3383.6639 -2920.1445 300.88185 11402.57 + 640 306.89182 121.41129 -3380.3762 -2923.8979 376.45557 11403.347 + 650 300.52127 121.30298 -3376.7659 -2929.7633 469.88722 11404.132 + 660 295.39559 121.24088 -3374.6961 -2935.3176 534.41022 11404.925 + 670 293.59119 121.20717 -3373.5724 -2936.8778 557.79376 11405.729 + 680 295.36949 121.2459 -3374.8633 -2935.5236 520.47729 11406.543 + 690 299.69654 121.34257 -3378.0857 -2932.3098 439.24953 11407.368 + 700 304.59438 121.47324 -3382.4412 -2929.3802 343.41809 11408.201 + 710 307.96318 121.55668 -3385.2225 -2927.1506 284.402 11409.041 + 720 308.35357 121.56263 -3385.4211 -2926.7686 286.21174 11409.886 + 730 305.33918 121.48732 -3382.9107 -2928.7418 350.49893 11410.738 + 740 300.03501 121.40623 -3380.2078 -2933.9285 432.74134 11411.596 + 750 295.12581 121.33235 -3377.7448 -2938.7676 498.71123 11412.463 + 760 293.47318 121.31724 -3377.2413 -2940.7222 500.40178 11413.339 + 770 296.15733 121.36068 -3378.6892 -2938.1776 430.22536 11414.225 + 780 301.50769 121.4365 -3381.2166 -2932.7467 318.64474 11415.119 + 790 306.13175 121.49937 -3383.3122 -2927.9645 219.00268 11416.02 + 800 307.37357 121.53662 -3384.554 -2927.3591 165.57164 11416.925 + 810 304.85262 121.4546 -3381.8199 -2928.3748 199.62236 11417.834 + 820 300.60164 121.32558 -3377.5193 -2930.3971 273.18602 11418.746 + 830 297.77967 121.28163 -3376.0544 -2933.1297 303.65329 11419.664 + 840 298.49364 121.32122 -3377.374 -2933.3873 268.86417 11420.588 + 850 302.57668 121.41376 -3380.4586 -2930.3987 179.21637 11421.517 + 860 308.14872 121.51752 -3383.9175 -2925.5696 66.802979 11422.449 + 870 313.06449 121.57803 -3385.9345 -2920.2748 -27.644002 11423.383 + 880 316.30535 121.70702 -3390.2339 -2919.7537 -134.25313 11424.317 + 890 317.74593 121.72456 -3390.8186 -2918.1956 -177.66609 11425.248 + 900 316.86746 121.71204 -3390.4013 -2919.085 -181.01119 11426.176 + 910 312.83916 121.63073 -3387.691 -2922.3665 -122.44293 11427.101 + 920 306.04955 121.52724 -3384.2412 -2929.0157 -26.251061 11428.024 + 930 298.70537 121.40199 -3380.0665 -2935.7648 85.194278 11428.946 + 940 293.16469 121.24629 -3374.8762 -2938.8159 191.47072 11429.87 + 950 290.52469 121.25346 -3375.1154 -2942.9819 203.84747 11430.798 + 960 291.09669 121.26724 -3375.5747 -2942.5904 178.59821 11431.73 + 970 293.99694 121.32293 -3377.4311 -2940.1329 112.43402 11432.665 + 980 297.31974 121.40213 -3380.071 -2937.8304 32.375746 11433.603 + 990 299.27867 121.46862 -3382.2872 -2937.1329 -28.673784 11434.542 + 1000 299.18538 121.45851 -3381.9504 -2936.9349 -39.701634 11435.48 + 1010 298.23484 121.43293 -3381.0978 -2937.4961 -33.404095 11436.418 + 1020 298.25068 121.43673 -3381.2242 -2937.5989 -43.442228 11437.355 + 1030 300.04566 121.44897 -3381.6325 -2935.3373 -71.253925 11438.291 + 1040 303.03618 121.49472 -3383.1573 -2932.4139 -123.1949 11439.227 + 1050 305.62588 121.56886 -3385.6285 -2931.0332 -184.60439 11440.16 + 1060 306.07572 121.55697 -3385.2324 -2929.968 -198.95981 11441.09 + 1070 304.58306 121.53369 -3384.4562 -2931.412 -196.21389 11442.016 + 1080 303.06947 121.52182 -3384.0606 -2933.2678 -198.57704 11442.939 + 1090 302.02905 121.49888 -3383.296 -2934.0506 -197.95326 11443.858 + 1100 300.12698 121.47618 -3382.5392 -2936.1231 -186.50374 11444.773 + 1110 297.09858 121.42122 -3380.7073 -2938.7957 -150.78343 11445.685 + 1120 294.34115 121.37517 -3379.1724 -2941.3623 -122.02811 11446.594 + 1130 293.53424 121.35643 -3378.5476 -2941.9377 -123.07716 11447.501 + 1140 294.65948 121.37256 -3379.0854 -2940.8018 -157.77335 11448.406 + 1150 296.41713 121.39221 -3379.7404 -2938.8424 -203.59962 11449.308 + 1160 297.79086 121.44045 -3381.3482 -2938.4069 -259.83749 11450.206 + 1170 298.3438 121.43053 -3381.0176 -2937.2538 -285.02956 11451.1 + 1180 297.93842 121.42704 -3380.9013 -2937.7405 -299.60577 11451.988 + 1190 297.07582 121.44281 -3381.4271 -2939.5494 -313.37642 11452.871 + 1200 296.14975 121.46928 -3382.3095 -2941.8092 -328.47519 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11356.817 + 9470 277.11445 112.07592 -3402.5305 -2990.3438 195.66591 11357.681 + 9480 276.24296 112.04597 -3401.5324 -2990.642 198.1981 11358.548 + 9490 279.18678 112.10317 -3403.4391 -2988.1699 131.96405 11359.419 + 9500 285.62232 112.22262 -3407.4208 -2982.5793 10.204022 11360.293 + 9510 292.92138 112.3565 -3411.8834 -2976.185 -123.66568 11361.168 + 9520 298.23784 112.46912 -3415.6372 -2972.031 -228.96731 11362.04 + 9530 300.44065 112.50596 -3416.8654 -2969.9827 -274.29938 11362.909 + 9540 300.1625 112.49335 -3416.4449 -2969.976 -274.83813 11363.774 + 9550 298.28409 112.46184 -3415.3945 -2971.7195 -250.45164 11364.633 + 9560 294.90643 112.39352 -3413.1173 -2974.4663 -199.16543 11365.488 + 9570 290.40096 112.35764 -3411.9212 -2979.9718 -153.13997 11366.34 + 9580 286.29201 112.28111 -3409.3702 -2983.5326 -96.522516 11367.19 + 9590 284.43019 112.24597 -3408.199 -2985.1307 -75.265393 11368.037 + 9600 285.51121 112.27581 -3409.1935 -2984.5173 -102.42078 11368.884 + 9610 288.45354 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112.25031 -3408.3435 -2975.4795 -514.96551 11393.129 + 9910 288.3146 102.21877 -3407.2925 -2978.4464 -552.6703 11393.854 + 9920 289.81888 102.2633 -3408.7767 -2977.6931 -595.04901 11394.569 + 9930 295.20081 102.38658 -3412.8859 -2973.797 -695.95493 11395.273 + 9940 301.57118 102.49325 -3416.4418 -2967.8775 -794.95454 11395.964 + 9950 305.76964 102.57072 -3419.024 -2964.2148 -862.85164 11396.64 + 9960 306.04627 102.5489 -3418.2967 -2963.076 -860.0359 11397.301 + 9970 302.3909 102.50659 -3416.8863 -2967.1028 -818.623 11397.945 + 9980 296.77037 102.38306 -3412.7686 -2971.3451 -733.14902 11398.574 + 9990 292.19734 102.29924 -3409.9746 -2975.3532 -674.286 11399.189 + 10000 290.66211 102.28541 -3409.5137 -2977.1759 -667.48493 11399.792 +Loop time of 2.5027 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.591 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.227 ns/day, 0.070 hours/ns, 3995.683 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5437 | 2.5437 | 2.5437 | 0.0 | 78.03 -Bond | 0.00067735 | 0.00067735 | 0.00067735 | 0.0 | 0.02 -Neigh | 0.017251 | 0.017251 | 0.017251 | 0.0 | 0.53 -Comm | 0.08847 | 0.08847 | 0.08847 | 0.0 | 2.71 -Output | 0.0010381 | 0.0010381 | 0.0010381 | 0.0 | 0.03 -Modify | 0.33628 | 0.33628 | 0.33628 | 0.0 | 10.32 -Other | | 0.2725 | | | 8.36 +Pair | 2.0312 | 2.0312 | 2.0312 | 0.0 | 81.16 +Bond | 0.00069571 | 0.00069571 | 0.00069571 | 0.0 | 0.03 +Neigh | 0.013799 | 0.013799 | 0.013799 | 0.0 | 0.55 +Comm | 0.073534 | 0.073534 | 0.073534 | 0.0 | 2.94 +Output | 0.0074136 | 0.0074136 | 0.0074136 | 0.0 | 0.30 +Modify | 0.23759 | 0.23759 | 0.23759 | 0.0 | 9.49 +Other | | 0.1385 | | | 5.53 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 18 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/3/log.lammps.3 b/examples/USER/misc/grem/lj-temper/3/log.lammps.3 index 2bd265431d..4d4060558f 100644 --- a/examples/USER/misc/grem/lj-temper/3/log.lammps.3 +++ b/examples/USER/misc/grem/lj-temper/3/log.lammps.3 @@ -16,10 +16,6 @@ read_data 3/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 100 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso ${press} ${press} 10000.0 @@ -27,135 +23,1044 @@ fix fxnpt all npt temp 300 300 1000.0 iso 0 ${press} 10000.0 fix fxnpt all npt temp 300 300 1000.0 iso 0 0 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt fix fxgREM all grem 930 -.03 -30000 fxnpt + +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol thermo_modify press fxgREM_press +timestep 1.0 temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} temper/grem 10000 100 930 fxgREM fxnpt 10294 98392 Neighbor list info ... - 1 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7 ghost atom cutoff = 7 - binsize = 3.5 -> bins = 7 7 7 -Memory usage per processor = 5.38075 Mbytes -Step Temp PotEng TotEng Press Volume - 0 290.839 -3356.3647 -2923.7637 13.376266 11488.157 - 100 285.69508 -3350.6878 -2925.738 167.78531 11487.986 - 200 303.33832 -3362.4442 -2911.2515 -285.77881 11487.825 - 300 296.08102 -3356.4942 -2916.0962 -14.958212 11487.267 - 400 293.47704 -3361.3097 -2924.7849 -10.620913 11486.528 - 500 299.4194 -3361.7955 -2916.4318 -50.507149 11485.642 - 600 305.29691 -3363.5524 -2909.4464 -108.7678 11484.625 - 700 303.76824 -3363.3253 -2911.493 -104.4867 11483.395 - 800 294.51417 -3359.4431 -2921.3756 69.012038 11481.959 - 900 317.06683 -3376.5605 -2904.9476 -394.53967 11480.603 - 1000 295.23442 -3359.4678 -2920.3289 140.84436 11479.118 - 1100 295.40528 -3359.5295 -2920.1365 238.50053 11477.82 - 1200 296.4057 -3358.2915 -2917.4104 187.0124 11476.739 - 1300 301.90051 -3364.4524 -2915.3982 37.401199 11475.788 - 1400 292.85338 -3358.8438 -2923.2466 166.77089 11474.892 - 1500 306.57141 -3367.7234 -2911.7217 -37.617278 11474.193 - 1600 303.60667 -3363.5842 -2911.9923 59.354855 11473.503 - 1700 309.11038 -3368.2542 -2908.4759 -77.354272 11473.036 - 1800 300.88534 -3360.8762 -2913.3321 157.35644 11472.739 - 1900 300.76857 -3362.1419 -2914.7714 64.474646 11472.846 - 2000 304.83747 -3362.6904 -2909.2678 74.697763 11473.205 - 2100 303.13383 -3361.2408 -2910.3522 23.427206 11473.697 - 2200 310.28177 -3369.0928 -2907.5722 -54.59024 11474.389 - 2300 301.49445 -3364.3099 -2915.8597 57.698577 11475.107 - 2400 302.32605 -3363.1745 -2913.4874 -101.51258 11475.951 - 2500 312.1335 -3371.5673 -2907.2924 -298.61384 11476.757 - 2600 311.48564 -3369.8118 -2906.5005 -248.29721 11477.348 - 2700 302.70772 -3366.2003 -2915.9455 -112.41764 11477.885 - 2800 296.91863 -3362.2907 -2920.6467 -11.436148 11478.398 - 2900 295.20791 -3360.1207 -2921.0213 28.151935 11478.849 - 3000 298.7181 -3363.3108 -2918.9903 -24.285938 11479.232 - 3100 299.63105 -3361.6655 -2915.987 -85.460877 11479.532 - 3200 299.2326 -3362.7204 -2917.6346 -1.4187391 11479.74 - 3300 292.01842 -3359.6831 -2925.3278 111.54019 11479.801 - 3400 300.40417 -3364.1372 -2917.3087 -35.829416 11479.821 - 3500 303.01655 -3366.1156 -2915.4014 -213.6144 11479.867 - 3600 300.80325 -3367.3344 -2919.9124 -108.94713 11479.727 - 3700 301.93871 -3365.3419 -2916.231 -108.25614 11479.485 - 3800 298.59542 -3364.1482 -2920.0102 -73.755956 11479.116 - 3900 296.82227 -3366.2208 -2924.7202 -102.3413 11478.537 - 4000 298.85366 -3363.1199 -2918.5977 -141.73373 11477.785 - 4100 285.93508 -3361.0953 -2935.7885 33.105452 11476.764 - 4200 294.13198 -3366.6662 -2929.1672 -61.017319 11475.527 - 4300 289.62881 -3360.4118 -2929.6109 72.508715 11474.117 - 4400 292.16548 -3363.2769 -2928.7029 69.460552 11472.679 - 4500 296.10391 -3364.7776 -2924.3455 -44.256514 11471.222 - 4600 298.19488 -3367.9838 -2924.4415 -79.787912 11469.536 - 4700 285.80539 -3358.8854 -2933.7716 197.88821 11467.664 - 4800 306.36811 -3371.2406 -2915.5413 -88.96311 11465.916 - 4900 292.49926 -3361.8643 -2926.7938 185.57775 11464.23 - 5000 290.88226 -3361.5861 -2928.9208 259.04414 11462.735 - 5100 307.58823 -3374.2434 -2916.7292 -29.448909 11461.464 - 5200 302.16928 -3370.5539 -2921.1 -33.25034 11460.298 - 5300 316.06674 -3376.741 -2906.6157 -242.91365 11458.915 - 5400 303.96005 -3370.8575 -2918.7399 -141.06744 11457.186 - 5500 311.74544 -3377.0044 -2913.3067 -274.23168 11455.241 - 5600 300.49781 -3366.7267 -2919.7589 112.99595 11452.946 - 5700 292.28467 -3363.6982 -2928.9469 345.58668 11450.884 - 5800 306.41131 -3375.5954 -2919.8318 44.031034 11449.306 - 5900 304.59946 -3373.6282 -2920.5596 11.550291 11447.886 - 6000 311.8961 -3377.6423 -2913.7205 -109.77328 11446.479 - 6100 291.20342 -3368.383 -2935.24 203.83576 11445.011 - 6200 297.89834 -3373.1747 -2930.0735 26.610471 11443.642 - 6300 300.56911 -3378.1564 -2931.0826 -35.208037 11442.15 - 6400 307.53502 -3382.2265 -2924.7914 -91.070456 11440.514 - 6500 303.68877 -3381.5242 -2929.8102 -47.863863 11438.647 - 6600 307.2743 -3383.4914 -2926.4441 -176.63601 11436.802 - 6700 294.30769 -3379.6274 -2941.8671 24.164729 11434.849 - 6800 303.13931 -3381.7922 -2930.8954 -111.95234 11432.875 - 6900 296.26164 -3381.8788 -2941.2121 -57.549381 11430.738 - 7000 289.01191 -3378.9354 -2949.0521 126.23987 11428.513 - 7100 302.81602 -3388.9706 -2938.5547 -237.78388 11426.322 - 7200 294.50663 -3383.9162 -2945.8599 -39.728782 11423.859 - 7300 290.35305 -3382.6487 -2950.7705 94.790713 11421.387 - 7400 282.82774 -3377.867 -2957.1822 250.1436 11419.087 - 7500 300.09907 -3388.5306 -2942.1559 -155.8278 11416.997 - 7600 297.08335 -3388.2429 -2946.354 -74.771931 11414.718 - 7700 296.10041 -3389.0183 -2948.5914 39.612836 11412.516 - 7800 302.26382 -3392.6735 -2943.079 -108.12678 11410.56 - 7900 299.45316 -3389.6586 -2944.2447 -67.016831 11408.644 - 8000 279.75796 -3383.3458 -2967.227 212.04894 11406.742 - 8100 296.1234 -3391.5243 -2951.0632 14.909942 11405.025 - 8200 283.90018 -3385.3372 -2963.0572 242.009 11403.233 - 8300 294.40491 -3390.3819 -2952.4769 144.49126 11401.685 - 8400 284.83989 -3386.3812 -2962.7034 294.44578 11400.452 - 8500 310.91803 -3399.32 -2936.853 -187.72128 11399.607 - 8600 280.73817 -3381.818 -2964.2413 368.28406 11398.828 - 8700 293.03064 -3389.802 -2953.9412 60.228584 11398.442 - 8800 284.38203 -3385.0501 -2962.0534 283.35374 11398.194 - 8900 296.26156 -3391.0805 -2950.4139 105.69366 11398.307 - 9000 293.15104 -3388.0276 -2951.9876 176.06272 11398.732 - 9100 296.37884 -3387.4524 -2946.6113 188.95802 11399.501 - 9200 299.22093 -3389.1839 -2944.1154 146.14576 11400.688 - 9300 284.90575 -3379.3036 -2955.5278 411.30367 11402.307 - 9400 300.14961 -3385.9354 -2939.4856 205.76471 11404.592 - 9500 298.23305 -3382.4734 -2938.8744 283.06153 11407.279 - 9600 282.24345 -3371.4137 -2951.598 615.47273 11410.426 - 9700 318.39873 -3390.0399 -2916.4459 -28.07165 11414.311 - 9800 311.94009 -3386.2127 -2922.2255 70.507396 11418.547 - 9900 317.20428 -3383.9541 -2912.1367 -26.751232 11423.218 - 10000 318.36799 -3382.5532 -2909.0049 -46.362454 11428.313 -Loop time of 3.25989 on 1 procs for 10000 steps with 500 atoms + binsize = 3.5, bins = 7 7 7 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 5.726 | 5.726 | 5.726 Mbytes +Step Temp f_fxgREM PotEng TotEng Press Volume + 0 290.839 130.69094 -3356.3647 -2923.7637 13.376266 11488.157 + 10 298.49016 130.86737 -3362.2456 -2918.2641 -139.01604 11488.157 + 20 305.83037 130.96693 -3365.5642 -2910.6647 -254.45224 11488.154 + 30 310.23182 131.06065 -3368.6884 -2907.2421 -332.60751 11488.147 + 40 310.27284 131.0497 -3368.3232 -2906.8159 -322.86391 11488.133 + 50 306.53667 130.92563 -3364.1878 -2908.2377 -229.32421 11488.113 + 60 301.05575 130.86235 -3362.0784 -2914.2808 -139.22921 11488.089 + 70 295.62185 130.74887 -3358.2958 -2918.5807 -30.488671 11488.062 + 80 291.00386 130.62365 -3354.1217 -2921.2755 71.019816 11488.035 + 90 287.64085 130.55052 -3351.684 -2923.84 136.24318 11488.009 + 100 285.69508 130.52063 -3350.6878 -2925.738 167.78531 11487.986 + 110 285.01446 130.47978 -3349.3259 -2925.3885 187.55076 11487.966 + 120 285.5602 130.50213 -3350.0709 -2925.3218 166.71919 11487.95 + 130 287.3227 130.55196 -3351.7321 -2924.3613 117.78775 11487.937 + 140 290.25957 130.63244 -3354.4147 -2922.6756 40.299682 11487.926 + 150 294.42021 130.70913 -3356.9709 -2919.0432 -49.667147 11487.916 + 160 299.06616 130.7992 -3359.9734 -2915.1351 -148.10202 11487.905 + 170 302.27193 130.85741 -3361.9138 -2912.3072 -219.90367 11487.892 + 180 303.13784 130.86602 -3362.2007 -2911.3062 -249.85871 11487.874 + 190 302.80628 130.87507 -3362.5024 -2912.101 -267.67656 11487.852 + 200 303.33832 130.87333 -3362.4442 -2911.2515 -285.77881 11487.825 + 210 305.5023 130.89943 -3363.3144 -2908.9029 -322.79381 11487.792 + 220 307.85065 130.92123 -3364.0411 -2906.1366 -351.67602 11487.753 + 230 308.22104 130.93218 -3364.406 -2905.9506 -348.91637 11487.707 + 240 305.74564 130.91929 -3363.9764 -2909.2029 -303.52406 11487.654 + 250 301.78413 130.84598 -3361.5326 -2912.6516 -216.19532 11487.596 + 260 298.46788 130.79715 -3359.9048 -2915.9565 -141.52764 11487.534 + 270 296.63349 130.7376 -3357.92 -2916.7002 -78.205751 11487.469 + 280 295.89932 130.72322 -3357.4406 -2917.3128 -46.177821 11487.402 + 290 295.70212 130.70344 -3356.7815 -2916.947 -22.759891 11487.335 + 300 296.08102 130.69483 -3356.4942 -2916.0962 -14.958212 11487.267 + 310 297.44455 130.7448 -3358.1599 -2915.7337 -42.692278 11487.199 + 320 299.60732 130.81428 -3360.4761 -2914.833 -85.527147 11487.13 + 330 301.41392 130.84528 -3361.5094 -2913.179 -109.23287 11487.059 + 340 301.95602 130.87141 -3362.3802 -2913.2435 -116.52949 11486.987 + 350 301.04313 130.87719 -3362.573 -2914.7942 -99.370101 11486.912 + 360 298.75171 130.86396 -3362.1319 -2917.7614 -61.477019 11486.836 + 370 295.31919 130.80085 -3360.0283 -2920.7634 2.7109805 11486.758 + 380 292.01147 130.74417 -3358.1391 -2923.7942 56.679543 11486.68 + 390 291.02267 130.76412 -3358.8039 -2925.9297 52.137334 11486.604 + 400 293.47704 130.83929 -3361.3097 -2924.7849 -10.620913 11486.528 + 410 298.04072 130.90419 -3363.4731 -2920.1601 -92.539319 11486.453 + 420 302.65763 130.9386 -3364.6201 -2914.4398 -161.34189 11486.375 + 430 305.58577 130.94802 -3364.9342 -2910.3985 -199.69054 11486.295 + 440 306.15192 130.96265 -3365.4217 -2910.0439 -210.24137 11486.211 + 450 304.70394 130.95 -3365.0002 -2911.7761 -185.30124 11486.122 + 460 302.72281 130.89534 -3363.178 -2912.9008 -135.5125 11486.031 + 470 301.565 130.87256 -3362.4188 -2913.8637 -103.42872 11485.936 + 480 301.09466 130.88295 -3362.7649 -2914.9094 -90.679055 11485.84 + 490 300.36785 130.88439 -3362.8128 -2916.0384 -75.984213 11485.742 + 500 299.4194 130.85387 -3361.7955 -2916.4318 -50.507149 11485.642 + 510 299.01319 130.85365 -3361.7883 -2917.0289 -42.892731 11485.542 + 520 299.3401 130.84795 -3361.5982 -2916.3525 -40.095555 11485.441 + 530 299.80119 130.82122 -3360.7075 -2914.7759 -29.794671 11485.339 + 540 299.83338 130.81373 -3360.4575 -2914.4781 -22.047344 11485.237 + 550 299.4037 130.80908 -3360.3026 -2914.9623 -9.5687775 11485.134 + 560 298.26531 130.81036 -3360.3454 -2916.6984 6.360308 11485.031 + 570 296.7951 130.74597 -3358.1989 -2916.7387 46.627791 11484.928 + 580 296.86944 130.75106 -3358.3685 -2916.7977 42.347178 11484.827 + 590 299.99401 130.76813 -3358.9377 -2912.7193 1.8547224 11484.726 + 600 305.29691 130.90657 -3363.5524 -2909.4464 -108.7678 11484.625 + 610 310.53262 131.03199 -3367.7329 -2905.8391 -214.98857 11484.522 + 620 313.26727 131.11668 -3370.5559 -2904.5946 -282.25441 11484.415 + 630 312.85585 131.1203 -3370.6767 -2905.3274 -288.19236 11484.303 + 640 311.07096 131.06565 -3368.8551 -2906.1606 -255.80573 11484.185 + 650 309.45998 131.02234 -3367.4112 -2907.1129 -224.31879 11484.062 + 660 307.97753 131.01314 -3367.1047 -2909.0115 -203.40277 11483.936 + 670 306.45975 130.95203 -3365.0678 -2909.2321 -160.61231 11483.805 + 680 305.20067 130.95516 -3365.1719 -2911.2091 -144.94169 11483.671 + 690 304.53788 130.9068 -3363.5599 -2910.5829 -116.21585 11483.534 + 700 303.76824 130.89976 -3363.3253 -2911.493 -104.4867 11483.395 + 710 302.08413 130.82356 -3360.7855 -2911.4582 -59.828868 11483.254 + 720 299.94321 130.81746 -3360.5821 -2914.4393 -37.62374 11483.112 + 730 298.41328 130.79559 -3359.8529 -2915.9857 -15.228868 11482.97 + 740 298.24134 130.78445 -3359.4815 -2915.8701 -8.1016813 11482.827 + 750 299.35763 130.83783 -3361.261 -2915.9892 -34.63294 11482.684 + 760 300.68466 130.88347 -3362.7823 -2915.5367 -56.018851 11482.54 + 770 300.46889 130.91881 -3363.9604 -2917.0357 -58.629961 11482.395 + 780 298.60969 130.84715 -3361.5716 -2917.4123 -6.2774696 11482.25 + 790 296.34564 130.80308 -3360.1027 -2919.3111 38.355568 11482.104 + 800 294.51417 130.78329 -3359.4431 -2921.3756 69.012038 11481.959 + 810 292.88964 130.75567 -3358.5224 -2922.8713 100.11987 11481.815 + 820 291.00259 130.68345 -3356.1148 -2923.2705 149.04294 11481.674 + 830 289.35715 130.65539 -3355.1797 -2924.7829 177.16152 11481.535 + 840 288.98728 130.64016 -3354.6719 -2924.8252 184.02622 11481.399 + 850 290.93491 130.73708 -3357.9026 -2925.159 120.8681 11481.268 + 860 295.66458 130.80129 -3360.0429 -2920.2643 38.832849 11481.138 + 870 302.5264 130.93467 -3364.4891 -2914.504 -92.377319 11481.009 + 880 309.52977 131.07094 -3369.0313 -2908.6292 -225.81971 11480.879 + 890 314.79857 131.22892 -3374.2973 -2906.0583 -345.569 11480.744 + 900 317.06683 131.29681 -3376.5605 -2904.9476 -394.53967 11480.603 + 910 315.46623 131.26165 -3375.3882 -2906.1561 -358.20311 11480.454 + 920 309.86806 131.12874 -3370.9581 -2910.0529 -239.56321 11480.299 + 930 301.86853 130.97293 -3365.7644 -2916.7579 -84.084273 11480.139 + 940 293.87732 130.75829 -3358.6098 -2921.4896 99.699044 11479.978 + 950 287.08521 130.63024 -3354.3413 -2927.3238 241.77818 11479.819 + 960 281.87799 130.53697 -3351.2325 -2931.9603 352.23356 11479.664 + 970 278.97756 130.50825 -3350.2749 -2935.317 408.09623 11479.516 + 980 279.5637 130.51545 -3350.5149 -2934.6851 405.94257 11479.376 + 990 285.08084 130.59476 -3353.1586 -2929.1224 318.75105 11479.244 + 1000 295.23442 130.78403 -3359.4678 -2920.3289 140.84436 11479.118 + 1010 306.39662 131.00504 -3366.8348 -2911.093 -57.300039 11478.994 + 1020 313.99268 131.17269 -3372.4229 -2905.3825 -196.39271 11478.87 + 1030 316.09081 131.17397 -3372.4657 -2902.3045 -212.08799 11478.742 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-3376.5631 -2937.0247 424.36683 11415.506 + 9740 293.69194 121.24535 -3374.845 -2938.0005 472.17246 11415.918 + 9750 295.82738 121.28075 -3376.0249 -2936.0041 436.99987 11416.34 + 9760 300.84709 121.36028 -3378.6761 -2931.1888 346.71992 11416.77 + 9770 306.75344 121.43996 -3381.3319 -2925.0594 241.24451 11417.208 + 9780 311.02557 121.5807 -3386.0235 -2923.3965 124.30422 11417.651 + 9790 312.54333 121.58098 -3386.0327 -2921.1481 86.777327 11418.098 + 9800 311.94009 121.58638 -3386.2127 -2922.2255 70.507396 11418.547 + 9810 310.63038 121.53963 -3384.6545 -2922.6153 85.926164 11418.997 + 9820 310.24158 121.54915 -3384.9716 -2923.5107 80.534768 11419.451 + 9830 310.26239 121.57399 -3385.7997 -2924.3079 74.796432 11419.906 + 9840 308.09463 121.48045 -3382.6815 -2924.4141 137.35072 11420.364 + 9850 303.25155 121.36246 -3378.7487 -2927.685 230.41562 11420.825 + 9860 298.15768 121.24027 -3374.6756 -2931.1886 319.73318 11421.291 + 9870 296.24967 121.20328 -3373.4426 -2932.7936 338.78078 11421.764 + 9880 299.74146 121.24008 -3374.6695 -2928.8268 273.4407 11422.244 + 9890 308.03575 121.3596 -3378.6534 -2920.4736 131.9849 11422.729 + 9900 317.20428 121.51862 -3383.9541 -2912.1367 -26.751232 11423.218 + 9910 322.01402 121.62253 -3387.4177 -2908.4463 -114.41883 11423.707 + 9920 319.17778 121.54485 -3384.8285 -2910.0757 -51.898249 11424.195 + 9930 309.068 121.37161 -3379.0535 -2919.3383 121.82333 11424.683 + 9940 295.19905 121.13123 -3371.0411 -2931.9549 355.38766 11425.174 + 9950 283.24166 120.94189 -3364.7297 -2943.4292 543.86415 11425.673 + 9960 278.89942 120.87426 -3362.4754 -2947.6337 605.50591 11426.182 + 9970 284.59829 120.96752 -3365.5839 -2942.2655 505.31899 11426.703 + 9980 297.42507 121.21278 -3373.7593 -2931.3621 277.96374 11427.235 + 9990 310.57569 121.40093 -3380.0309 -2918.0731 68.495001 11427.773 + 10000 318.36799 121.47659 -3382.5532 -2909.0049 -46.362454 11428.313 +Loop time of 2.5028 on 1 procs for 10000 steps with 500 atoms -Performance: 265.040 ns/day, 0.091 hours/ns, 3067.588 timesteps/s -100.0% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 345.213 ns/day, 0.070 hours/ns, 3995.527 timesteps/s +99.9% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 2.5437 | 2.5437 | 2.5437 | 0.0 | 78.03 -Bond | 0.00088167 | 0.00088167 | 0.00088167 | 0.0 | 0.03 -Neigh | 0.027397 | 0.027397 | 0.027397 | 0.0 | 0.84 -Comm | 0.088112 | 0.088112 | 0.088112 | 0.0 | 2.70 -Output | 0.0010602 | 0.0010602 | 0.0010602 | 0.0 | 0.03 -Modify | 0.33726 | 0.33726 | 0.33726 | 0.0 | 10.35 -Other | | 0.2614 | | | 8.02 +Pair | 2.0314 | 2.0314 | 2.0314 | 0.0 | 81.16 +Bond | 0.00091743 | 0.00091743 | 0.00091743 | 0.0 | 0.04 +Neigh | 0.022412 | 0.022412 | 0.022412 | 0.0 | 0.90 +Comm | 0.074236 | 0.074236 | 0.074236 | 0.0 | 2.97 +Output | 0.0073647 | 0.0073647 | 0.0073647 | 0.0 | 0.29 +Modify | 0.23464 | 0.23464 | 0.23464 | 0.0 | 9.38 +Other | | 0.1319 | | | 5.27 Nlocal: 500 ave 500 max 500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -171,4 +1076,4 @@ Neighbor list builds = 29 Dangerous builds = 0 #write_data ${rep}/lj-out.data -Total wall time: 0:00:03 +Total wall time: 0:00:02 diff --git a/examples/USER/misc/grem/lj-temper/in.gREM-temper b/examples/USER/misc/grem/lj-temper/in.gREM-temper index 9e94edec79..8aa495d9d2 100644 --- a/examples/USER/misc/grem/lj-temper/in.gREM-temper +++ b/examples/USER/misc/grem/lj-temper/in.gREM-temper @@ -18,14 +18,14 @@ read_data ${rep}/lj.data #dump dump all xyz 1000 ${rep}/dump.xyz -thermo 10 -thermo_style custom step temp pe etotal press vol -timestep 1.0 - fix fxnpt all npt temp ${T0} ${T0} 1000.0 iso ${press} ${press} 10000.0 fix fxgREM all grem ${lambda} -.03 -30000 fxnpt -thermo_modify press fxgREM_press -temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} +thermo 10 +thermo_style custom step temp f_fxgREM pe etotal press vol +thermo_modify press fxgREM_press +timestep 1.0 + +temper/grem 10000 100 ${lambda} fxgREM fxnpt 10294 98392 #${walker} #write_data ${rep}/lj-out.data diff --git a/examples/USER/tally/log.12Jun17.force.1 b/examples/USER/tally/log.12Jun17.force.1 new file mode 100644 index 0000000000..98b3bad245 --- /dev/null +++ b/examples/USER/tally/log.12Jun17.force.1 @@ -0,0 +1,177 @@ +LAMMPS (19 May 2017) + +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-4 + +pair_coeff 1 1 0.15535 3.166 +pair_coeff * 2 0.0000 0.0000 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 3e-06 on 1 procs for 0 steps with 4500 atoms + + +group one molecule 1 2 +6 atoms in group one + +# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords + +# compute pairwise force between two molecules and everybody +compute fpa one group/group all pair yes kspace no boundary no +# tally pairwise force between two molecules and the all molecules +compute c1 one force/tally all +# tally the force of all with all (should be zero) +compute c2 all force/tally all +# collect per atom data. only reduce over the first group. +compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] +compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] +# determine magnitude of force +variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) +variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) +# round to 10**-10 absolute precision. +variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 +variable all equal round(1e10*c_c2)*1e-10 + +velocity all create 300 432567 dist uniform + +timestep 2.0 + +# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero +thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all +thermo 10 + +run 50 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 28.47 | 28.47 | 28.47 Mbytes +Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all + 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0 + 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0 + 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0 + 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0 + 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0 + 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0 +Loop time of 13.9507 on 1 procs for 50 steps with 4500 atoms + +Performance: 0.619 ns/day, 38.752 hours/ns, 3.584 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.594 | 12.594 | 12.594 | 0.0 | 90.27 +Bond | 7.3e-05 | 7.3e-05 | 7.3e-05 | 0.0 | 0.00 +Kspace | 0.56296 | 0.56296 | 0.56296 | 0.0 | 4.04 +Neigh | 0.65858 | 0.65858 | 0.65858 | 0.0 | 4.72 +Comm | 0.019093 | 0.019093 | 0.019093 | 0.0 | 0.14 +Output | 0.055025 | 0.055025 | 0.055025 | 0.0 | 0.39 +Modify | 0.057276 | 0.057276 | 0.057276 | 0.0 | 0.41 +Other | | 0.004003 | | | 0.03 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21131 ave 21131 max 21131 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 +Ave special neighs/atom = 2 +Neighbor list builds = 4 +Dangerous builds = 1 + +Total wall time: 0:00:15 diff --git a/examples/USER/tally/log.12Jun17.force.4 b/examples/USER/tally/log.12Jun17.force.4 new file mode 100644 index 0000000000..4238173fb6 --- /dev/null +++ b/examples/USER/tally/log.12Jun17.force.4 @@ -0,0 +1,177 @@ +LAMMPS (19 May 2017) + +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style lj/cut/coul/long 12.0 12.0 +kspace_style pppm 1.0e-4 + +pair_coeff 1 1 0.15535 3.166 +pair_coeff * 2 0.0000 0.0000 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 4.5e-06 on 4 procs for 0 steps with 4500 atoms + + +group one molecule 1 2 +6 atoms in group one + +# the following section shows equivalences between using the force/tally compute and other computes and thermo keywords + +# compute pairwise force between two molecules and everybody +compute fpa one group/group all pair yes kspace no boundary no +# tally pairwise force between two molecules and the all molecules +compute c1 one force/tally all +# tally the force of all with all (should be zero) +compute c2 all force/tally all +# collect per atom data. only reduce over the first group. +compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] +compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] +# determine magnitude of force +variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) +variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) +# round to 10**-10 absolute precision. +variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 +variable all equal round(1e10*c_c2)*1e-10 + +velocity all create 300 432567 dist uniform + +timestep 2.0 + +# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero +thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all +thermo 10 + +run 50 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:77) +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.58 | 11.59 | 11.6 Mbytes +Step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref v_all + 0 22.7331 22.7331 22.7331 -17.068295 -17.068295 -8.8348335 -8.8348334 -12.141369 -12.141369 0 0 + 10 11.736901 11.736901 11.736901 -3.3897029 -3.3897029 9.1193856 9.1193856 -6.5651786 -6.5651786 0 0 + 20 5.6120339 5.6120339 5.6120339 -0.60046861 -0.60046861 -4.4481306 -4.4481306 3.3687528 3.3687528 0 0 + 30 17.29261 17.29261 17.29261 6.179302 6.179302 -10.593979 -10.593979 12.190906 12.190906 0 0 + 40 18.664433 18.664433 18.664433 5.4727782 5.4727782 -6.9329319 -6.9329319 16.442148 16.442148 0 0 + 50 12.130407 12.130407 12.130407 -1.0321196 -1.0321196 8.0035558 8.0035558 -9.0567428 -9.0567428 0 0 +Loop time of 4.31614 on 4 procs for 50 steps with 4500 atoms + +Performance: 2.002 ns/day, 11.989 hours/ns, 11.584 timesteps/s +31.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 3.5075 | 3.6114 | 3.7489 | 4.7 | 83.67 +Bond | 8.6e-05 | 0.00010525 | 0.000141 | 0.0 | 0.00 +Kspace | 0.2581 | 0.39489 | 0.49723 | 14.2 | 9.15 +Neigh | 0.19826 | 0.19888 | 0.19918 | 0.1 | 4.61 +Comm | 0.034639 | 0.037137 | 0.038938 | 0.9 | 0.86 +Output | 0.025465 | 0.025997 | 0.027558 | 0.6 | 0.60 +Modify | 0.044022 | 0.044175 | 0.044407 | 0.1 | 1.02 +Other | | 0.003593 | | | 0.08 + +Nlocal: 1125 ave 1148 max 1097 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +Nghost: 12212.5 ave 12269 max 12162 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Neighs: 650496 ave 675112 max 631353 min +Histogram: 1 0 0 1 1 0 0 0 0 1 + +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 +Ave special neighs/atom = 2 +Neighbor list builds = 4 +Dangerous builds = 1 + +Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.pe.1 b/examples/USER/tally/log.12Jun17.pe.1 similarity index 50% rename from examples/USER/tally/log.21Aug15.pe.1 rename to examples/USER/tally/log.12Jun17.pe.1 index aea5530038..8b0f753414 100644 --- a/examples/USER/tally/log.21Aug15.pe.1 +++ b/examples/USER/tally/log.12Jun17.pe.1 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 1e-06 on 1 procs for 0 steps with 4500 atoms + + group oxy type 1 1500 atoms in group oxy group hyd type 2 @@ -88,6 +116,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -95,38 +124,49 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 17.381 Mbytes -Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair - 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827 - 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972 - 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572 - 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165 - 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345 - 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 29.08 | 29.08 | 29.08 Mbytes +Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair + 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425 + 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003 + 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594 + 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191 + 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369 + 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935 +Loop time of 15.3339 on 1 procs for 50 steps with 4500 atoms -Loop time of 4.31105 on 1 procs for 50 steps with 4500 atoms -100.1% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.004 ns/day 11.975 hours/ns 11.598 timesteps/s +Performance: 0.563 ns/day, 42.594 hours/ns, 3.261 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.5071 | 3.5071 | 3.5071 | 0.0 | 81.35 -Bond | 0.00025034 | 0.00025034 | 0.00025034 | 0.0 | 0.01 -Kspace | 0.19991 | 0.19991 | 0.19991 | 0.0 | 4.64 -Neigh | 0.31459 | 0.31459 | 0.31459 | 0.0 | 7.30 -Comm | 0.010338 | 0.010338 | 0.010338 | 0.0 | 0.24 -Output | 0.24722 | 0.24722 | 0.24722 | 0.0 | 5.73 -Modify | 0.029466 | 0.029466 | 0.029466 | 0.0 | 0.68 -Other | | 0.002182 | | | 0.05 +Pair | 13.432 | 13.432 | 13.432 | 0.0 | 87.60 +Bond | 0.000365 | 0.000365 | 0.000365 | 0.0 | 0.00 +Kspace | 0.581 | 0.581 | 0.581 | 0.0 | 3.79 +Neigh | 0.66081 | 0.66081 | 0.66081 | 0.0 | 4.31 +Comm | 0.019908 | 0.019908 | 0.019908 | 0.0 | 0.13 +Output | 0.57731 | 0.57731 | 0.57731 | 0.0 | 3.76 +Modify | 0.058515 | 0.058515 | 0.058515 | 0.0 | 0.38 +Other | | 0.003889 | | | 0.03 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -135,10 +175,10 @@ Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 -Total wall time: 0:00:04 +Total wall time: 0:00:16 diff --git a/examples/USER/tally/log.21Aug15.pe.4 b/examples/USER/tally/log.12Jun17.pe.4 similarity index 50% rename from examples/USER/tally/log.21Aug15.pe.4 rename to examples/USER/tally/log.12Jun17.pe.4 index 303af555ff..f684fabe01 100644 --- a/examples/USER/tally/log.21Aug15.pe.4 +++ b/examples/USER/tally/log.12Jun17.pe.4 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 1.75e-06 on 4 procs for 0 steps with 4500 atoms + + group oxy type 1 1500 atoms in group oxy group hyd type 2 @@ -88,6 +116,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -95,38 +124,49 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) -WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:75) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) +WARNING: Compute pe/tally only called from pair style (../compute_pe_tally.cpp:77) Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 14 ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 8.44413 Mbytes -Step epa epa E_vdwl vdwl E_coul coul eref pe c2 pair - 0 -516632.19 -516632.19 3169.9382 3169.9382 46213.889 46213.889 49383.827 49383.827 49383.827 49383.827 - 10 -517027.36 -517027.36 3099.1322 3099.1322 45891.84 45891.84 48990.972 48990.972 48990.972 48990.972 - 20 -516828.06 -516828.06 3101.4321 3101.4321 45884.14 45884.14 48985.572 48985.572 48985.572 48985.572 - 30 -517032.1 -517032.1 3198.5939 3198.5939 45793.571 45793.571 48992.165 48992.165 48992.165 48992.165 - 40 -517095.56 -517095.56 3244.0797 3244.0797 45715.265 45715.265 48959.345 48959.345 48959.345 48959.345 - 50 -517273.54 -517273.54 3274.9142 3274.9142 45665.997 45665.997 48940.911 48940.911 48940.911 48940.911 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 1 1 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) compute group/group, occasional, copy from (1) + attributes: half, newton on + pair build: copy + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 11.86 | 11.87 | 11.88 Mbytes +Step c_epa v_epa E_vdwl v_vdwl E_coul v_coul v_eref v_pe c_c2 v_pair + 0 -516634.27 -516634.27 3169.9427 3169.9427 46212.482 46212.482 49382.425 49382.425 49382.425 49382.425 + 10 -517027.35 -517027.35 3099.1374 3099.1374 45891.866 45891.866 48991.003 48991.003 48991.003 48991.003 + 20 -516828.05 -516828.05 3101.4373 3101.4373 45884.156 45884.156 48985.594 48985.594 48985.594 48985.594 + 30 -517032.07 -517032.07 3198.5951 3198.5951 45793.595 45793.595 48992.191 48992.191 48992.191 48992.191 + 40 -517095.54 -517095.54 3244.0771 3244.0771 45715.292 45715.292 48959.369 48959.369 48959.369 48959.369 + 50 -517273.5 -517273.5 3274.9097 3274.9097 45666.025 45666.025 48940.935 48940.935 48940.935 48940.935 +Loop time of 2.32344 on 4 procs for 50 steps with 4500 atoms -Loop time of 1.20533 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.168 ns/day 3.348 hours/ns 41.482 timesteps/s +Performance: 3.719 ns/day, 6.454 hours/ns, 21.520 timesteps/s +64.0% CPU use with 4 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.87053 | 0.90325 | 0.94364 | 2.8 | 74.94 -Bond | 0.00015402 | 0.00018191 | 0.00020909 | 0.2 | 0.02 -Kspace | 0.061657 | 0.10164 | 0.13394 | 8.4 | 8.43 -Neigh | 0.088292 | 0.088332 | 0.088373 | 0.0 | 7.33 -Comm | 0.017319 | 0.017806 | 0.018291 | 0.4 | 1.48 -Output | 0.07067 | 0.070706 | 0.070813 | 0.0 | 5.87 -Modify | 0.021655 | 0.021694 | 0.02173 | 0.0 | 1.80 -Other | | 0.001719 | | | 0.14 +Pair | 1.5561 | 1.8883 | 2.0327 | 14.1 | 81.27 +Bond | 8.8e-05 | 0.000116 | 0.000135 | 0.0 | 0.00 +Kspace | 0.094718 | 0.1933 | 0.26055 | 14.1 | 8.32 +Neigh | 0.085117 | 0.1073 | 0.1147 | 3.9 | 4.62 +Comm | 0.014156 | 0.017907 | 0.020005 | 1.8 | 0.77 +Output | 0.071634 | 0.090599 | 0.097665 | 3.6 | 3.90 +Modify | 0.019447 | 0.024101 | 0.026277 | 1.8 | 1.04 +Other | | 0.001804 | | | 0.08 Nlocal: 1125 ave 1148 max 1097 min Histogram: 1 0 0 1 0 0 0 0 1 1 @@ -135,10 +175,10 @@ Histogram: 1 0 0 1 0 1 0 0 0 1 Neighs: 650496 ave 675112 max 631353 min Histogram: 1 0 0 1 1 0 0 0 0 1 -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 +Total # of neighbors = 2601983 +Ave neighs/atom = 578.218 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 1 -Total wall time: 0:00:01 +Total wall time: 0:00:02 diff --git a/examples/USER/tally/log.21Aug15.stress.1 b/examples/USER/tally/log.12Jun17.stress.1 similarity index 56% rename from examples/USER/tally/log.21Aug15.stress.1 rename to examples/USER/tally/log.12Jun17.stress.1 index c20b515596..a76012487c 100644 --- a/examples/USER/tally/log.21Aug15.stress.1 +++ b/examples/USER/tally/log.12Jun17.stress.1 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 8000 3375 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 26.54 | 26.54 | 26.54 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 2e-06 on 1 procs for 0 steps with 4500 atoms + + group one molecule 1 2 6 atoms in group one @@ -79,6 +107,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -86,38 +115,32 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 24.631 Mbytes -Step press spa press one ref - 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6 - 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3 - 20 23338.149 23338.149 23338.149 -2034283 -2034283 - 30 25946.4 25946.4 25946.4 -2002817 -2002817 - 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5 - 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3 +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +Per MPI rank memory allocation (min/avg/max) = 35.9 | 35.9 | 35.9 Mbytes +Step c_press v_spa v_press v_one v_ref + 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7 + 10 23665.129 23665.129 23665.129 -2096059 -2096059 + 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1 + 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3 + 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7 + 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5 +Loop time of 14.2089 on 1 procs for 50 steps with 4500 atoms -Loop time of 4.15609 on 1 procs for 50 steps with 4500 atoms -100.1% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.079 ns/day 11.545 hours/ns 12.031 timesteps/s +Performance: 0.608 ns/day, 39.469 hours/ns, 3.519 timesteps/s +32.0% CPU use with 1 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 3.6444 | 3.6444 | 3.6444 | 0.0 | 87.69 -Bond | 0.0016105 | 0.0016105 | 0.0016105 | 0.0 | 0.04 -Kspace | 0.22345 | 0.22345 | 0.22345 | 0.0 | 5.38 -Neigh | 0.23588 | 0.23588 | 0.23588 | 0.0 | 5.68 -Comm | 0.010035 | 0.010035 | 0.010035 | 0.0 | 0.24 -Output | 0.0084085 | 0.0084085 | 0.0084085 | 0.0 | 0.20 -Modify | 0.029978 | 0.029978 | 0.029978 | 0.0 | 0.72 -Other | | 0.002368 | | | 0.06 +Pair | 12.983 | 12.983 | 12.983 | 0.0 | 91.37 +Bond | 0.002788 | 0.002788 | 0.002788 | 0.0 | 0.02 +Kspace | 0.62745 | 0.62745 | 0.62745 | 0.0 | 4.42 +Neigh | 0.49839 | 0.49839 | 0.49839 | 0.0 | 3.51 +Comm | 0.018597 | 0.018597 | 0.018597 | 0.0 | 0.13 +Output | 0.015852 | 0.015852 | 0.015852 | 0.0 | 0.11 +Modify | 0.058415 | 0.058415 | 0.058415 | 0.0 | 0.41 +Other | | 0.004126 | | | 0.03 Nlocal: 4500 ave 4500 max 4500 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -132,4 +155,4 @@ Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:04 +Total wall time: 0:00:15 diff --git a/examples/USER/tally/log.21Aug15.stress.4 b/examples/USER/tally/log.12Jun17.stress.4 similarity index 55% rename from examples/USER/tally/log.21Aug15.stress.4 rename to examples/USER/tally/log.12Jun17.stress.4 index c681960c99..37bb60f013 100644 --- a/examples/USER/tally/log.21Aug15.stress.4 +++ b/examples/USER/tally/log.12Jun17.stress.4 @@ -1,5 +1,4 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task +LAMMPS (19 May 2017) units real atom_style full @@ -50,6 +49,35 @@ fix 1 all shake 0.0001 20 0 b 1 a 1 1500 = # of frozen angles fix 2 all nvt temp 300.0 300.0 100.0 +# make certain that shake constraints are satisfied +run 0 post no +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.218482 + grid = 15 15 15 + stencil order = 5 + estimated absolute RMS force accuracy = 0.0319435 + estimated relative force accuracy = 9.61968e-05 + using double precision FFTs + 3d grid and FFT values/proc = 3380 960 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair lj/cut/coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 10.6 | 10.61 | 10.61 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.358 0 -16692.358 -1289.8319 +Loop time of 4e-06 on 4 procs for 0 steps with 4500 atoms + + group one molecule 1 2 6 atoms in group one @@ -79,6 +107,7 @@ thermo 10 run 50 PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.218482 grid = 15 15 15 stencil order = 5 @@ -86,44 +115,38 @@ PPPM initialization ... estimated relative force accuracy = 9.61968e-05 using double precision FFTs 3d grid and FFT values/proc = 3380 960 -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:75) -Neighbor list info ... - 1 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 12.0691 Mbytes -Step press spa press one ref - 0 26497.547 26497.547 26497.547 -2357033.6 -2357033.6 - 10 23665.073 23665.073 23665.073 -2096057.3 -2096057.3 - 20 23338.149 23338.149 23338.149 -2034283 -2034283 - 30 25946.4 25946.4 25946.4 -2002817 -2002817 - 40 27238.349 27238.349 27238.349 -2155411.5 -2155411.5 - 50 27783.092 27783.092 27783.092 -1862190.3 -1862190.3 +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +WARNING: Compute stress/tally only called from pair style (../compute_stress_tally.cpp:79) +Per MPI rank memory allocation (min/avg/max) = 15.25 | 15.26 | 15.27 Mbytes +Step c_press v_spa v_press v_one v_ref + 0 26496.811 26496.811 26496.811 -2356992.7 -2356992.7 + 10 23665.129 23665.129 23665.129 -2096059 -2096059 + 20 23338.197 23338.197 23338.197 -2034284.1 -2034284.1 + 30 25946.434 25946.434 25946.434 -2002815.3 -2002815.3 + 40 27238.374 27238.374 27238.374 -2155408.7 -2155408.7 + 50 27783.107 27783.107 27783.107 -1862191.5 -1862191.5 +Loop time of 4.32017 on 4 procs for 50 steps with 4500 atoms -Loop time of 1.17266 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.368 ns/day 3.257 hours/ns 42.638 timesteps/s +Performance: 2.000 ns/day, 12.000 hours/ns, 11.574 timesteps/s +31.8% CPU use with 4 MPI tasks x no OpenMP threads -MPI task timings breakdown: +MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.89832 | 0.93222 | 0.98611 | 3.4 | 79.50 -Bond | 0.00081754 | 0.00096095 | 0.0011327 | 0.4 | 0.08 -Kspace | 0.068058 | 0.12154 | 0.15522 | 9.4 | 10.36 -Neigh | 0.065756 | 0.065785 | 0.065824 | 0.0 | 5.61 -Comm | 0.017489 | 0.017982 | 0.018623 | 0.4 | 1.53 -Output | 0.010985 | 0.011017 | 0.011111 | 0.1 | 0.94 -Modify | 0.021429 | 0.021491 | 0.021551 | 0.0 | 1.83 -Other | | 0.001671 | | | 0.14 +Pair | 3.5816 | 3.6917 | 3.839 | 4.9 | 85.45 +Bond | 0.001579 | 0.0016563 | 0.001709 | 0.1 | 0.04 +Kspace | 0.22505 | 0.3716 | 0.48023 | 15.3 | 8.60 +Neigh | 0.14558 | 0.14568 | 0.14575 | 0.0 | 3.37 +Comm | 0.032009 | 0.03441 | 0.036274 | 0.8 | 0.80 +Output | 0.02253 | 0.023115 | 0.024844 | 0.7 | 0.54 +Modify | 0.046954 | 0.047086 | 0.047132 | 0.0 | 1.09 +Other | | 0.004935 | | | 0.11 Nlocal: 1125 ave 1154 max 1092 min Histogram: 1 0 0 0 1 0 1 0 0 1 Nghost: 12263.5 ave 12300 max 12219 min Histogram: 1 0 1 0 0 0 0 0 0 2 -Neighs: 650438 ave 678786 max 626279 min +Neighs: 650438 ave 678787 max 626279 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 2601750 @@ -132,4 +155,4 @@ Ave special neighs/atom = 2 Neighbor list builds = 3 Dangerous builds = 0 -Total wall time: 0:00:01 +Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.force.1 b/examples/USER/tally/log.21Aug15.force.1 deleted file mode 100644 index 8e7bdb9520..0000000000 --- a/examples/USER/tally/log.21Aug15.force.1 +++ /dev/null @@ -1,136 +0,0 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task - -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 1 by 1 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-4 - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -group one molecule 1 2 -6 atoms in group one - -# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords - -# compute pairwise force between two molecules and everybody -compute fpa one group/group all pair yes kspace no boundary no -# tally pairwise force between two molecules and the all molecules -compute c1 one force/tally all -# tally the force of all with all (should be zero) -compute c2 all force/tally all -# collect per atom data. only reduce over the first group. -compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] -compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] -# determine magnitude of force -variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) -variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) -# round to 10**-10 absolute precision. -variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 - -velocity all create 300 432567 dist uniform - -timestep 2.0 - -# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero -thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2 -thermo 10 - -run 50 -PPPM initialization ... - G vector (1/distance) = 0.218482 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0319435 - estimated relative force accuracy = 9.61968e-05 - using double precision FFTs - 3d grid and FFT values/proc = 8000 3375 -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 16.7648 Mbytes -Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2 - 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0 - 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0 - 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0 - 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0 - 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0 - 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0 - -Loop time of 4.11825 on 1 procs for 50 steps with 4500 atoms -100.0% CPU use with 1 MPI tasks x 1 OpenMP threads -Performance: 2.098 ns/day 11.440 hours/ns 12.141 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 3.5286 | 3.5286 | 3.5286 | 0.0 | 85.68 -Bond | 6.1274e-05 | 6.1274e-05 | 6.1274e-05 | 0.0 | 0.00 -Kspace | 0.1937 | 0.1937 | 0.1937 | 0.0 | 4.70 -Neigh | 0.31454 | 0.31454 | 0.31454 | 0.0 | 7.64 -Comm | 0.01037 | 0.01037 | 0.01037 | 0.0 | 0.25 -Output | 0.039355 | 0.039355 | 0.039355 | 0.0 | 0.96 -Modify | 0.029273 | 0.029273 | 0.029273 | 0.0 | 0.71 -Other | | 0.002351 | | | 0.06 - -Nlocal: 4500 ave 4500 max 4500 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 21131 ave 21131 max 21131 min -Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 2.60198e+06 ave 2.60198e+06 max 2.60198e+06 min -Histogram: 1 0 0 0 0 0 0 0 0 0 - -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 -Ave special neighs/atom = 2 -Neighbor list builds = 4 -Dangerous builds = 1 - -Total wall time: 0:00:04 diff --git a/examples/USER/tally/log.21Aug15.force.4 b/examples/USER/tally/log.21Aug15.force.4 deleted file mode 100644 index 17cbc50f02..0000000000 --- a/examples/USER/tally/log.21Aug15.force.4 +++ /dev/null @@ -1,136 +0,0 @@ -LAMMPS (21 Aug 2015-ICMS) - using 1 OpenMP thread(s) per MPI task - -units real -atom_style full - -read_data data.spce - orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) - 2 by 2 by 1 MPI processor grid - reading atoms ... - 4500 atoms - scanning bonds ... - 2 = max bonds/atom - scanning angles ... - 1 = max angles/atom - reading bonds ... - 3000 bonds - reading angles ... - 1500 angles - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 1 = max # of 1-4 neighbors - 2 = max # of special neighbors - -pair_style lj/cut/coul/long 12.0 12.0 -kspace_style pppm 1.0e-4 - -pair_coeff 1 1 0.15535 3.166 -pair_coeff * 2 0.0000 0.0000 - -bond_style harmonic -angle_style harmonic -dihedral_style none -improper_style none - -bond_coeff 1 1000.00 1.000 -angle_coeff 1 100.0 109.47 - -special_bonds lj/coul 0.0 0.0 1.0 - 2 = max # of 1-2 neighbors - 1 = max # of 1-3 neighbors - 2 = max # of special neighbors - -neighbor 2.0 bin - -fix 1 all shake 0.0001 20 0 b 1 a 1 - 0 = # of size 2 clusters - 0 = # of size 3 clusters - 0 = # of size 4 clusters - 1500 = # of frozen angles -fix 2 all nvt temp 300.0 300.0 100.0 - -group one molecule 1 2 -6 atoms in group one - -# the following section shows equivalences between using the pe/tally compute and other computes and thermo keywords - -# compute pairwise force between two molecules and everybody -compute fpa one group/group all pair yes kspace no boundary no -# tally pairwise force between two molecules and the all molecules -compute c1 one force/tally all -# tally the force of all with all (should be zero) -compute c2 all force/tally all -# collect per atom data. only reduce over the first group. -compute one one reduce sum c_c1[1] c_c1[2] c_c1[3] -compute red all reduce sum c_c2[1] c_c2[2] c_c2[3] -# determine magnitude of force -variable fpa equal sqrt(c_fpa[1]*c_fpa[1]+c_fpa[2]*c_fpa[2]+c_fpa[3]*c_fpa[3]) -variable for equal sqrt(c_one[1]*c_one[1]+c_one[2]*c_one[2]+c_one[3]*c_one[3]) -# round to 10**-10 absolute precision. -variable ref equal round(1e10*sqrt(c_red[1]*c_red[1]+c_red[2]*c_red[2]+c_red[3]*c_red[3]))*1e-10 - -velocity all create 300 432567 dist uniform - -timestep 2.0 - -# v_fpa and v_for and c_c1, c_fpa[] and c_one[] should all each have the same value. v_ref and c_c2 should be zero -thermo_style custom step v_fpa v_for c_c1 c_fpa[1] c_one[1] c_fpa[2] c_one[2] c_fpa[3] c_one[3] v_ref c_c2 -thermo 10 - -run 50 -PPPM initialization ... - G vector (1/distance) = 0.218482 - grid = 15 15 15 - stencil order = 5 - estimated absolute RMS force accuracy = 0.0319435 - estimated relative force accuracy = 9.61968e-05 - using double precision FFTs - 3d grid and FFT values/proc = 3380 960 -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -WARNING: Compute force/tally only called from pair style (../compute_force_tally.cpp:75) -Neighbor list info ... - 2 neighbor list requests - update every 1 steps, delay 10 steps, check yes - master list distance cutoff = 14 - ghost atom cutoff = 14 - binsize = 7 -> bins = 6 6 6 -Memory usage per processor = 8.16441 Mbytes -Step fpa for c1 fpa[1] one[1] fpa[2] one[2] fpa[3] one[3] ref c2 - 0 22.732789 22.732789 22.732789 -17.068392 -17.068392 -8.8345214 -8.8345214 -12.140878 -12.140878 0 0 - 10 11.736915 11.736915 11.736915 -3.3898298 -3.3898298 9.119272 9.119272 -6.5652948 -6.5652948 0 0 - 20 5.6119761 5.6119761 5.6119761 -0.60028931 -0.60028931 -4.4479886 -4.4479886 3.368876 3.368876 0 0 - 30 17.292617 17.292617 17.292617 6.1793856 6.1793856 -10.593927 -10.593927 12.190919 12.190919 0 0 - 40 18.664226 18.664226 18.664226 5.4725079 5.4725079 -6.933046 -6.933046 16.441955 16.441955 0 0 - 50 12.130282 12.130282 12.130282 -1.0321244 -1.0321244 8.0032646 8.0032646 -9.0568326 -9.0568326 0 0 - -Loop time of 1.13658 on 4 procs for 50 steps with 4500 atoms -100.0% CPU use with 4 MPI tasks x 1 OpenMP threads -Performance: 7.602 ns/day 3.157 hours/ns 43.991 timesteps/s - -MPI task timings breakdown: -Section | min time | avg time | max time |%varavg| %total ---------------------------------------------------------------- -Pair | 0.85795 | 0.89088 | 0.93636 | 3.0 | 78.38 -Bond | 3.4571e-05 | 4.4644e-05 | 5.4598e-05 | 0.1 | 0.00 -Kspace | 0.059847 | 0.1051 | 0.1384 | 8.9 | 9.25 -Neigh | 0.085891 | 0.085954 | 0.086 | 0.0 | 7.56 -Comm | 0.01758 | 0.018091 | 0.019178 | 0.5 | 1.59 -Output | 0.013697 | 0.013725 | 0.013805 | 0.0 | 1.21 -Modify | 0.021068 | 0.021137 | 0.021205 | 0.0 | 1.86 -Other | | 0.001656 | | | 0.15 - -Nlocal: 1125 ave 1148 max 1097 min -Histogram: 1 0 0 1 0 0 0 0 1 1 -Nghost: 12212.5 ave 12269 max 12162 min -Histogram: 1 0 0 1 0 1 0 0 0 1 -Neighs: 650496 ave 675112 max 631353 min -Histogram: 1 0 0 1 1 0 0 0 0 1 - -Total # of neighbors = 2601984 -Ave neighs/atom = 578.219 -Ave special neighs/atom = 2 -Neighbor list builds = 4 -Dangerous builds = 1 - -Total wall time: 0:00:01 diff --git a/examples/balance/in.balance.bond.fast b/examples/balance/in.balance.bond.fast index d2cecd2bfc..3bfcea033e 100644 --- a/examples/balance/in.balance.bond.fast +++ b/examples/balance/in.balance.bond.fast @@ -32,7 +32,7 @@ bond_coeff 1 10.0 1.2 # need to preserve 1-3, 1-4 pairwise interactions during hard collisions special_bonds lj/coul 0 1 1 -create_bonds all all 1 1.0 1.5 +create_bonds many all all 1 1.0 1.5 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes diff --git a/examples/balance/in.balance.bond.slow b/examples/balance/in.balance.bond.slow index fdf0ea6c48..68b1110c3d 100644 --- a/examples/balance/in.balance.bond.slow +++ b/examples/balance/in.balance.bond.slow @@ -32,7 +32,7 @@ pair_coeff 1 1 10.0 1.0 2.5 bond_style harmonic bond_coeff 1 10.0 1.2 -create_bonds all all 1 1.0 1.5 +create_bonds many all all 1 1.0 1.5 neighbor 0.3 bin neigh_modify delay 0 every 1 check yes diff --git a/examples/meam/in.meamc b/examples/meam/in.meamc new file mode 100644 index 0000000000..f6815cd7d4 --- /dev/null +++ b/examples/meam/in.meamc @@ -0,0 +1,30 @@ +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.meam + +pair_style meam/c +pair_coeff * * library.meam Si C SiC.meam Si C + +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element & +# axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 diff --git a/examples/meam/in.meamc.shear b/examples/meam/in.meamc.shear new file mode 100644 index 0000000000..e4584d9744 --- /dev/null +++ b/examples/meam/in.meamc.shear @@ -0,0 +1,79 @@ +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 & + origin 0.5 0 0 +create_atoms 1 box + +pair_style meam/c +pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +group upper region upper +group boundary union lower upper +group mobile subtract all boundary + +set group lower type 2 +set group upper type 3 + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d + +timestep 0.001 +run 100 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +#dump 1 all atom 500 dump.meam.shear + +#dump 2 all image 100 image.*.jpg type type & +# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 2 pad 4 + +#dump 3 all movie 100 movie.mpg type type & +# axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 3 pad 4 + +thermo 100 +thermo_modify temp new2d + +reset_timestep 0 +run 3000 diff --git a/examples/meam/log.5Oct16.meam.icc.1 b/examples/meam/log.19May17.meam.g++.1 similarity index 68% rename from examples/meam/log.5Oct16.meam.icc.1 rename to examples/meam/log.19May17.meam.g++.1 index 200da68e06..a98de97f8e 100644 --- a/examples/meam/log.5Oct16.meam.icc.1 +++ b/examples/meam/log.19May17.meam.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal @@ -34,13 +35,23 @@ timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.39054 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 @@ -53,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 2126.0903 -671.43755 0 -636.53557 -97475.831 90 2065.755 -670.4349 0 -636.52338 -95858.837 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.094512 on 1 procs for 100 steps with 128 atoms +Loop time of 0.0864418 on 1 procs for 100 steps with 128 atoms -Performance: 91.417 ns/day, 0.263 hours/ns, 1058.067 timesteps/s -99.4% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 99.952 ns/day, 0.240 hours/ns, 1156.848 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.091268 | 0.091268 | 0.091268 | 0.0 | 96.57 -Neigh | 0.0021861 | 0.0021861 | 0.0021861 | 0.0 | 2.31 -Comm | 0.00059438 | 0.00059438 | 0.00059438 | 0.0 | 0.63 -Output | 9.0837e-05 | 9.0837e-05 | 9.0837e-05 | 0.0 | 0.10 -Modify | 0.00024438 | 0.00024438 | 0.00024438 | 0.0 | 0.26 -Other | | 0.000128 | | | 0.14 +Pair | 0.082592 | 0.082592 | 0.082592 | 0.0 | 95.55 +Neigh | 0.0028124 | 0.0028124 | 0.0028124 | 0.0 | 3.25 +Comm | 0.00049043 | 0.00049043 | 0.00049043 | 0.0 | 0.57 +Output | 0.00014329 | 0.00014329 | 0.00014329 | 0.0 | 0.17 +Modify | 0.00025415 | 0.00025415 | 0.00025415 | 0.0 | 0.29 +Other | | 0.0001497 | | | 0.17 Nlocal: 128 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 diff --git a/examples/meam/log.5Oct16.meam.icc.4 b/examples/meam/log.19May17.meam.g++.4 similarity index 68% rename from examples/meam/log.5Oct16.meam.icc.4 rename to examples/meam/log.19May17.meam.g++.4 index 51a6619e3b..adc34d08aa 100644 --- a/examples/meam/log.5Oct16.meam.icc.4 +++ b/examples/meam/log.19May17.meam.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # Test of MEAM potential for SiC system units metal @@ -34,13 +35,23 @@ timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 6 6 6 -Memory usage per processor = 7.319 Mbytes + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -636.38121 0 -636.38121 -76571.819 10 1807.8862 -666.21959 0 -636.54126 -150571.49 @@ -53,20 +64,20 @@ Step Temp E_pair E_mol TotEng Press 80 2126.0903 -671.43755 0 -636.53557 -97475.831 90 2065.755 -670.4349 0 -636.52338 -95858.837 100 2051.4553 -670.20799 0 -636.53122 -107068.9 -Loop time of 0.0350628 on 4 procs for 100 steps with 128 atoms +Loop time of 0.0389078 on 4 procs for 100 steps with 128 atoms -Performance: 246.415 ns/day, 0.097 hours/ns, 2852.026 timesteps/s -98.4% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 222.063 ns/day, 0.108 hours/ns, 2570.177 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.030952 | 0.031776 | 0.032203 | 0.3 | 90.63 -Neigh | 0.00058937 | 0.00061423 | 0.00063896 | 0.1 | 1.75 -Comm | 0.0018125 | 0.0022421 | 0.0030777 | 1.1 | 6.39 -Output | 0.00018525 | 0.00019765 | 0.00021911 | 0.1 | 0.56 -Modify | 8.0585e-05 | 9.0539e-05 | 9.7752e-05 | 0.1 | 0.26 -Other | | 0.0001422 | | | 0.41 +Pair | 0.031958 | 0.033267 | 0.034691 | 0.6 | 85.50 +Neigh | 0.00079155 | 0.00086409 | 0.00098801 | 0.0 | 2.22 +Comm | 0.0025704 | 0.0041765 | 0.005573 | 1.9 | 10.73 +Output | 0.0002749 | 0.00029588 | 0.00033569 | 0.0 | 0.76 +Modify | 9.4891e-05 | 0.00010347 | 0.00011587 | 0.0 | 0.27 +Other | | 0.000201 | | | 0.52 Nlocal: 32 ave 36 max 30 min Histogram: 1 2 0 0 0 0 0 0 0 1 diff --git a/examples/meam/log.5Oct16.meam.shear.icc.1 b/examples/meam/log.19May17.meam.shear.g++.1 similarity index 55% rename from examples/meam/log.5Oct16.meam.shear.icc.1 rename to examples/meam/log.19May17.meam.shear.g++.1 index 57f48d5ee2..77b9688455 100644 --- a/examples/meam/log.5Oct16.meam.shear.icc.1 +++ b/examples/meam/log.19May17.meam.shear.g++.1 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -62,38 +63,48 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 27 17 5 -Memory usage per processor = 8.55725 Mbytes + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02 50 300 -8149.7654 0 -8096.1353 10633.141 19684.382 75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745 100 300 -8173.6884 0 -8120.0584 5952.521 19886.589 -Loop time of 1.72323 on 1 procs for 100 steps with 1912 atoms +Loop time of 1.58103 on 1 procs for 100 steps with 1912 atoms -Performance: 5.014 ns/day, 4.787 hours/ns, 58.031 timesteps/s -99.8% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 5.465 ns/day, 4.392 hours/ns, 63.250 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 1.7026 | 1.7026 | 1.7026 | 0.0 | 98.80 -Neigh | 0.014496 | 0.014496 | 0.014496 | 0.0 | 0.84 -Comm | 0.0015783 | 0.0015783 | 0.0015783 | 0.0 | 0.09 -Output | 6.0081e-05 | 6.0081e-05 | 6.0081e-05 | 0.0 | 0.00 -Modify | 0.0034628 | 0.0034628 | 0.0034628 | 0.0 | 0.20 -Other | | 0.00101 | | | 0.06 +Pair | 1.5561 | 1.5561 | 1.5561 | 0.0 | 98.42 +Neigh | 0.018544 | 0.018544 | 0.018544 | 0.0 | 1.17 +Comm | 0.0013864 | 0.0013864 | 0.0013864 | 0.0 | 0.09 +Output | 0.00011396 | 0.00011396 | 0.00011396 | 0.0 | 0.01 +Modify | 0.0038245 | 0.0038245 | 0.0038245 | 0.0 | 0.24 +Other | | 0.001096 | | | 0.07 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 @@ -128,11 +139,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) reset_timestep 0 run 3000 -Memory usage per processor = 8.73384 Mbytes +Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300.39988 -8173.6884 0 -8137.8874 4992.9811 19894.297 100 292.06374 -8177.7096 0 -8142.9021 2568.3762 19871.53 @@ -144,53 +155,53 @@ Step Temp E_pair E_mol TotEng Press Volume 700 300 -8148.1328 0 -8112.3794 3506.9234 20435.302 800 300 -8139.1821 0 -8103.4288 3628.3957 20509.519 900 305.03425 -8126.7734 0 -8090.4201 5316.2206 20638.992 - 1000 304.00321 -8112.1616 0 -8075.9311 7441.9639 20767.243 - 1100 304.14051 -8096.5041 0 -8060.2573 9646.698 20888.167 - 1200 302.78461 -8080.5931 0 -8044.5079 11516.21 20995.917 - 1300 308.67046 -8061.6724 0 -8024.8857 11496.487 21130.013 - 1400 309.83019 -8046.2701 0 -8009.3452 12926.847 21247.271 - 1500 300 -8035.0322 0 -7999.2789 15346.188 21370.637 - 1600 300 -8030.6678 0 -7994.9144 14802.342 21496.446 - 1700 300 -8024.5988 0 -7988.8454 13177.445 21611.262 - 1800 300 -8023.045 0 -7987.2916 10240.041 21740.735 - 1900 300 -8028.2797 0 -7992.5263 6912.1441 21866.544 - 2000 300 -8036.4487 0 -8000.6953 3561.8365 21977.695 - 2100 300 -8037.8249 0 -8002.0715 2879.2618 22109.611 - 2200 300 -8033.6682 0 -7997.9148 4936.3695 22224.427 - 2300 304.49349 -8033.4561 0 -7997.1673 5593.0915 22356.343 - 2400 300 -8033.2969 0 -7997.5436 7537.0891 22473.601 - 2500 300 -8033.1874 0 -7997.4341 11476.447 22598.189 - 2600 307.77395 -8026.9234 0 -7990.2436 15758.81 22720.333 - 2700 300 -8021.1736 0 -7985.4203 17948.896 22832.706 - 2800 300 -8017.0863 0 -7981.3329 17154.618 22957.293 - 2900 300 -8012.0514 0 -7976.298 13224.292 23089.209 - 3000 304.58031 -8008.1654 0 -7971.8661 8572.9227 23211.354 -Loop time of 55.136 on 1 procs for 3000 steps with 1912 atoms + 1000 304.00321 -8112.1616 0 -8075.9311 7441.9638 20767.243 + 1100 304.14047 -8096.5041 0 -8060.2573 9646.6976 20888.167 + 1200 302.78457 -8080.5931 0 -8044.5079 11516.209 20995.917 + 1300 308.67054 -8061.6724 0 -8024.8857 11496.479 21130.013 + 1400 309.8301 -8046.27 0 -8009.3452 12926.835 21247.271 + 1500 300 -8035.0321 0 -7999.2788 15346.455 21370.637 + 1600 300 -8030.6657 0 -7994.9123 14802.869 21496.446 + 1700 300 -8024.5251 0 -7988.7718 13176.923 21611.262 + 1800 300 -8022.9963 0 -7987.243 10260.665 21741.956 + 1900 300 -8028.0522 0 -7992.2988 6955.1367 21867.765 + 2000 300 -8037.2708 0 -8001.5175 3520.3749 21987.467 + 2100 300 -8035.9945 0 -8000.2412 3237.6121 22109.611 + 2200 300 -8036.1882 0 -8000.4348 4295.1386 22223.205 + 2300 300 -8032.7689 0 -7997.0155 6231.2346 22355.121 + 2400 300 -8034.6621 0 -7998.9088 8585.3799 22468.716 + 2500 300 -8031.7774 0 -7996.0241 11627.871 22587.196 + 2600 300 -8024.032 0 -7988.2786 16254.69 22716.669 + 2700 308.64215 -8017.407 0 -7980.6237 18440.226 22835.149 + 2800 300 -8015.7348 0 -7979.9814 17601.716 22957.293 + 2900 305.82558 -8013.7448 0 -7977.2972 14123.494 23089.209 + 3000 300 -8011.0289 0 -7975.2755 9957.2884 23205.247 +Loop time of 51.9315 on 1 procs for 3000 steps with 1912 atoms -Performance: 4.701 ns/day, 5.105 hours/ns, 54.411 timesteps/s -99.9% CPU use with 1 MPI tasks x no OpenMP threads +Performance: 4.991 ns/day, 4.808 hours/ns, 57.768 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 54.317 | 54.317 | 54.317 | -nan | 98.51 -Neigh | 0.63189 | 0.63189 | 0.63189 | 0.0 | 1.15 -Comm | 0.051245 | 0.051245 | 0.051245 | 0.0 | 0.09 -Output | 0.0005548 | 0.0005548 | 0.0005548 | 0.0 | 0.00 -Modify | 0.10452 | 0.10452 | 0.10452 | 0.0 | 0.19 -Other | | 0.03128 | | | 0.06 +Pair | 50.918 | 50.918 | 50.918 | 0.0 | 98.05 +Neigh | 0.81033 | 0.81033 | 0.81033 | 0.0 | 1.56 +Comm | 0.047331 | 0.047331 | 0.047331 | 0.0 | 0.09 +Output | 0.0011976 | 0.0011976 | 0.0011976 | 0.0 | 0.00 +Modify | 0.11889 | 0.11889 | 0.11889 | 0.0 | 0.23 +Other | | 0.03606 | | | 0.07 Nlocal: 1912 ave 1912 max 1912 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Nghost: 1667 ave 1667 max 1667 min +Nghost: 1672 ave 1672 max 1672 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Neighs: 23365 ave 23365 max 23365 min +Neighs: 23557 ave 23557 max 23557 min Histogram: 1 0 0 0 0 0 0 0 0 0 -FullNghs: 46730 ave 46730 max 46730 min +FullNghs: 47114 ave 47114 max 47114 min Histogram: 1 0 0 0 0 0 0 0 0 0 -Total # of neighbors = 46730 -Ave neighs/atom = 24.4404 +Total # of neighbors = 47114 +Ave neighs/atom = 24.6412 Neighbor list builds = 221 Dangerous builds = 0 -Total wall time: 0:00:56 +Total wall time: 0:00:53 diff --git a/examples/meam/log.5Oct16.meam.shear.icc.4 b/examples/meam/log.19May17.meam.shear.g++.4 similarity index 55% rename from examples/meam/log.5Oct16.meam.shear.icc.4 rename to examples/meam/log.19May17.meam.shear.g++.4 index 2f197de920..84cb94f4b9 100644 --- a/examples/meam/log.5Oct16.meam.shear.icc.4 +++ b/examples/meam/log.19May17.meam.shear.g++.4 @@ -1,4 +1,5 @@ -LAMMPS (5 Oct 2016) +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task # 3d metal shear simulation units metal @@ -62,38 +63,48 @@ fix_modify 3 temp new3d thermo 25 thermo_modify temp new3d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) timestep 0.001 run 100 Neighbor list info ... - 2 neighbor list requests update every 1 steps, delay 5 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 4.3 ghost atom cutoff = 4.3 - binsize = 2.15 -> bins = 27 17 5 -Memory usage per processor = 7.74146 Mbytes + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02 50 300 -8150.0685 0 -8096.4384 10317.407 19685.743 75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814 100 300 -8176.5141 0 -8122.884 4162.2559 19873.327 -Loop time of 0.469502 on 4 procs for 100 steps with 1912 atoms +Loop time of 0.482293 on 4 procs for 100 steps with 1912 atoms -Performance: 18.402 ns/day, 1.304 hours/ns, 212.992 timesteps/s -99.7% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 17.914 ns/day, 1.340 hours/ns, 207.343 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 0.44052 | 0.45213 | 0.45813 | 1.0 | 96.30 -Neigh | 0.0036478 | 0.0037832 | 0.003854 | 0.1 | 0.81 -Comm | 0.0055377 | 0.011533 | 0.02316 | 6.5 | 2.46 -Output | 9.0837e-05 | 9.8228e-05 | 0.00011325 | 0.1 | 0.02 -Modify | 0.00098062 | 0.0010158 | 0.0010564 | 0.1 | 0.22 -Other | | 0.0009408 | | | 0.20 +Pair | 0.44374 | 0.45604 | 0.46922 | 1.4 | 94.56 +Neigh | 0.0047338 | 0.0049097 | 0.0051899 | 0.2 | 1.02 +Comm | 0.0054841 | 0.019044 | 0.031472 | 6.9 | 3.95 +Output | 0.00012755 | 0.00013644 | 0.00015831 | 0.0 | 0.03 +Modify | 0.0011139 | 0.0011852 | 0.0012643 | 0.2 | 0.25 +Other | | 0.0009753 | | | 0.20 Nlocal: 478 ave 492 max 465 min Histogram: 2 0 0 0 0 0 0 0 1 1 @@ -128,11 +139,11 @@ fix_modify 3 temp new2d thermo 100 thermo_modify temp new2d -WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:474) +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) reset_timestep 0 run 3000 -Memory usage per processor = 7.78572 Mbytes +Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 295.32113 -8176.5141 0 -8141.3183 3169.3113 19886.93 100 292.00251 -8176.5358 0 -8141.7356 -825.04802 19918.765 @@ -144,53 +155,53 @@ Step Temp E_pair E_mol TotEng Press Volume 700 296.44479 -8149.7914 0 -8114.4618 1985.4155 20421.046 800 307.75738 -8139.1649 0 -8102.487 4319.078 20513.183 900 304.61422 -8126.9246 0 -8090.6214 6654.0963 20640.213 - 1000 300 -8113.8464 0 -8078.0931 7760.1242 20768.465 - 1100 300.17874 -8097.7469 0 -8061.9722 8438.1263 20874.731 - 1200 306.01444 -8083.3367 0 -8046.8665 10835.585 20994.432 + 1000 300 -8113.8464 0 -8078.0931 7760.1239 20768.465 + 1100 300.17873 -8097.7469 0 -8061.9722 8438.126 20874.731 + 1200 306.01441 -8083.3367 0 -8046.8665 10835.586 20994.432 1300 300 -8067.022 0 -8031.2686 11216.067 21126.348 - 1400 300 -8053.223 0 -8017.4697 10570.21 21253.378 - 1500 300 -8043.4848 0 -8007.7314 11360.829 21375.523 - 1600 300 -8034.6216 0 -7998.8683 11371.642 21498.889 - 1700 300 -8028.6774 0 -7992.924 9595.8772 21613.705 - 1800 300 -8033.0808 0 -7997.3274 8767.6261 21743.178 - 1900 303.30302 -8035.1958 0 -7999.0488 8059.5152 21859.215 - 2000 300 -8025.0857 0 -7989.3323 9308.9938 21980.138 - 2100 300 -8041.5796 0 -8005.8263 6656.0066 22108.39 - 2200 300 -8039.6315 0 -8003.8781 7532.9687 22226.87 - 2300 300 -8053.203 0 -8017.4497 8466.9094 22356.343 - 2400 300 -8050.9154 0 -8015.162 11784.136 22467.494 - 2500 300 -8037.6394 0 -8001.886 16464.786 22588.417 - 2600 300 -8030.9221 0 -7995.1688 16807.326 22719.112 - 2700 300 -8025.2102 0 -7989.4569 13729.61 22837.592 - 2800 300 -8014.5312 0 -7978.7779 6784.6283 22953.629 - 2900 300 -8007.4768 0 -7971.7234 1362.3131 23084.324 - 3000 300 -7994.5614 0 -7958.808 -1726.5273 23194.254 -Loop time of 14.8108 on 4 procs for 3000 steps with 1912 atoms + 1400 300 -8053.223 0 -8017.4697 10570.206 21253.378 + 1500 300 -8043.4849 0 -8007.7315 11360.766 21375.523 + 1600 300 -8034.621 0 -7998.8676 11371.584 21498.889 + 1700 300 -8028.6783 0 -7992.925 9596.524 21613.705 + 1800 300 -8033.0818 0 -7997.3285 8767.2651 21743.178 + 1900 303.18912 -8035.194 0 -7999.0606 8059.9558 21859.215 + 2000 300 -8025.0327 0 -7989.2794 9305.7521 21980.138 + 2100 300 -8041.4626 0 -8005.7092 6623.8789 22108.39 + 2200 300 -8040.3133 0 -8004.5599 7512.9368 22225.648 + 2300 300 -8055.6567 0 -8019.9033 8281.354 22344.128 + 2400 304.05922 -8050.289 0 -8014.0518 11964.826 22476.044 + 2500 305.75646 -8037.0481 0 -8000.6087 16594.032 22595.746 + 2600 307.71105 -8031.2253 0 -7994.5529 18381.745 22708.119 + 2700 307.397 -8026.5338 0 -7989.8988 13944.653 22829.042 + 2800 309.3455 -8020.2305 0 -7983.3634 7037.4046 22954.851 + 2900 301.2859 -8010.4731 0 -7974.5665 3843.8972 23072.109 + 3000 303.29908 -8000.0395 0 -7963.8929 364.90172 23207.69 +Loop time of 14.5278 on 4 procs for 3000 steps with 1912 atoms -Performance: 17.501 ns/day, 1.371 hours/ns, 202.555 timesteps/s -99.8% CPU use with 4 MPI tasks x no OpenMP threads +Performance: 17.842 ns/day, 1.345 hours/ns, 206.500 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- -Pair | 14.05 | 14.237 | 14.332 | 2.9 | 96.12 -Neigh | 0.1592 | 0.16414 | 0.1671 | 0.8 | 1.11 -Comm | 0.26002 | 0.35589 | 0.54696 | 18.8 | 2.40 -Output | 0.00061679 | 0.00065172 | 0.0007441 | 0.2 | 0.00 -Modify | 0.02895 | 0.030174 | 0.03104 | 0.5 | 0.20 -Other | | 0.02338 | | | 0.16 +Pair | 13.872 | 13.929 | 13.998 | 1.4 | 95.88 +Neigh | 0.20891 | 0.21114 | 0.21272 | 0.3 | 1.45 +Comm | 0.25364 | 0.32377 | 0.37706 | 8.9 | 2.23 +Output | 0.0011427 | 0.0012097 | 0.0013931 | 0.3 | 0.01 +Modify | 0.033687 | 0.033991 | 0.034694 | 0.2 | 0.23 +Other | | 0.02871 | | | 0.20 -Nlocal: 478 ave 509 max 448 min -Histogram: 2 0 0 0 0 0 0 0 0 2 -Nghost: 799.25 ave 844 max 756 min -Histogram: 1 1 0 0 0 0 0 1 0 1 -Neighs: 5813.25 ave 6081 max 5602 min -Histogram: 2 0 0 0 0 0 1 0 0 1 -FullNghs: 11626.5 ave 12151 max 11205 min -Histogram: 1 1 0 0 0 0 1 0 0 1 +Nlocal: 478 ave 509 max 445 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Nghost: 804 ave 845 max 759 min +Histogram: 1 1 0 0 0 0 0 0 1 1 +Neighs: 5827 ave 6177 max 5496 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +FullNghs: 11654 ave 12330 max 11039 min +Histogram: 1 0 0 1 0 1 0 0 0 1 -Total # of neighbors = 46506 -Ave neighs/atom = 24.3232 -Neighbor list builds = 225 +Total # of neighbors = 46616 +Ave neighs/atom = 24.3808 +Neighbor list builds = 223 Dangerous builds = 0 Total wall time: 0:00:15 diff --git a/examples/meam/log.19May17.meamc.g++.1 b/examples/meam/log.19May17.meamc.g++.1 new file mode 100644 index 0000000000..4aa1f7bcc3 --- /dev/null +++ b/examples/meam/log.19May17.meamc.g++.1 @@ -0,0 +1,95 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.meam + orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 128 atoms + +pair_style meam/c +pair_coeff * * library.meam Si C SiC.meam Si C +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file SiC.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.103 | 8.103 | 8.103 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -636.38121 0 -636.38121 -76571.819 + 10 1807.8862 -666.21959 0 -636.54126 -150571.49 + 20 1932.4467 -668.2581 0 -636.53498 -120223.52 + 30 1951.3652 -668.58139 0 -636.54771 -100508.4 + 40 2172.5974 -672.22715 0 -636.5617 -110753.34 + 50 2056.9149 -670.33108 0 -636.56468 -105418.07 + 60 1947.9564 -668.52788 0 -636.55015 -111413.04 + 70 1994.7712 -669.28849 0 -636.54225 -109645.76 + 80 2126.0903 -671.43755 0 -636.53557 -97475.832 + 90 2065.7549 -670.4349 0 -636.52338 -95858.836 + 100 2051.4553 -670.20799 0 -636.53122 -107068.89 +Loop time of 0.0778153 on 1 procs for 100 steps with 128 atoms + +Performance: 111.032 ns/day, 0.216 hours/ns, 1285.094 timesteps/s +99.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.073801 | 0.073801 | 0.073801 | 0.0 | 94.84 +Neigh | 0.0029731 | 0.0029731 | 0.0029731 | 0.0 | 3.82 +Comm | 0.00047708 | 0.00047708 | 0.00047708 | 0.0 | 0.61 +Output | 0.00015664 | 0.00015664 | 0.00015664 | 0.0 | 0.20 +Modify | 0.00025702 | 0.00025702 | 0.00025702 | 0.0 | 0.33 +Other | | 0.0001504 | | | 0.19 + +Nlocal: 128 ave 128 max 128 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 543 ave 543 max 543 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 1526 ave 1526 max 1526 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 3052 ave 3052 max 3052 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 3052 +Ave neighs/atom = 23.8438 +Neighbor list builds = 10 +Dangerous builds = 10 +Total wall time: 0:00:00 diff --git a/examples/meam/log.19May17.meamc.g++.4 b/examples/meam/log.19May17.meamc.g++.4 new file mode 100644 index 0000000000..3701fb80d8 --- /dev/null +++ b/examples/meam/log.19May17.meamc.g++.4 @@ -0,0 +1,95 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# Test of MEAM potential for SiC system + +units metal +boundary p p p + +atom_style atomic + +read_data data.meam + orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 128 atoms + +pair_style meam/c +pair_coeff * * library.meam Si C SiC.meam Si C +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file SiC.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 10 + +fix 1 all nve +thermo 10 +timestep 0.001 + +#dump 1 all atom 50 dump.meam + +#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 2 pad 3 element Si C + +#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30 +#dump_modify 3 pad 3 element Si C + +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.024 | 8.026 | 8.027 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -636.38121 0 -636.38121 -76571.819 + 10 1807.8862 -666.21959 0 -636.54126 -150571.49 + 20 1932.4467 -668.2581 0 -636.53498 -120223.52 + 30 1951.3652 -668.58139 0 -636.54771 -100508.4 + 40 2172.5974 -672.22715 0 -636.5617 -110753.34 + 50 2056.9149 -670.33108 0 -636.56468 -105418.07 + 60 1947.9564 -668.52788 0 -636.55015 -111413.04 + 70 1994.7712 -669.28849 0 -636.54225 -109645.76 + 80 2126.0903 -671.43755 0 -636.53557 -97475.832 + 90 2065.7549 -670.4349 0 -636.52338 -95858.836 + 100 2051.4553 -670.20799 0 -636.53122 -107068.89 +Loop time of 0.037066 on 4 procs for 100 steps with 128 atoms + +Performance: 233.097 ns/day, 0.103 hours/ns, 2697.887 timesteps/s +97.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.029985 | 0.031596 | 0.033021 | 0.8 | 85.24 +Neigh | 0.0007906 | 0.00085384 | 0.00088596 | 0.0 | 2.30 +Comm | 0.0025654 | 0.0040313 | 0.0057514 | 2.2 | 10.88 +Output | 0.00027013 | 0.00029153 | 0.00033426 | 0.0 | 0.79 +Modify | 9.5367e-05 | 0.00010639 | 0.00012016 | 0.0 | 0.29 +Other | | 0.0001866 | | | 0.50 + +Nlocal: 32 ave 36 max 30 min +Histogram: 1 2 0 0 0 0 0 0 0 1 +Nghost: 293.75 ave 305 max 285 min +Histogram: 2 0 0 0 0 0 0 1 0 1 +Neighs: 381.5 ave 413 max 334 min +Histogram: 1 0 0 0 1 0 0 0 0 2 +FullNghs: 763 ave 866 max 678 min +Histogram: 1 0 1 0 0 1 0 0 0 1 + +Total # of neighbors = 3052 +Ave neighs/atom = 23.8438 +Neighbor list builds = 10 +Dangerous builds = 10 +Total wall time: 0:00:00 diff --git a/examples/meam/log.19May17.meamc.shear.g++.1 b/examples/meam/log.19May17.meamc.shear.g++.1 new file mode 100644 index 0000000000..5eb06592d8 --- /dev/null +++ b/examples/meam/log.19May17.meamc.shear.g++.1 @@ -0,0 +1,207 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) + 1 by 1 by 1 MPI processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 box +Created 1912 atoms + +pair_style meam/c +pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file Ni.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set group lower type 2 + 264 settings made for type +set group upper type 3 + 264 settings made for type + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +timestep 0.001 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 9.788 | 9.788 | 9.788 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 + 25 222.78953 -8188.1215 0 -8148.2941 9095.9003 19547.02 + 50 300 -8149.7654 0 -8096.1353 10633.139 19684.382 + 75 304.80657 -8163.4557 0 -8108.9665 7045.4555 19759.745 + 100 300 -8173.6884 0 -8120.0584 5952.5197 19886.589 +Loop time of 1.46986 on 1 procs for 100 steps with 1912 atoms + +Performance: 5.878 ns/day, 4.083 hours/ns, 68.034 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.445 | 1.445 | 1.445 | 0.0 | 98.31 +Neigh | 0.018564 | 0.018564 | 0.018564 | 0.0 | 1.26 +Comm | 0.0012956 | 0.0012956 | 0.0012956 | 0.0 | 0.09 +Output | 0.00012612 | 0.00012612 | 0.00012612 | 0.0 | 0.01 +Modify | 0.0038197 | 0.0038197 | 0.0038197 | 0.0 | 0.26 +Other | | 0.001095 | | | 0.07 + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1672 ave 1672 max 1672 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23806 ave 23806 max 23806 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 47612 ave 47612 max 47612 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 47612 +Ave neighs/atom = 24.9017 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +#dump 1 all atom 500 dump.meam.shear + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 2 pad 4 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 3 pad 4 + +thermo 100 +thermo_modify temp new2d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +reset_timestep 0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 9.964 | 9.964 | 9.964 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300.39988 -8173.6884 0 -8137.8874 4992.9799 19894.297 + 100 292.06374 -8177.7096 0 -8142.9021 2568.3756 19871.53 + 200 306.69894 -8177.1357 0 -8140.584 874.24118 20047.24 + 300 295.68216 -8172.9213 0 -8137.6825 -1049.0799 20091.759 + 400 308.99955 -8169.6355 0 -8132.8096 -1785.9554 20121.698 + 500 303.85688 -8163.9842 0 -8127.7712 -150.60892 20183.813 + 600 300 -8157.7627 0 -8122.0093 1492.8514 20279.887 + 700 300 -8148.1314 0 -8112.3781 3507.1949 20435.297 + 800 300 -8139.1805 0 -8103.4272 3628.5908 20509.519 + 900 305.03217 -8126.7741 0 -8090.421 5313.7881 20638.992 + 1000 303.7648 -8112.1574 0 -8075.9554 7433.3181 20767.243 + 1100 302.39719 -8096.1399 0 -8060.1009 9681.7685 20888.167 + 1200 304.04919 -8080.7022 0 -8044.4663 11621.974 21011.532 + 1300 303.56395 -8062.0984 0 -8025.9203 11410.793 21125.127 + 1400 309.92338 -8046.0008 0 -8009.0648 12408.158 21246.05 + 1500 300 -8034.7094 0 -7998.956 14845.312 21363.308 + 1600 300 -8028.4585 0 -7992.7051 15120.908 21489.117 + 1700 308.23904 -8015.9618 0 -7979.2265 14714.73 21612.483 + 1800 300 -8013.5458 0 -7977.7924 11955.065 21737.07 + 1900 300 -8012.2984 0 -7976.545 6667.1353 21854.329 + 2000 300 -8025.6019 0 -7989.8485 2006.6545 21981.359 + 2100 300 -8027.6823 0 -7991.9289 16.47633 22109.611 + 2200 300 -8029.6905 0 -7993.9372 -603.98293 22224.427 + 2300 300 -8033.2663 0 -7997.513 -464.68645 22351.457 + 2400 300 -8040.6863 0 -8004.9329 -640.54641 22467.494 + 2500 300 -8037.0332 0 -8001.2799 1504.2444 22587.196 + 2600 300 -8036.0909 0 -8000.3375 4190.2052 22708.119 + 2700 308.97892 -8028.5269 0 -7991.7035 5755.7418 22832.706 + 2800 305.27189 -8023.8286 0 -7987.4469 2611.7551 22962.179 + 2900 301.94251 -8017.4523 0 -7981.4675 358.11928 23078.216 + 3000 305.67682 -8009.853 0 -7973.4231 -2345.487 23197.918 +Loop time of 48.351 on 1 procs for 3000 steps with 1912 atoms + +Performance: 5.361 ns/day, 4.477 hours/ns, 62.046 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 47.356 | 47.356 | 47.356 | 0.0 | 97.94 +Neigh | 0.79977 | 0.79977 | 0.79977 | 0.0 | 1.65 +Comm | 0.043133 | 0.043133 | 0.043133 | 0.0 | 0.09 +Output | 0.0011899 | 0.0011899 | 0.0011899 | 0.0 | 0.00 +Modify | 0.11648 | 0.11648 | 0.11648 | 0.0 | 0.24 +Other | | 0.03404 | | | 0.07 + +Nlocal: 1912 ave 1912 max 1912 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 1662 ave 1662 max 1662 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 23143 ave 23143 max 23143 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +FullNghs: 46286 ave 46286 max 46286 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 46286 +Ave neighs/atom = 24.2082 +Neighbor list builds = 220 +Dangerous builds = 0 +Total wall time: 0:00:49 diff --git a/examples/meam/log.19May17.meamc.shear.g++.4 b/examples/meam/log.19May17.meamc.shear.g++.4 new file mode 100644 index 0000000000..136459a44a --- /dev/null +++ b/examples/meam/log.19May17.meamc.shear.g++.4 @@ -0,0 +1,207 @@ +LAMMPS (19 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d metal shear simulation + +units metal +boundary s s p + +atom_style atomic +lattice fcc 3.52 +Lattice spacing in x,y,z = 3.52 3.52 3.52 +region box block 0 16.0 0 10.0 0 2.828427 +create_box 3 box +Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606) + 2 by 2 by 1 MPI processor grid + +lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0 +Lattice spacing in x,y,z = 3.52 4.97803 4.97803 +create_atoms 1 box +Created 1912 atoms + +pair_style meam/c +pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4 +Reading potential file library.meam with DATE: 2012-06-29 +Reading potential file Ni.meam with DATE: 2007-06-11 + +neighbor 0.3 bin +neigh_modify delay 5 + +region lower block INF INF INF 0.9 INF INF +region upper block INF INF 6.1 INF INF INF +group lower region lower +264 atoms in group lower +group upper region upper +264 atoms in group upper +group boundary union lower upper +528 atoms in group boundary +group mobile subtract all boundary +1384 atoms in group mobile + +set group lower type 2 + 264 settings made for type +set group upper type 3 + 264 settings made for type + +# void + +#region void cylinder z 8 5 2.5 INF INF +#delete_atoms region void + +# temp controllers + +compute new3d mobile temp +compute new2d mobile temp/partial 0 1 1 + +# equilibrate + +velocity mobile create 300.0 5812775 temp new3d +fix 1 all nve +fix 2 boundary setforce 0.0 0.0 0.0 + +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new3d + +thermo 25 +thermo_modify temp new3d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +timestep 0.001 +run 100 +Neighbor list info ... + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 4.3 + ghost atom cutoff = 4.3 + binsize = 2.15, bins = 27 17 5 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair meam/c, perpetual + attributes: full, newton on + pair build: full/bin/atomonly + stencil: full/bin/3d + bin: standard + (2) pair meam/c, perpetual, half/full from (1) + attributes: half, newton on + pair build: halffull/newton + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 8.954 | 8.957 | 8.959 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02 + 25 221.59546 -8187.6813 0 -8148.0673 9100.4505 19547.02 + 50 300 -8150.0685 0 -8096.4384 10317.406 19685.743 + 75 307.76021 -8164.6669 0 -8109.6496 6289.7123 19757.814 + 100 300 -8176.5141 0 -8122.884 4162.2548 19873.327 +Loop time of 0.435874 on 4 procs for 100 steps with 1912 atoms + +Performance: 19.822 ns/day, 1.211 hours/ns, 229.424 timesteps/s +98.8% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.4092 | 0.41563 | 0.42184 | 0.7 | 95.35 +Neigh | 0.0048575 | 0.004932 | 0.0049984 | 0.1 | 1.13 +Comm | 0.0069079 | 0.013151 | 0.019513 | 4.2 | 3.02 +Output | 0.00012398 | 0.00013405 | 0.00015688 | 0.0 | 0.03 +Modify | 0.0011275 | 0.0011509 | 0.0011735 | 0.1 | 0.26 +Other | | 0.0008795 | | | 0.20 + +Nlocal: 478 ave 492 max 465 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Nghost: 809 ave 822 max 795 min +Histogram: 1 1 0 0 0 0 0 0 0 2 +Neighs: 5916 ave 6133 max 5658 min +Histogram: 1 0 0 1 0 0 0 0 1 1 +FullNghs: 11832 ave 12277 max 11299 min +Histogram: 1 0 0 1 0 0 0 0 1 1 + +Total # of neighbors = 47328 +Ave neighs/atom = 24.7531 +Neighbor list builds = 5 +Dangerous builds = 0 + +# shear + +velocity upper set 1.0 0 0 +velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes + +unfix 3 +fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0 +fix_modify 3 temp new2d + +#dump 1 all atom 500 dump.meam.shear + +#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 2 pad 4 + +#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0 +#dump_modify 3 pad 4 + +thermo 100 +thermo_modify temp new2d +WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:489) + +reset_timestep 0 +run 3000 +Per MPI rank memory allocation (min/avg/max) = 8.999 | 9.002 | 9.005 Mbytes +Step Temp E_pair E_mol TotEng Press Volume + 0 295.32113 -8176.5141 0 -8141.3183 3169.3102 19886.93 + 100 292.0025 -8176.5358 0 -8141.7356 -825.04852 19918.765 + 200 306.11682 -8176.7718 0 -8140.2895 -1370.6881 19948.878 + 300 300 -8172.6262 0 -8136.8729 -1735.9794 20085.715 + 400 306.88504 -8168.4351 0 -8131.8612 -933.05532 20117.008 + 500 308.99111 -8166.2909 0 -8129.466 -1049.3442 20198.267 + 600 304.22555 -8158.0946 0 -8121.8377 583.69142 20328.753 + 700 296.41606 -8149.7777 0 -8114.4515 1986.7982 20421.032 + 800 307.88628 -8139.1709 0 -8102.4776 4311.4142 20513.183 + 900 303.37209 -8126.9382 0 -8090.7829 6712.7316 20640.213 + 1000 300 -8113.7973 0 -8078.044 7630.2594 20750.143 + 1100 300.07815 -8098.1383 0 -8062.3756 8423.7063 20879.616 + 1200 300 -8083.3163 0 -8047.563 10772.917 21000.539 + 1300 300 -8066.6741 0 -8030.9208 10834.336 21128.791 + 1400 300 -8050.8799 0 -8015.1265 10842.382 21257.043 + 1500 300 -8040.3206 0 -8004.5673 11852.589 21362.087 + 1600 300 -8033.2471 0 -7997.4937 11298.745 21492.782 + 1700 300 -8030.6375 0 -7994.8842 10850.43 21610.04 + 1800 300 -8035.1631 0 -7999.4097 9985.6107 21734.628 + 1900 308.56562 -8040.1954 0 -8003.4213 9865.7107 21859.215 + 2000 300 -8030.1651 0 -7994.4117 11817.502 21980.138 + 2100 300 -8031.6147 0 -7995.8613 12791.357 22101.061 + 2200 300 -8033.7793 0 -7998.0259 13823.043 22234.198 + 2300 300 -8040.5964 0 -8004.8431 16204.549 22350.236 + 2400 309.42867 -8045.9414 0 -8009.0644 18506.386 22465.051 + 2500 300 -8054.2629 0 -8018.5095 20099.612 22593.303 + 2600 300 -8054.9562 0 -8019.2028 20036.318 22721.555 + 2700 300 -8051.4788 0 -8015.7254 16993.437 22844.921 + 2800 300 -8050.6908 0 -8014.9374 9048.5896 22964.622 + 2900 309.90783 -8044.3096 0 -8007.3754 5017.0198 23080.659 + 3000 300 -8035.8165 0 -8000.0632 2084.8999 23207.69 +Loop time of 13.4901 on 4 procs for 3000 steps with 1912 atoms + +Performance: 19.214 ns/day, 1.249 hours/ns, 222.386 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 12.851 | 12.919 | 12.945 | 1.1 | 95.76 +Neigh | 0.20449 | 0.20777 | 0.21169 | 0.6 | 1.54 +Comm | 0.27479 | 0.30264 | 0.36667 | 6.8 | 2.24 +Output | 0.0010171 | 0.0010971 | 0.0012388 | 0.3 | 0.01 +Modify | 0.033248 | 0.033878 | 0.034567 | 0.3 | 0.25 +Other | | 0.02594 | | | 0.19 + +Nlocal: 478 ave 506 max 450 min +Histogram: 2 0 0 0 0 0 0 0 0 2 +Nghost: 790.5 ave 822 max 751 min +Histogram: 1 0 1 0 0 0 0 0 0 2 +Neighs: 5829.5 ave 6014 max 5672 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +FullNghs: 11659 ave 12027 max 11320 min +Histogram: 2 0 0 0 0 0 0 0 1 1 + +Total # of neighbors = 46636 +Ave neighs/atom = 24.3912 +Neighbor list builds = 220 +Dangerous builds = 0 +Total wall time: 0:00:13 diff --git a/examples/neb/README b/examples/neb/README index 130d0fd2e3..5ef32f2ba6 100644 --- a/examples/neb/README +++ b/examples/neb/README @@ -2,12 +2,16 @@ Run these examples as: mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1 mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop2 +mpirun -np 4 lmp_g++ -partition 4x1 -in in.neb.hop1.end mpirun -np 3 lmp_g++ -partition 3x1 -in in.neb.sivac mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1 mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop2 -mpirun -np 6 lmp_g++ -partition 3x2 -in in.neb.sivac -mpirun -np 9 lmp_g++ -partition 3x3 -in in.neb.sivac +mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.hop1.end +mpirun -np 8 lmp_g++ -partition 4x2 -in in.neb.sivac + +Note that more than 4 replicas should be used for a precise estimate +of the activation energy corresponding to a transition. If you uncomment the dump command lines in the input scripts, you can create dump files to do visualization from via Python tools: (see diff --git a/examples/neb/in.neb.hop1 b/examples/neb/in.neb.hop1 index 9a3d7579f3..f26b52a28a 100644 --- a/examples/neb/in.neb.hop1 +++ b/examples/neb/in.neb.hop1 @@ -51,7 +51,7 @@ set group nebatoms type 3 group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 +fix 2 nebatoms neb 1.0 parallel ideal fix 3 all enforce2d thermo 100 diff --git a/examples/neb/in.neb.hop1.end b/examples/neb/in.neb.hop1.end new file mode 100644 index 0000000000..81e5315306 --- /dev/null +++ b/examples/neb/in.neb.hop1.end @@ -0,0 +1,56 @@ +# 2d NEB surface simulation, hop from surface to become adatom + +dimension 2 +boundary p s p + +atom_style atomic +neighbor 0.3 bin +neigh_modify delay 5 +atom_modify map array sort 0 0.0 + +variable u uloop 20 + +# create geometry with flat surface + +lattice hex 0.9 +region box block 0 20 0 10 -0.25 0.25 + +read_data initial.hop1.end + +# LJ potentials + +pair_style lj/cut 2.5 +pair_coeff * * 1.0 1.0 2.5 +pair_modify shift yes + +# define groups + +region 1 block INF INF INF 1.25 INF INF +group lower region 1 +group mobile subtract all lower +set group lower type 2 + +timestep 0.05 + +# group of NEB atoms - either block or single atom ID 412 + +region surround block 10 18 17 20 0 0 units box +group nebatoms region surround +#group nebatoms id 412 +set group nebatoms type 3 +group nonneb subtract all nebatoms + +fix 1 lower setforce 0.0 0.0 0.0 +fix 2 nebatoms neb 1.0 parallel ideal end first 1.0 +fix 3 all enforce2d + +thermo 100 + +#dump 1 nebatoms atom 10 dump.neb.$u +#dump 2 nonneb atom 10 dump.nonneb.$u + +# run NEB for 2000 steps or to force tolerance + +min_style quickmin + +neb 0.0 0.1 1000 1000 100 final final.hop1 diff --git a/examples/neb/in.neb.hop2 b/examples/neb/in.neb.hop2 index 3eb16248e1..e69fb338cd 100644 --- a/examples/neb/in.neb.hop2 +++ b/examples/neb/in.neb.hop2 @@ -53,7 +53,7 @@ set group nebatoms type 3 group nonneb subtract all nebatoms fix 1 lower setforce 0.0 0.0 0.0 -fix 2 nebatoms neb 1.0 +fix 2 nebatoms neb 1.0 fix 3 all enforce2d thermo 100 @@ -65,4 +65,4 @@ thermo 100 min_style fire -neb 0.0 0.01 1000 1000 100 final final.hop2 +neb 0.0 0.05 1000 1000 100 final final.hop2 diff --git a/examples/neb/in.neb.sivac b/examples/neb/in.neb.sivac index 566a380627..941d063b90 100644 --- a/examples/neb/in.neb.sivac +++ b/examples/neb/in.neb.sivac @@ -66,7 +66,7 @@ minimize 1.0e-6 1.0e-4 1000 10000 reset_timestep 0 -fix 1 all neb 1.0 +fix 1 all neb 1.0 thermo 100 diff --git a/examples/neb/initial.hop1.end b/examples/neb/initial.hop1.end new file mode 100644 index 0000000000..0357431fda --- /dev/null +++ b/examples/neb/initial.hop1.end @@ -0,0 +1,860 @@ +LAMMPS data file via write_data, version 4 May 2017, timestep = 155 + +420 atoms +3 atom types + +0.0000000000000000e+00 2.2653923264628304e+01 xlo xhi 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8.4550353671555104e-05 0.0000000000000000e+00 +418 2.2486305540664193e-04 4.3653832482456800e-05 0.0000000000000000e+00 +419 2.2188236489361566e-04 7.6524745655054321e-06 0.0000000000000000e+00 +420 2.0949238720629205e-04 -1.7218568434280989e-05 0.0000000000000000e+00 diff --git a/examples/neb/log.19Jun17.neb.hop1.end.g++.4 b/examples/neb/log.19Jun17.neb.hop1.end.g++.4 new file mode 100644 index 0000000000..4878b86566 --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop1.end.g++.4 @@ -0,0 +1,11 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 +100 0.11027532 0.085410308 3.0967938 0.024201563 0.38551033 0.0017583261 0.0021866943 1.7710358 0 -3.0483469 0.31192818 -3.0465886 0.61093022 -3.0466143 1 -3.0487752 +130 0.09954083 0.075481108 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 +Climbing replica = 2 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +130 0.37838747 0.3502435 3.0927626 0.015664388 0.37491833 0.0017573704 0.0021913201 1.7713726 0 -3.048342 0.31428487 -3.0465846 0.61762817 -3.0466296 1 -3.048776 +230 0.22757286 0.12027481 3.1250243 0.0081260569 0.14019507 0.0018364585 0.002278918 1.76926 0 -3.0483347 0.39730698 -3.0464983 0.64450769 -3.0466973 1 -3.0487772 +278 0.096184498 0.085088496 3.1405655 0.0068164307 0.093861113 0.0018426056 0.002286256 1.7684765 0 -3.0483338 0.41277997 -3.0464912 0.65562984 -3.0467294 1 -3.0487775 diff --git a/examples/neb/log.19Jun17.neb.hop1.end.g++.8 b/examples/neb/log.19Jun17.neb.hop1.end.g++.8 new file mode 100644 index 0000000000..62344b3da5 --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop1.end.g++.8 @@ -0,0 +1,11 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 229.26196 146.68251 2.9774577 4.4127369 233.11559 0.023301843 0.0224626 1.4763579 0 -3.048332 0.33333333 -3.0250302 0.66666667 -3.0291888 1 -3.0474928 +100 0.11375359 0.085350745 3.0966418 0.0236765 0.38531777 0.0017582606 0.0021868783 1.7710738 0 -3.0483467 0.31201141 -3.0465884 0.61117406 -3.0466149 1 -3.0487753 +119 0.09996986 0.078639268 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 +Climbing replica = 2 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +119 0.3793192 0.35281863 3.0937691 0.017444108 0.3780308 0.0017574935 0.0021899317 1.7713574 0 -3.0483433 0.31354192 -3.0465858 0.61555533 -3.0466249 1 -3.0487758 +219 0.20159133 0.12247026 3.1244061 0.0085896057 0.13938632 0.0018362816 0.0022783681 1.7693295 0 -3.048335 0.39646633 -3.0464988 0.64277703 -3.0466925 1 -3.0487771 +266 0.099868725 0.086180598 3.1401661 0.0070922949 0.095128081 0.001842608 0.002286044 1.7685191 0 -3.048334 0.41231024 -3.0464914 0.65425179 -3.0467252 1 -3.0487774 diff --git a/examples/neb/log.19Jun17.neb.hop1.g++.4 b/examples/neb/log.19Jun17.neb.hop1.g++.4 new file mode 100644 index 0000000000..e2984c031c --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop1.g++.4 @@ -0,0 +1,9 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969 +87 0.095951502 0.052720903 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +87 0.14137277 0.11108954 0.005588927 0.065110105 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775 +124 0.099583263 0.085936899 0.0044220372 0.023873795 0.091308308 0.0071061754 0.0022863931 2.308121 0 -3.0535968 0.32223905 -3.0473329 0.61673898 -3.0464906 1 -3.048777 diff --git a/examples/neb/log.19Jun17.neb.hop1.g++.8 b/examples/neb/log.19Jun17.neb.hop1.g++.8 new file mode 100644 index 0000000000..d1be1284fa --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop1.g++.8 @@ -0,0 +1,9 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 4327.2753 2746.3378 0.082169072 4.9967651 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969 +87 0.095951792 0.052720902 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +87 0.14137297 0.11108954 0.0055889267 0.065110091 0.12467831 0.0071014928 0.0022798007 2.3003372 0 -3.0535967 0.32435271 -3.0473127 0.62805027 -3.0464952 1 -3.048775 +124 0.099582186 0.08593683 0.0044220345 0.023873731 0.091308197 0.0071061754 0.0022863931 2.3081211 0 -3.0535968 0.32223904 -3.0473329 0.61673896 -3.0464906 1 -3.048777 diff --git a/examples/neb/log.19Jun17.neb.hop2.g++.4 b/examples/neb/log.19Jun17.neb.hop2.g++.4 new file mode 100644 index 0000000000..c6b6cbe2ce --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop2.g++.4 @@ -0,0 +1,12 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305 +100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923 +200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938 +261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494 +361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942 +381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942 diff --git a/examples/neb/log.19Jun17.neb.hop2.g++.8 b/examples/neb/log.19Jun17.neb.hop2.g++.8 new file mode 100644 index 0000000000..c6b6cbe2ce --- /dev/null +++ b/examples/neb/log.19Jun17.neb.hop2.g++.8 @@ -0,0 +1,12 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 14.104748 10.419633 0.1227071 4.999238 8.2087606 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305 +100 0.24646695 0.10792196 0.0077146918 0.058733261 0.63504706 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923 +200 0.061777741 0.050288749 0.0047486883 0.0095236035 0.88698597 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938 +261 0.048699591 0.038138604 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +261 0.95753855 0.94297239 0.0040083594 0.0074854409 0.95722712 0.0014243579 0.0014241377 1.1696848 0 -3.0514942 0.30525481 -3.0502812 0.6357998 -3.0500698 1 -3.051494 +361 0.072509627 0.06580631 0.0027545765 0.0044749366 0.016746483 0.0016018879 0.0016017805 1.1704611 0 -3.0514943 0.28176307 -3.0503855 0.50355454 -3.0498924 1 -3.0514942 +381 0.04884836 0.040787876 0.0023445904 0.0035162935 0.017959209 0.0016017716 0.0016016898 1.1713862 0 -3.0514943 0.27120138 -3.0504399 0.50428218 -3.0498925 1 -3.0514942 diff --git a/examples/neb/log.19Jun17.neb.sivac.g++.4 b/examples/neb/log.19Jun17.neb.sivac.g++.4 new file mode 100644 index 0000000000..0d9880ca81 --- /dev/null +++ b/examples/neb/log.19Jun17.neb.sivac.g++.4 @@ -0,0 +1,17 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253 +20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346 +30 0.094973707 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367 +40 0.027727472 0.0044528145 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337 +50 0.019429348 0.0030110281 0.0087135563 0.015391975 0.76952681 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372 +60 0.019009471 0.0016234562 0.0053426307 0.0086166186 0.77759617 0.38936861 0.38933364 1.7610433 0 -2213.3374 0.33187548 -2212.9523 0.66497617 -2212.948 1 -2213.3373 +63 0.0097365134 0.0012734598 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +63 0.77865149 0.31085821 0.004777604 0.0076121987 0.77865149 0.38888778 0.38886047 1.7615294 0 -2213.3374 0.33212107 -2212.952 0.66525385 -2212.9485 1 -2213.3373 +73 0.098175496 0.033609035 0.0027886955 0.0042742148 0.036594003 0.51024838 0.51023983 1.7607181 0 -2213.3374 0.27574151 -2213.0416 0.50432348 -2212.8271 1 -2213.3374 +83 0.03341862 0.012760857 0.0020868177 0.0031625649 0.010189924 0.51014634 0.51014168 1.7602562 0 -2213.3374 0.26045338 -2213.0672 0.50355193 -2212.8272 1 -2213.3374 +93 0.0097374358 0.0028416114 0.0014003718 0.0020986584 0.0053485291 0.51011052 0.51010848 1.7601202 0 -2213.3374 0.25397887 -2213.0783 0.50388111 -2212.8273 1 -2213.3374 diff --git a/examples/neb/log.19Jun17.neb.sivac.g++.8 b/examples/neb/log.19Jun17.neb.sivac.g++.8 new file mode 100644 index 0000000000..260eb9e18b --- /dev/null +++ b/examples/neb/log.19Jun17.neb.sivac.g++.8 @@ -0,0 +1,18 @@ +LAMMPS (19 May 2017) +Running on 4 partitions of processors +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.33333333 -2212.7428 0.66666667 -2212.2247 1 -2211.7959 +10 0.24005275 0.036502104 0.036483049 0.24005275 0.68351722 0.42916118 0.41794425 1.6989349 0 -2213.3365 0.32909183 -2212.9587 0.65386736 -2212.9073 1 -2213.3253 +20 0.07940898 0.016398055 0.024706844 0.07940898 0.71637784 0.41387872 0.41157886 1.7343662 0 -2213.3369 0.32478734 -2212.9621 0.65348766 -2212.923 1 -2213.3346 +30 0.094973708 0.0083631681 0.015145947 0.035267404 0.7535772 0.40072717 0.40024605 1.7504612 0 -2213.3372 0.32705584 -2212.9584 0.65894506 -2212.9365 1 -2213.3367 +40 0.027727472 0.0044528144 0.011618173 0.022562656 0.76133752 0.39614635 0.39591731 1.7547519 0 -2213.3373 0.32873163 -2212.9562 0.66124255 -2212.9411 1 -2213.337 +50 0.019429341 0.0030110281 0.0087135565 0.015391975 0.7695268 0.39274846 0.3926388 1.7578616 0 -2213.3373 0.33022595 -2212.9543 0.66307279 -2212.9446 1 -2213.3372 +60 0.019048963 0.0016262345 0.0053426844 0.0086167196 0.77759655 0.38936867 0.3893337 1.7610433 0 -2213.3374 0.33187545 -2212.9523 0.66497615 -2212.948 1 -2213.3373 +63 0.0097037048 0.0012761841 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373 +Climbing replica = 3 +Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN +63 0.77865545 0.3108551 0.0047749367 0.0076075138 0.77865545 0.38888554 0.38885827 1.7615318 0 -2213.3374 0.33212221 -2212.952 0.66525512 -2212.9485 1 -2213.3373 +73 0.098595989 0.033659485 0.0027927196 0.0042813387 0.038224344 0.51024759 0.51023901 1.7607156 0 -2213.3374 0.27595612 -2213.0413 0.50453988 -2212.8271 1 -2213.3374 +83 0.033344977 0.012868685 0.0020880608 0.0031645847 0.010250413 0.51014677 0.5101421 1.7602601 0 -2213.3374 0.26053624 -2213.067 0.50358775 -2212.8272 1 -2213.3374 +93 0.013254873 0.0038176141 0.0014928226 0.0022407967 0.0058577818 0.51011371 0.51011138 1.7601272 0 -2213.3374 0.25452741 -2213.0774 0.50382161 -2212.8273 1 -2213.3374 +95 0.0099964951 0.0031053214 0.0014131665 0.0021184362 0.0053683638 0.51011105 0.51010897 1.7601232 0 -2213.3374 0.2540975 -2213.0781 0.50387313 -2212.8273 1 -2213.3374 diff --git a/examples/neb/log.5Oct16.neb.hop1.g++.4 b/examples/neb/log.5Oct16.neb.hop1.g++.4 deleted file mode 100644 index c678e69493..0000000000 --- a/examples/neb/log.5Oct16.neb.hop1.g++.4 +++ /dev/null @@ -1,10 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 4 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969 -100 0.10482184 0.085218486 0.014588241 0.066178594 0.19602237 0.0070900402 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.63987598 -3.0465067 1 -3.0487759 -111 0.096708467 0.07803707 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764 -Climbing replica = 3 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -111 0.2023467 0.1777038 0.013922973 0.05417562 0.2023467 0.0070871172 0.0022668002 2.3052945 0 -3.0535968 0.31853431 -3.0473633 0.64178871 -3.0465096 1 -3.0487764 -179 0.096874474 0.090676856 0.01040177 0.023364005 0.096874474 0.0071047642 0.0022856172 2.3122768 0 -3.0535969 0.31577311 -3.0473955 0.61798541 -3.0464922 1 -3.0487778 diff --git a/examples/neb/log.5Oct16.neb.hop1.g++.8 b/examples/neb/log.5Oct16.neb.hop1.g++.8 deleted file mode 100644 index d70f02bd16..0000000000 --- a/examples/neb/log.5Oct16.neb.hop1.g++.8 +++ /dev/null @@ -1,10 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 4 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 4327.2753 2746.3378 0.3387091 5.0075576 4514.5424 0.42933428 0.42323635 1.8941131 0 -3.0535948 0.33333333 -2.6242605 0.66666667 -2.7623811 1 -3.0474969 -100 0.10482171 0.085218406 0.014588234 0.066178435 0.19602242 0.0070900401 0.0022691875 2.3031875 0 -3.0535967 0.31839181 -3.0473647 0.639876 -3.0465067 1 -3.0487759 -111 0.096708718 0.078036984 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764 -Climbing replica = 3 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -111 0.20234693 0.17770387 0.013922966 0.054175505 0.20234693 0.0070871172 0.0022668002 2.3052946 0 -3.0535968 0.31853431 -3.0473633 0.64178873 -3.0465096 1 -3.0487764 -178 0.09975409 0.093814031 0.010577358 0.024247224 0.09975409 0.0071042931 0.0022851195 2.312004 0 -3.0535969 0.31607934 -3.0473923 0.618931 -3.0464926 1 -3.0487777 diff --git a/examples/neb/log.5Oct16.neb.hop2.g++.4 b/examples/neb/log.5Oct16.neb.hop2.g++.4 deleted file mode 100644 index 9977287303..0000000000 --- a/examples/neb/log.5Oct16.neb.hop2.g++.4 +++ /dev/null @@ -1,18 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 4 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305 -100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923 -200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938 -300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941 -400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943 -500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943 -600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944 -633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944 -Climbing replica = 3 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944 -733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944 -833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944 -933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944 -996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944 diff --git a/examples/neb/log.5Oct16.neb.hop2.g++.8 b/examples/neb/log.5Oct16.neb.hop2.g++.8 deleted file mode 100644 index 9977287303..0000000000 --- a/examples/neb/log.5Oct16.neb.hop2.g++.8 +++ /dev/null @@ -1,18 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 4 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 14.104748 10.419633 0.24852044 5.0039071 8.2116049 0.0018276223 0.00064050211 0.98401186 0 -3.0514921 0.33333333 -3.0496673 0.66666667 -3.0496645 1 -3.050305 -100 0.24646695 0.10792196 0.01781018 0.098854684 0.63725646 0.001516756 0.0015151635 1.165391 0 -3.0514939 0.2890334 -3.0503533 0.59718494 -3.0499771 1 -3.0514923 -200 0.061777741 0.050288749 0.012466513 0.020420207 0.88741041 0.0014465772 0.0014462528 1.1692938 0 -3.0514941 0.29975094 -3.0503052 0.62768286 -3.0500476 1 -3.0514938 -300 0.056346766 0.030000618 0.0093152917 0.013765031 1.0101529 0.0014069751 0.0014068154 1.1699608 0 -3.0514942 0.30992449 -3.0502613 0.64174291 -3.0500873 1 -3.0514941 -400 0.025589489 0.015671005 0.0061287063 0.008588518 1.1136424 0.001370987 0.0013709154 1.1704204 0 -3.0514943 0.32016645 -3.0502198 0.65324019 -3.0501233 1 -3.0514943 -500 0.014778626 0.0092108366 0.0042668521 0.0059963914 1.1636579 0.0013527466 0.0013527072 1.1706283 0 -3.0514944 0.32550275 -3.0501993 0.65875414 -3.0501416 1 -3.0514943 -600 0.08786211 0.020876327 0.0031421548 0.0051657363 1.1898894 0.0013430848 0.0013430599 1.1707681 0 -3.0514944 0.32831927 -3.0501889 0.66160681 -3.0501513 1 -3.0514944 -633 0.0098132678 0.0055392541 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944 -Climbing replica = 3 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -633 1.1924486 1.1648685 0.0030063464 0.0043091323 1.1924486 0.0013420127 0.0013419893 1.1707818 0 -3.0514944 0.32862625 -3.0501878 0.66191769 -3.0501524 1 -3.0514944 -733 0.095331134 0.089136608 0.0021551441 0.0031844438 0.043042998 0.0016022317 0.0016022168 1.170789 0 -3.0514944 0.29157063 -3.0503375 0.50358402 -3.0498922 1 -3.0514944 -833 0.10539135 0.030724373 0.0013749699 0.002221013 0.10539135 0.0016019798 0.001601971 1.1732118 0 -3.0514944 0.26249002 -3.0504848 0.50415223 -3.0498924 1 -3.0514944 -933 0.01883894 0.011496399 0.0011058925 0.0018178041 0.014621806 0.0016018934 0.0016018865 1.173866 0 -3.0514944 0.25788763 -3.0505113 0.50466375 -3.0498925 1 -3.0514944 -996 0.0082457876 0.0036336551 0.00077325986 0.0013910671 0.0068823708 0.0016018293 0.0016018244 1.174511 0 -3.0514944 0.2544553 -3.0505324 0.50520462 -3.0498926 1 -3.0514944 diff --git a/examples/neb/log.5Oct16.neb.sivac.g++.3 b/examples/neb/log.5Oct16.neb.sivac.g++.3 deleted file mode 100644 index f6adae4a18..0000000000 --- a/examples/neb/log.5Oct16.neb.sivac.g++.3 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 3 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959 -10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211 -20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347 -30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364 -40 0.0421393 0.0037035761 0.01173707 0.0421393 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371 -50 0.025897844 0.0022804241 0.0081056535 0.025897844 0.016908913 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923344 -2212.8272 1 -2213.3373 -59 0.00962839 0.0012946076 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373 -Climbing replica = 2 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -59 0.012040803 0.0031505502 0.005657505 0.009365729 0.012040803 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373 -63 0.009152118 0.0016692472 0.0049645771 0.0081967836 0.009152118 0.51013743 0.51010776 1.7409028 0 -2213.3374 0.50022239 -2212.8272 1 -2213.3373 diff --git a/examples/neb/log.5Oct16.neb.sivac.g++.6 b/examples/neb/log.5Oct16.neb.sivac.g++.6 deleted file mode 100644 index e00069d052..0000000000 --- a/examples/neb/log.5Oct16.neb.sivac.g++.6 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 3 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959 -10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211 -20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347 -30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364 -40 0.042139305 0.0037035764 0.01173707 0.042139305 0.026104735 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371 -50 0.025899631 0.0022805513 0.0081057075 0.025899631 0.016908929 0.5101712 0.51008591 1.739143 0 -2213.3373 0.49923345 -2212.8272 1 -2213.3373 -59 0.0096285044 0.0012946258 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373 -Climbing replica = 2 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -59 0.012040919 0.0031505771 0.0056576061 0.0093678253 0.012040919 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955698 -2212.8272 1 -2213.3373 -63 0.0091523813 0.0016692845 0.0049647607 0.0081998372 0.0091523813 0.51013743 0.51010775 1.7409028 0 -2213.3374 0.50022236 -2212.8272 1 -2213.3373 diff --git a/examples/neb/log.5Oct16.neb.sivac.g++.9 b/examples/neb/log.5Oct16.neb.sivac.g++.9 deleted file mode 100644 index 31ab7c9ac6..0000000000 --- a/examples/neb/log.5Oct16.neb.sivac.g++.9 +++ /dev/null @@ -1,14 +0,0 @@ -LAMMPS (5 Oct 2016) -Running on 3 partitions of processors -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -0 7.5525391 1.6345605 0.16683659 7.5525391 7.5525391 1.5383951 0 1.6207355 0 -2213.3343 0.5 -2212.4096 1 -2211.7959 -10 0.27332818 0.040944923 0.039164338 0.27332818 0.17804882 0.51235911 0.497084 1.6790474 0 -2213.3364 0.49024121 -2212.824 1 -2213.3211 -20 0.1820396 0.018049916 0.024428411 0.1820396 0.08601739 0.51038174 0.5080746 1.7224961 0 -2213.337 0.49199582 -2212.8266 1 -2213.3347 -30 0.043288796 0.0068108825 0.017372479 0.043288796 0.049466709 0.51032316 0.5095943 1.7304745 0 -2213.3371 0.49553568 -2212.8268 1 -2213.3364 -40 0.042139318 0.0037035773 0.011737071 0.042139318 0.026104737 0.51022733 0.5100163 1.7366752 0 -2213.3373 0.49838067 -2212.8271 1 -2213.3371 -50 0.025904121 0.0022808707 0.0081058431 0.025904121 0.016908969 0.5101712 0.51008591 1.7391431 0 -2213.3373 0.49923346 -2212.8272 1 -2213.3373 -59 0.0096287928 0.0012946716 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373 -Climbing replica = 2 -Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN -59 0.01204121 0.0031506449 0.005657861 0.0093731008 0.01204121 0.51014185 0.51010207 1.7404554 0 -2213.3374 0.49955696 -2212.8272 1 -2213.3373 -63 0.0091530442 0.0016693787 0.0049652227 0.0082075097 0.0091530442 0.51013743 0.51010775 1.7409027 0 -2213.3374 0.50022228 -2212.8272 1 -2213.3373 diff --git a/examples/python/README.pair_python b/examples/python/README.pair_python new file mode 100644 index 0000000000..3844a2676e --- /dev/null +++ b/examples/python/README.pair_python @@ -0,0 +1,41 @@ +This folder contains several LAMMPS input scripts and a python module +file py_pot.py to demonstrate the use of the pair style python. + +in.pair_python_melt: +This is a version of the melt example using the python pair style. The first +part of the output should have identical energies, temperature and pressure +than the melt example. The following two sections then demonstrate how to +restart with pair style python from a restart file and a data file. + +in.pair_python_hybrid: +This versions shows how to mix regular pair styles with a python pair style. +However, in this case both potentials are the same, so the energies and +pressure in the output should be identical to that of the previous example. + +in.pair_python_spce: +This input shows a simulation of small bulk water system with the SPC/E +water potential. Since the python pair style does not support computing +coulomb contributions, pair style hybrid/overload is used to combine +the python style containing the Lennard-Jones part with the long-range coulomb. +Same as for the previous example, it also showcases restarting. + +in.pair_python_table: +This input demonstrates the use of using the python pair style to build +a table file for use with pair style table. This will run much faster +than the python pair style. This example tabulates the melt example from +above. Note that tabulation is approximative, so the output will only +agree with the melt result to some degree. + +in.pair_python_coulomb: +This is another tabulation example, this time for the SPC/E water example +with cutoff coulomb interactions. +Please note, that tabulating long-range coulomb has a systematic error in +forces and energies for all systems with bonds, angle and dihedrals. +In this case, this will only affect the energies, since the water molecules +are held rigid with fix shake. To enable long-range coulomb the coul/cut +style needs to be replaced with coul/long, a suitable kspace style added +and the pppm keyword added to the table pair style definition. + +in.pair_python_long: +The final example shows how to combine long-range coulomb with tabulation +for only the short range interactions via pair style hybrid/overlay. diff --git a/examples/python/data.spce b/examples/python/data.spce new file mode 100644 index 0000000000..1e8a4a0913 --- /dev/null +++ b/examples/python/data.spce @@ -0,0 +1,9029 @@ +LAMMPS Atom File + + 4500 atoms + 3000 bonds + 1500 angles + 0 dihedrals + 0 impropers + + 2 atom types + 1 bond types + 1 angle types + + 0.02645 35.53280 xlo xhi + 0.02645 35.53280 ylo yhi + 0.02641 35.47360 zlo zhi + +Masses + + 1 15.9994 + 2 1.00794 + +Atoms + + 1 1 1 -0.8472 12.12456 28.09298 22.27452 0 1 0 + 2 1 2 0.4236 12.53683 28.75606 22.89928 0 1 0 + 3 1 2 0.4236 11.49482 28.56390 21.65678 0 1 0 + 4 2 1 -0.8472 1.17079 29.37777 23.72984 1 -1 0 + 5 2 2 0.4236 1.91804 29.48483 23.07399 1 -1 0 + 6 2 2 0.4236 0.40074 28.91964 23.28586 1 -1 0 + 7 3 1 -0.8472 29.68313 14.73733 21.62793 -1 0 0 + 8 3 2 0.4236 30.54284 14.93741 21.15800 -1 0 0 + 9 3 2 0.4236 29.73135 15.07344 22.56848 -1 0 0 + 10 4 1 -0.8472 10.87272 7.00153 35.10920 0 1 0 + 11 4 2 0.4236 11.11057 6.21663 34.53712 0 1 0 + 12 4 2 0.4236 9.95658 7.32301 34.86983 0 1 0 + 13 5 1 -0.8472 9.46588 6.43648 19.79899 0 1 0 + 14 5 2 0.4236 9.04840 6.32936 18.89668 0 1 0 + 15 5 2 0.4236 10.31722 5.91326 19.83657 0 1 0 + 16 6 1 -0.8472 3.17905 29.69801 22.11922 0 0 0 + 17 6 2 0.4236 3.19240 30.63289 21.76465 0 0 0 + 18 6 2 0.4236 3.38651 29.05797 21.37944 0 0 0 + 19 7 1 -0.8472 23.38618 11.29979 30.78238 0 0 0 + 20 7 2 0.4236 23.69882 10.46688 31.23897 0 0 0 + 21 7 2 0.4236 24.17354 11.79208 30.41132 0 0 0 + 22 8 1 -0.8472 11.03761 10.46106 30.14741 0 1 0 + 23 8 2 0.4236 10.94682 11.45112 30.25464 0 1 0 + 24 8 2 0.4236 11.60678 10.09680 30.88450 0 1 0 + 25 9 1 -0.8472 26.24001 25.40937 21.06754 0 0 0 + 26 9 2 0.4236 25.67045 26.09258 21.52442 0 0 0 + 27 9 2 0.4236 26.22311 25.56759 20.08030 0 0 0 + 28 10 1 -0.8472 10.84087 35.33915 19.78347 0 -1 0 + 29 10 2 0.4236 10.20697 0.54421 19.48018 0 0 0 + 30 10 2 0.4236 11.06253 34.74012 19.01405 0 -1 0 + 31 11 1 -0.8472 20.07383 4.95885 33.62365 0 1 0 + 32 11 2 0.4236 19.77359 5.87080 33.90322 0 1 0 + 33 11 2 0.4236 20.68149 4.57954 34.32139 0 1 0 + 34 12 1 -0.8472 12.43897 28.56656 17.39837 0 0 0 + 35 12 2 0.4236 12.80348 27.99505 18.13354 0 0 0 + 36 12 2 0.4236 11.63887 28.12177 16.99597 0 0 0 + 37 13 1 -0.8472 14.80338 7.14199 1.42116 0 0 0 + 38 13 2 0.4236 14.86001 6.68442 0.53382 0 0 0 + 39 13 2 0.4236 14.13589 6.67036 1.99737 0 0 0 + 40 14 1 -0.8472 15.87968 22.18330 24.13468 1 -1 0 + 41 14 2 0.4236 15.97100 22.71526 23.29285 1 -1 0 + 42 14 2 0.4236 16.69618 22.30846 24.69826 1 -1 0 + 43 15 1 -0.8472 13.29194 18.30473 12.37157 1 0 0 + 44 15 2 0.4236 12.55838 18.63231 12.96701 1 0 0 + 45 15 2 0.4236 13.24823 18.78335 11.49467 1 0 0 + 46 16 1 -0.8472 20.27409 23.94157 15.50212 0 0 0 + 47 16 2 0.4236 20.17851 24.67734 14.83167 0 0 0 + 48 16 2 0.4236 20.62006 23.12024 15.04857 0 0 0 + 49 17 1 -0.8472 30.10203 10.78182 14.24321 1 0 0 + 50 17 2 0.4236 29.40171 11.00523 13.56532 1 0 0 + 51 17 2 0.4236 29.70120 10.21329 14.96159 1 0 0 + 52 18 1 -0.8472 19.71525 12.98975 25.40578 0 0 0 + 53 18 2 0.4236 20.21522 13.35852 26.18938 0 0 0 + 54 18 2 0.4236 18.75253 12.87297 25.64962 0 0 0 + 55 19 1 -0.8472 4.22362 18.99305 32.62946 1 0 0 + 56 19 2 0.4236 4.05067 18.17865 32.07556 1 0 0 + 57 19 2 0.4236 3.38513 19.53353 32.69833 1 0 0 + 58 20 1 -0.8472 17.67279 30.86798 34.86933 1 -1 0 + 59 20 2 0.4236 17.18866 31.74218 34.90528 1 -1 0 + 60 20 2 0.4236 18.18607 30.80612 34.01339 1 -1 0 + 61 21 1 -0.8472 7.49194 27.84024 34.65598 0 0 0 + 62 21 2 0.4236 7.36412 27.37987 33.77752 0 0 0 + 63 21 2 0.4236 7.83650 27.18529 35.32848 0 0 0 + 64 22 1 -0.8472 9.58199 8.75878 28.38767 0 0 0 + 65 22 2 0.4236 8.89931 8.96106 27.68557 0 0 0 + 66 22 2 0.4236 9.61451 9.50981 29.04713 0 0 0 + 67 23 1 -0.8472 18.15447 7.97877 4.02967 1 0 0 + 68 23 2 0.4236 17.65379 8.02465 3.16529 1 0 0 + 69 23 2 0.4236 17.56073 7.59903 4.73904 1 0 0 + 70 24 1 -0.8472 13.45467 10.30195 21.94603 0 0 0 + 71 24 2 0.4236 14.12655 11.01716 21.75366 0 0 0 + 72 24 2 0.4236 13.15542 10.37304 22.89754 0 0 0 + 73 25 1 -0.8472 28.77370 1.83495 6.23711 0 0 0 + 74 25 2 0.4236 29.55410 1.23316 6.06742 0 0 0 + 75 25 2 0.4236 28.43863 1.69170 7.16831 0 0 0 + 76 26 1 -0.8472 21.17410 3.00906 4.56251 0 1 0 + 77 26 2 0.4236 21.00772 2.96011 5.54734 0 1 0 + 78 26 2 0.4236 21.17488 3.96581 4.27178 0 1 0 + 79 27 1 -0.8472 15.86257 20.77629 10.34675 1 -1 0 + 80 27 2 0.4236 15.84751 19.99231 10.96732 1 -1 0 + 81 27 2 0.4236 15.76759 20.45695 9.40393 1 -1 0 + 82 28 1 -0.8472 19.37283 6.41248 28.33230 0 0 0 + 83 28 2 0.4236 19.86925 6.14505 27.50645 0 0 0 + 84 28 2 0.4236 19.23659 7.40311 28.33322 0 0 0 + 85 29 1 -0.8472 19.69874 26.80111 22.56675 -1 -1 0 + 86 29 2 0.4236 20.51873 26.54536 22.05471 -1 -1 0 + 87 29 2 0.4236 19.52519 26.12131 23.27927 -1 -1 0 + 88 30 1 -0.8472 10.44934 1.95847 4.23874 1 1 0 + 89 30 2 0.4236 10.99436 1.49085 4.93460 1 1 0 + 90 30 2 0.4236 10.84502 2.85816 4.05448 1 1 0 + 91 31 1 -0.8472 6.35411 29.19722 23.17920 0 0 0 + 92 31 2 0.4236 5.50252 29.65394 23.43641 0 0 0 + 93 31 2 0.4236 7.01350 29.87731 22.85887 0 0 0 + 94 32 1 -0.8472 27.70305 33.63868 1.45545 0 0 0 + 95 32 2 0.4236 27.45511 34.56848 1.72731 0 0 0 + 96 32 2 0.4236 28.23820 33.21008 2.18338 0 0 0 + 97 33 1 -0.8472 34.54150 25.90721 10.97268 0 0 0 + 98 33 2 0.4236 34.26945 25.07242 10.49403 0 0 0 + 99 33 2 0.4236 34.74630 26.62266 10.30478 0 0 0 + 100 34 1 -0.8472 35.13701 10.35159 32.75388 -1 0 0 + 101 34 2 0.4236 35.31674 9.89658 31.88174 -1 0 0 + 102 34 2 0.4236 35.40693 9.74994 33.50557 -1 0 0 + 103 35 1 -0.8472 19.45549 25.22953 13.06888 1 0 0 + 104 35 2 0.4236 18.63554 25.79082 12.95680 1 0 0 + 105 35 2 0.4236 19.57263 24.64638 12.26505 1 0 0 + 106 36 1 -0.8472 8.76637 34.60601 24.20146 0 0 0 + 107 36 2 0.4236 9.50956 34.70873 24.86259 0 0 0 + 108 36 2 0.4236 9.11640 34.17220 23.37125 0 0 0 + 109 37 1 -0.8472 18.52185 34.00287 24.76220 0 0 0 + 110 37 2 0.4236 19.50193 33.87409 24.61123 0 0 0 + 111 37 2 0.4236 18.00811 33.44318 24.11196 0 0 0 + 112 38 1 -0.8472 5.46879 16.75651 12.09359 0 -1 0 + 113 38 2 0.4236 5.19937 17.67659 11.80934 0 -1 0 + 114 38 2 0.4236 5.65240 16.75172 13.07654 0 -1 0 +115 39 1 -0.8472 26.78187 26.54273 35.17124 1 0 0 +116 39 2 0.4236 27.38399 26.93341 0.42029 1 0 1 +117 39 2 0.4236 27.18089 25.69431 34.82353 1 0 0 + 118 40 1 -0.8472 14.04248 15.27305 12.41517 0 0 0 + 119 40 2 0.4236 14.36157 15.76500 13.22517 0 0 0 + 120 40 2 0.4236 14.30963 15.77579 11.59307 0 0 0 + 121 41 1 -0.8472 6.75576 6.34672 6.04938 1 1 0 + 122 41 2 0.4236 7.58170 5.78427 6.08735 1 1 0 + 123 41 2 0.4236 5.98388 5.83092 6.42094 1 1 0 + 124 42 1 -0.8472 10.86576 34.93065 25.98166 0 0 0 + 125 42 2 0.4236 10.69405 35.32452 26.88460 0 0 0 + 126 42 2 0.4236 11.59169 35.44574 25.52591 0 0 0 + 127 43 1 -0.8472 18.34531 30.51202 26.27445 0 0 0 + 128 43 2 0.4236 18.04166 30.29551 25.34662 0 0 0 + 129 43 2 0.4236 19.17552 31.06784 26.23227 0 0 0 + 130 44 1 -0.8472 13.18486 0.77946 20.62491 -1 1 0 + 131 44 2 0.4236 13.44906 0.56426 21.56501 -1 1 0 + 132 44 2 0.4236 12.29152 0.37510 20.42885 -1 1 0 + 133 45 1 -0.8472 24.47790 24.05885 28.20937 -1 0 0 + 134 45 2 0.4236 24.15706 23.14172 27.97301 -1 0 0 + 135 45 2 0.4236 23.74391 24.71952 28.05213 -1 0 0 +136 46 1 -0.8472 30.79103 15.33785 34.86738 0 0 0 +137 46 2 0.4236 31.17614 15.32312 0.34290 0 0 1 +138 46 2 0.4236 29.97833 14.75605 34.83605 0 0 0 + 139 47 1 -0.8472 18.30892 19.76908 34.23734 0 0 0 + 140 47 2 0.4236 17.75981 20.19846 33.52035 0 0 0 + 141 47 2 0.4236 19.04827 19.24096 33.81970 0 0 0 + 142 48 1 -0.8472 24.18923 16.21113 25.53917 0 0 0 + 143 48 2 0.4236 24.35093 17.17602 25.33219 0 0 0 + 144 48 2 0.4236 24.25573 16.06630 26.52637 0 0 0 + 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28.37248 19.48784 -1 -1 0 + 165 55 2 0.4236 33.66659 29.16225 18.56621 -1 -1 0 + 166 56 1 -0.8472 9.78186 33.73160 21.96701 0 -1 0 + 167 56 2 0.4236 9.24351 33.11436 21.39330 0 -1 0 + 168 56 2 0.4236 10.15276 34.47066 21.40475 0 -1 0 + 169 57 1 -0.8472 7.86139 6.97451 8.72713 0 0 0 + 170 57 2 0.4236 8.16632 6.08021 9.05452 0 0 0 + 171 57 2 0.4236 7.15204 6.85123 8.03315 0 0 0 + 172 58 1 -0.8472 34.25223 27.81706 31.79312 -1 -1 0 + 173 58 2 0.4236 34.70046 28.60821 31.37704 -1 -1 0 + 174 58 2 0.4236 33.75216 28.10807 32.60872 -1 -1 0 + 175 59 1 -0.8472 34.94048 26.84844 19.52041 -1 -1 0 + 176 59 2 0.4236 35.40459 26.00577 19.79339 -1 -1 0 + 177 59 2 0.4236 34.15050 26.62404 18.94986 -1 -1 0 + 178 60 1 -0.8472 21.76411 32.20568 20.89158 0 0 0 + 179 60 2 0.4236 22.66239 31.82480 21.11072 0 0 0 + 180 60 2 0.4236 21.76667 33.18956 21.07031 0 0 0 + 181 61 1 -0.8472 34.30787 3.43694 14.24158 -1 0 0 + 182 61 2 0.4236 34.88829 2.82261 13.70711 -1 0 0 + 183 61 2 0.4236 34.87977 4.10183 14.72200 -1 0 0 + 184 62 1 -0.8472 17.88110 18.91029 14.42187 0 1 0 + 185 62 2 0.4236 17.92538 18.97676 15.41864 0 1 0 + 186 62 2 0.4236 18.59574 19.48109 14.01766 0 1 0 + 187 63 1 -0.8472 19.08402 14.22906 20.78379 0 0 0 + 188 63 2 0.4236 19.62169 13.82628 21.52446 0 0 0 + 189 63 2 0.4236 18.62450 13.50292 20.27246 0 0 0 + 190 64 1 -0.8472 7.85997 17.97828 9.48138 1 0 0 + 191 64 2 0.4236 7.51843 18.85870 9.15243 1 0 0 + 192 64 2 0.4236 8.12328 17.41050 8.70147 1 0 0 + 193 65 1 -0.8472 0.30367 23.18327 0.38100 1 -1 0 + 194 65 2 0.4236 35.34479 24.06840 0.38922 0 -1 0 + 195 65 2 0.4236 35.13158 22.44974 0.42108 0 -1 0 + 196 66 1 -0.8472 4.53675 21.21621 29.86203 1 0 0 + 197 66 2 0.4236 5.08827 22.03780 29.71779 1 0 0 + 198 66 2 0.4236 5.02017 20.59411 30.47781 1 0 0 + 199 67 1 -0.8472 3.76321 1.66558 34.11622 0 0 0 + 200 67 2 0.4236 4.72980 1.83277 33.92193 0 0 0 + 201 67 2 0.4236 3.56027 1.93821 35.05667 0 0 0 + 202 68 1 -0.8472 35.17951 34.70220 7.53093 0 0 0 + 203 68 2 0.4236 34.22070 34.47397 7.36203 0 0 0 + 204 68 2 0.4236 0.09341 33.98533 8.08720 1 0 0 + 205 69 1 -0.8472 24.82000 8.21485 16.09338 0 0 0 + 206 69 2 0.4236 25.55821 8.87272 15.94450 0 0 0 + 207 69 2 0.4236 25.00950 7.68219 16.91816 0 0 0 + 208 70 1 -0.8472 4.18282 28.52828 29.70840 1 0 0 + 209 70 2 0.4236 5.11675 28.38566 30.03614 1 0 0 + 210 70 2 0.4236 4.20438 29.05790 28.86047 1 0 0 + 211 71 1 -0.8472 26.43717 31.27303 3.91741 -1 0 0 + 212 71 2 0.4236 26.51838 30.56852 3.21243 -1 0 0 + 213 71 2 0.4236 27.32007 31.72670 4.03853 -1 0 0 + 214 72 1 -0.8472 35.11244 7.70363 27.08017 -1 0 0 + 215 72 2 0.4236 35.17419 7.38841 28.02717 -1 0 0 + 216 72 2 0.4236 34.54388 7.07077 26.55463 -1 0 0 + 217 73 1 -0.8472 21.45404 34.05655 2.90167 0 0 0 + 218 73 2 0.4236 21.02487 33.76274 3.75574 0 0 0 + 219 73 2 0.4236 22.28101 34.57992 3.10701 0 0 0 + 220 74 1 -0.8472 31.21242 3.31299 25.80396 -1 1 0 + 221 74 2 0.4236 30.72513 4.00625 25.27307 -1 1 0 + 222 74 2 0.4236 31.51511 3.70889 26.67093 -1 1 0 + 223 75 1 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+neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +pair_coeff 1 2 spce.table OW-HW +pair_coeff 2 2 spce.table HW-HW + +thermo 10 +run 100 + +shell rm spce.table + diff --git a/examples/python/in.pair_python_hybrid b/examples/python/in.pair_python_hybrid new file mode 100644 index 0000000000..5d5157ae6d --- /dev/null +++ b/examples/python/in.pair_python_hybrid @@ -0,0 +1,63 @@ +# 3d Lennard-Jones hybrid + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 2 box +create_atoms 1 box +mass * 1.0 +region half block -0.1 4.9 0 10 0 10 +set region half type 2 + +velocity all create 3.0 87287 + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 + +write_data hybrid.data +write_restart hybrid.restart + +clear + +read_restart hybrid.restart + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +fix 1 all nve + +thermo 50 +run 250 + +clear + +units lj +atom_style atomic + +read_data hybrid.data + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 + +shell rm hybrid.data hybrid.restart diff --git a/examples/python/in.pair_python_long b/examples/python/in.pair_python_long new file mode 100644 index 0000000000..a600e824df --- /dev/null +++ b/examples/python/in.pair_python_long @@ -0,0 +1,38 @@ +units real +atom_style full + +read_data data.spce + +pair_style python 12.0 +pair_coeff * * py_pot.LJCutSPCE OW HW + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 +fix 2 all nvt temp 300.0 300.0 100.0 + +# create only lj/cut table for the oxygen atoms from python +shell rm -f spce.table +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW + +# switch to tabulated potential with long-range coulomb as overlay +pair_style hybrid/overlay coul/long 12.0 table linear 2000 +kspace_style pppm 1.0e-6 +pair_coeff * * coul/long +pair_coeff 1 1 table spce.table OW-OW + +thermo 10 +run 100 + +shell rm spce.table + diff --git a/examples/python/in.pair_python_melt b/examples/python/in.pair_python_melt new file mode 100644 index 0000000000..3f775e6651 --- /dev/null +++ b/examples/python/in.pair_python_melt @@ -0,0 +1,58 @@ +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 box +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 + +write_data melt.data +write_restart melt.restart + +clear + +read_restart melt.restart + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +fix 1 all nve + +thermo 50 +run 250 + +clear + +units lj +atom_style atomic + +read_data melt.data + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 + +shell rm melt.data melt.restart diff --git a/examples/python/in.pair_python_spce b/examples/python/in.pair_python_spce new file mode 100644 index 0000000000..5bd9e1e23a --- /dev/null +++ b/examples/python/in.pair_python_spce @@ -0,0 +1,28 @@ +units real +atom_style full + +read_data data.spce + +pair_style hybrid/overlay coul/long 12.0 python 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 +fix 2 all nvt temp 300.0 300.0 100.0 + +thermo 10 +run 100 diff --git a/examples/python/in.pair_python_table b/examples/python/in.pair_python_table new file mode 100644 index 0000000000..761a6efd78 --- /dev/null +++ b/examples/python/in.pair_python_table @@ -0,0 +1,32 @@ +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +region box block 0 10 0 10 0 10 +create_box 1 box +create_atoms 1 box +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ + +pair_style table linear 2000 +pair_coeff 1 1 lj_1_1.table LJ + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 + +shell rm lj_1_1.table + diff --git a/examples/python/log.4May17.pair_python_coulomb.1 b/examples/python/log.4May17.pair_python_coulomb.1 new file mode 100644 index 0000000000..97826eda47 --- /dev/null +++ b/examples/python/log.4May17.pair_python_coulomb.1 @@ -0,0 +1,178 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay python 12.0 coul/long 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python potentials.LJCutSPCE OW NULL + +pair_modify table 0 + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +PPPM initialization ... +WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394206 + estimated relative force accuracy = 1.18714e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair python, perpetual, skip from (2) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +PPPM initialization ... +WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394206 + estimated relative force accuracy = 1.18714e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 +PPPM initialization ... +WARNING: Using polynomial approximation for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394206 + estimated relative force accuracy = 1.18714e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +pair_coeff 1 2 spce.table OW-HW +pair_coeff 2 2 spce.table HW-HW + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 35.26 | 35.26 | 35.26 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -100272.97 0 -100272.97 -1282.0708 + 10 120.61568 -101350.63 0 -100272.39 -4077.5051 + 20 136.11379 -101465.43 0 -100248.65 -5136.5677 + 30 137.01602 -101455.3 0 -100230.46 -5347.8311 + 40 153.424 -101582.46 0 -100210.93 -5223.1676 + 50 167.73654 -101686.24 0 -100186.77 -4468.6687 + 60 163.11642 -101618.16 0 -100159.99 -3291.7815 + 70 169.64512 -101647.89 0 -100131.35 -2611.638 + 80 182.9979 -101737.01 0 -100101.11 -2390.6293 + 90 191.33873 -101778.71 0 -100068.24 -2239.386 + 100 194.7458 -101775.84 0 -100034.92 -1951.9128 +Loop time of 7.60221 on 1 procs for 100 steps with 4500 atoms + +Performance: 1.137 ns/day, 21.117 hours/ns, 13.154 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.7401 | 5.7401 | 5.7401 | 0.0 | 75.51 +Bond | 0.00017881 | 0.00017881 | 0.00017881 | 0.0 | 0.00 +Kspace | 1.5387 | 1.5387 | 1.5387 | 0.0 | 20.24 +Neigh | 0.2299 | 0.2299 | 0.2299 | 0.0 | 3.02 +Comm | 0.024311 | 0.024311 | 0.024311 | 0.0 | 0.32 +Output | 0.00057936 | 0.00057936 | 0.00057936 | 0.0 | 0.01 +Modify | 0.063158 | 0.063158 | 0.063158 | 0.0 | 0.83 +Other | | 0.005243 | | | 0.07 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21216 ave 21216 max 21216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2601766 +Ave neighs/atom = 578.17 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:07 diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.1 b/examples/python/log.4May17.pair_python_coulomb.g++.1 new file mode 100644 index 0000000000..b08d4b939c --- /dev/null +++ b/examples/python/log.4May17.pair_python_coulomb.g++.1 @@ -0,0 +1,138 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/cut 12.0 python 12.0 + +pair_coeff * * coul/cut +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +pair_coeff 1 2 spce.table OW-HW +pair_coeff 2 2 spce.table HW-HW + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 25.08 | 25.08 | 25.08 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -18284.922 0 -18284.922 -2080.7739 + 10 146.83806 -19552.072 0 -18239.421 -4865.31 + 20 183.15761 -18706.872 0 -17069.543 -4865.6695 + 30 205.96203 -18901.541 0 -17060.354 -4454.8634 + 40 241.62768 -18323.117 0 -16163.099 -3269.1475 + 50 265.98384 -19883.562 0 -17505.813 -2788.5194 + 60 274.01897 -21320.575 0 -18870.996 -2387.0708 + 70 288.7601 -19849.269 0 -17267.913 -1235.818 + 80 300.64724 -20958.602 0 -18270.981 -1714.7988 + 90 304.19113 -21580.4 0 -18861.099 -2144.1614 + 100 304.22027 -21239.014 0 -18519.452 -2092.6759 +Loop time of 6.01861 on 1 procs for 100 steps with 4500 atoms + +Performance: 1.436 ns/day, 16.718 hours/ns, 16.615 timesteps/s +99.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.698 | 5.698 | 5.698 | 0.0 | 94.67 +Bond | 0.0001626 | 0.0001626 | 0.0001626 | 0.0 | 0.00 +Neigh | 0.23235 | 0.23235 | 0.23235 | 0.0 | 3.86 +Comm | 0.018961 | 0.018961 | 0.018961 | 0.0 | 0.32 +Output | 0.00058126 | 0.00058126 | 0.00058126 | 0.0 | 0.01 +Modify | 0.063452 | 0.063452 | 0.063452 | 0.0 | 1.05 +Other | | 0.005146 | | | 0.09 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21285 ave 21285 max 21285 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.59766e+06 ave 2.59766e+06 max 2.59766e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2597662 +Ave neighs/atom = 577.258 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:06 diff --git a/examples/python/log.4May17.pair_python_coulomb.g++.4 b/examples/python/log.4May17.pair_python_coulomb.g++.4 new file mode 100644 index 0000000000..b002d5c1ab --- /dev/null +++ b/examples/python/log.4May17.pair_python_coulomb.g++.4 @@ -0,0 +1,138 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/cut 12.0 python 12.0 + +pair_coeff * * coul/cut +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create combined lj/coul table for all atom types +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW -0.8472 -0.8472 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/cut, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +pair_write 1 2 2000 rsq 0.1 12 spce.table OW-HW -0.8472 0.4236 +pair_write 2 2 2000 rsq 0.1 12 spce.table HW-HW 0.4236 0.4236 + +# switch to tabulated potential +pair_style table linear 2000 pppm +pair_coeff 1 1 spce.table OW-OW +pair_coeff 1 2 spce.table OW-HW +pair_coeff 2 2 spce.table HW-HW + +thermo 10 +run 100 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 9.962 | 9.963 | 9.963 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -18284.922 0 -18284.922 -2080.7739 + 10 146.83806 -19552.072 0 -18239.421 -4865.31 + 20 183.15761 -18706.872 0 -17069.543 -4865.6695 + 30 205.96203 -18901.541 0 -17060.354 -4454.8634 + 40 241.62768 -18323.117 0 -16163.099 -3269.1475 + 50 265.98384 -19883.562 0 -17505.813 -2788.5194 + 60 274.01897 -21320.575 0 -18870.996 -2387.0708 + 70 288.7601 -19849.269 0 -17267.913 -1235.818 + 80 300.64724 -20958.602 0 -18270.981 -1714.7988 + 90 304.19113 -21580.4 0 -18861.099 -2144.1614 + 100 304.22027 -21239.014 0 -18519.452 -2092.6759 +Loop time of 1.7361 on 4 procs for 100 steps with 4500 atoms + +Performance: 4.977 ns/day, 4.823 hours/ns, 57.600 timesteps/s +99.2% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.4424 | 1.5149 | 1.6066 | 5.3 | 87.26 +Bond | 8.9407e-05 | 0.00010258 | 0.00012374 | 0.0 | 0.01 +Neigh | 0.064205 | 0.064241 | 0.064295 | 0.0 | 3.70 +Comm | 0.023643 | 0.1155 | 0.18821 | 19.2 | 6.65 +Output | 0.00038004 | 0.00042355 | 0.00054145 | 0.0 | 0.02 +Modify | 0.037507 | 0.037787 | 0.038042 | 0.1 | 2.18 +Other | | 0.003148 | | | 0.18 + +Nlocal: 1125 ave 1162 max 1098 min +Histogram: 1 1 0 0 0 1 0 0 0 1 +Nghost: 12267.8 ave 12302 max 12238 min +Histogram: 2 0 0 0 0 0 0 0 1 1 +Neighs: 649416 ave 681458 max 630541 min +Histogram: 1 0 2 0 0 0 0 0 0 1 + +Total # of neighbors = 2597662 +Ave neighs/atom = 577.258 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:01 diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.1 b/examples/python/log.4May17.pair_python_hybrid.g++.1 new file mode 100644 index 0000000000..718f794a57 --- /dev/null +++ b/examples/python/log.4May17.pair_python_hybrid.g++.1 @@ -0,0 +1,250 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones hybrid + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 2 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 +region half block -0.1 4.9 0 10 0 10 +set region half type 2 + 2000 settings made for type + +velocity all create 3.0 87287 + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.446 | 4.446 | 4.446 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 + 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 + 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 + 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 +Loop time of 10.0384 on 1 procs for 250 steps with 4000 atoms + +Performance: 10758.705 tau/day, 24.904 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.913 | 9.913 | 9.913 | 0.0 | 98.75 +Neigh | 0.095569 | 0.095569 | 0.095569 | 0.0 | 0.95 +Comm | 0.012686 | 0.012686 | 0.012686 | 0.0 | 0.13 +Output | 0.00027537 | 0.00027537 | 0.00027537 | 0.0 | 0.00 +Modify | 0.01386 | 0.01386 | 0.01386 | 0.0 | 0.14 +Other | | 0.003027 | | | 0.03 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5499 ave 5499 max 5499 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 85978 ave 85978 max 85978 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 85978 +Ave neighs/atom = 21.4945 +Neighbor list builds = 12 +Dangerous builds not checked + +write_data hybrid.data +write_restart hybrid.restart + +clear + using 1 OpenMP thread(s) per MPI task + +read_restart hybrid.restart + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid + 4000 atoms + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 4.245 | 4.245 | 4.245 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 + 300 1.645592 -4.7496711 0 -2.2819002 5.8734193 + 350 1.6514972 -4.7580756 0 -2.2814491 5.810167 + 400 1.6540555 -4.7622999 0 -2.281837 5.8200413 + 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 + 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 +Loop time of 10.0803 on 1 procs for 250 steps with 4000 atoms + +Performance: 10713.932 tau/day, 24.801 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.8479 | 9.8479 | 9.8479 | 0.0 | 97.69 +Neigh | 0.20002 | 0.20002 | 0.20002 | 0.0 | 1.98 +Comm | 0.01437 | 0.01437 | 0.01437 | 0.0 | 0.14 +Output | 0.00024033 | 0.00024033 | 0.00024033 | 0.0 | 0.00 +Modify | 0.013422 | 0.013422 | 0.013422 | 0.0 | 0.13 +Other | | 0.004348 | | | 0.04 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5472 ave 5472 max 5472 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 86930 ave 86930 max 86930 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 86930 +Ave neighs/atom = 21.7325 +Neighbor list builds = 25 +Dangerous builds = 25 + +clear + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style atomic + +read_data hybrid.data + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4000 atoms + reading velocities ... + 4000 velocities + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.745 | 3.745 | 3.745 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.6275257 -4.7224992 0 -2.281821 5.9567365 + 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 + 100 1.6512008 -4.7582693 0 -2.2820874 5.8090548 + 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 + 200 1.6258731 -4.7205017 0 -2.2823017 5.952511 + 250 1.6370862 -4.7373176 0 -2.2823022 5.925807 +Loop time of 9.93686 on 1 procs for 250 steps with 4000 atoms + +Performance: 10868.626 tau/day, 25.159 timesteps/s +98.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 9.8119 | 9.8119 | 9.8119 | 0.0 | 98.74 +Neigh | 0.096041 | 0.096041 | 0.096041 | 0.0 | 0.97 +Comm | 0.01243 | 0.01243 | 0.01243 | 0.0 | 0.13 +Output | 0.00028133 | 0.00028133 | 0.00028133 | 0.0 | 0.00 +Modify | 0.013261 | 0.013261 | 0.013261 | 0.0 | 0.13 +Other | | 0.002994 | | | 0.03 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5487 ave 5487 max 5487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 86831 ave 86831 max 86831 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 86831 +Ave neighs/atom = 21.7078 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm hybrid.data hybrid.restart +Total wall time: 0:00:30 diff --git a/examples/python/log.4May17.pair_python_hybrid.g++.4 b/examples/python/log.4May17.pair_python_hybrid.g++.4 new file mode 100644 index 0000000000..32d9fc1740 --- /dev/null +++ b/examples/python/log.4May17.pair_python_hybrid.g++.4 @@ -0,0 +1,250 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones hybrid + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 2 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 +region half block -0.1 4.9 0 10 0 10 +set region half type 2 + 2000 settings made for type + +velocity all create 3.0 87287 + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.953 | 3.953 | 3.953 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 + 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 + 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 + 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 + 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 +Loop time of 2.71748 on 4 procs for 250 steps with 4000 atoms + +Performance: 39742.745 tau/day, 91.997 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.4777 | 2.5639 | 2.6253 | 3.9 | 94.35 +Neigh | 0.024626 | 0.025331 | 0.02598 | 0.3 | 0.93 +Comm | 0.061933 | 0.12297 | 0.20987 | 18.0 | 4.53 +Output | 0.00026131 | 0.00027591 | 0.00031352 | 0.0 | 0.01 +Modify | 0.0036087 | 0.0036573 | 0.0037553 | 0.1 | 0.13 +Other | | 0.001337 | | | 0.05 + +Nlocal: 1000 ave 1010 max 982 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703.75 ave 2713 max 2689 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +Neighs: 21469.8 ave 22167 max 20546 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 85879 +Ave neighs/atom = 21.4698 +Neighbor list builds = 12 +Dangerous builds not checked + +write_data hybrid.data +write_restart hybrid.restart + +clear + using 1 OpenMP thread(s) per MPI task + +read_restart hybrid.restart + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid + 4000 atoms + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.612 | 3.612 | 3.612 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 + 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 + 350 1.6171909 -4.7064928 0 -2.2813129 6.0094235 + 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 + 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 + 500 1.643316 -4.7454222 0 -2.2810644 5.8454817 +Loop time of 2.75827 on 4 procs for 250 steps with 4000 atoms + +Performance: 39155.038 tau/day, 90.637 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3631 | 2.5412 | 2.6672 | 7.2 | 92.13 +Neigh | 0.050358 | 0.052316 | 0.053312 | 0.5 | 1.90 +Comm | 0.032793 | 0.15893 | 0.33904 | 29.1 | 5.76 +Output | 0.00018525 | 0.00020212 | 0.00024509 | 0.0 | 0.01 +Modify | 0.0034482 | 0.0035321 | 0.0036578 | 0.1 | 0.13 +Other | | 0.002039 | | | 0.07 + +Nlocal: 1000 ave 1012 max 983 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 2699 ave 2706 max 2693 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 21802 ave 22700 max 21236 min +Histogram: 1 1 0 1 0 0 0 0 0 1 + +Total # of neighbors = 87208 +Ave neighs/atom = 21.802 +Neighbor list builds = 25 +Dangerous builds = 25 + +clear + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style atomic + +read_data hybrid.data + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 4000 atoms + reading velocities ... + 4000 velocities + +pair_style hybrid lj/cut 2.5 python 2.5 +pair_coeff * * python py_pot.LJCutMelt lj NULL +pair_coeff * 2 lj/cut 1.0 1.0 + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 3 neighbor lists, perpetual/occasional/extra = 3 0 0 + (1) pair lj/cut, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (2) pair python, perpetual, skip from (3) + attributes: half, newton on + pair build: skip + stencil: none + bin: none + (3) neighbor class addition, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 + 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 + 100 1.6169004 -4.7066969 0 -2.2819526 6.0082546 + 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 + 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 + 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 +Loop time of 2.71936 on 4 procs for 250 steps with 4000 atoms + +Performance: 39715.257 tau/day, 91.933 timesteps/s +98.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.3769 | 2.5432 | 2.6447 | 6.6 | 93.52 +Neigh | 0.024088 | 0.025093 | 0.025748 | 0.4 | 0.92 +Comm | 0.044614 | 0.14598 | 0.31339 | 27.5 | 5.37 +Output | 0.00026488 | 0.00028872 | 0.00034189 | 0.0 | 0.01 +Modify | 0.0034099 | 0.0035709 | 0.0036535 | 0.2 | 0.13 +Other | | 0.001215 | | | 0.04 + +Nlocal: 1000 ave 1013 max 989 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 2695.5 ave 2706 max 2682 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 21792 ave 22490 max 21457 min +Histogram: 2 0 1 0 0 0 0 0 0 1 + +Total # of neighbors = 87168 +Ave neighs/atom = 21.792 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm hybrid.data hybrid.restart +Total wall time: 0:00:08 diff --git a/examples/python/log.4May17.pair_python_long.g++.1 b/examples/python/log.4May17.pair_python_long.g++.1 new file mode 100644 index 0000000000..e2d7cf1bde --- /dev/null +++ b/examples/python/log.4May17.pair_python_long.g++.1 @@ -0,0 +1,146 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style python 12.0 +pair_coeff * * py_pot.LJCutSPCE OW HW + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create only lj/cut table for the oxygen atoms from python +shell rm -f spce.table +WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + +# switch to tabulated potential with long-range coulomb as overlay +pair_style hybrid/overlay coul/long 12.0 table linear 2000 +kspace_style pppm 1.0e-6 +pair_coeff * * coul/long +pair_coeff 1 1 table spce.table OW-OW + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair table, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 36.47 | 36.47 | 36.47 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16690.032 0 -16690.032 -1268.9538 + 10 120.58553 -17767.504 0 -16689.536 -4063.8589 + 20 136.11736 -17882.557 0 -16665.742 -5124.6758 + 30 137.00764 -17872.318 0 -16647.545 -5337.2022 + 40 153.38868 -17999.269 0 -16628.059 -5213.6001 + 50 167.70342 -18103.06 0 -16603.883 -4460.6632 + 60 163.07134 -18034.856 0 -16577.088 -3285.0037 + 70 169.59286 -18064.636 0 -16548.57 -2606.407 + 80 182.92893 -18153.499 0 -16518.215 -2385.5152 + 90 191.2793 -18195.356 0 -16485.425 -2235.3701 + 100 194.68587 -18192.458 0 -16452.073 -1948.3746 +Loop time of 7.90705 on 1 procs for 100 steps with 4500 atoms + +Performance: 1.093 ns/day, 21.964 hours/ns, 12.647 timesteps/s +99.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.0343 | 6.0343 | 6.0343 | 0.0 | 76.32 +Bond | 0.00019622 | 0.00019622 | 0.00019622 | 0.0 | 0.00 +Kspace | 1.5311 | 1.5311 | 1.5311 | 0.0 | 19.36 +Neigh | 0.246 | 0.246 | 0.246 | 0.0 | 3.11 +Comm | 0.023937 | 0.023937 | 0.023937 | 0.0 | 0.30 +Output | 0.00060368 | 0.00060368 | 0.00060368 | 0.0 | 0.01 +Modify | 0.065543 | 0.065543 | 0.065543 | 0.0 | 0.83 +Other | | 0.005364 | | | 0.07 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21216 ave 21216 max 21216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60177e+06 ave 2.60177e+06 max 2.60177e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2601769 +Ave neighs/atom = 578.171 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:08 diff --git a/examples/python/log.4May17.pair_python_long.g++.4 b/examples/python/log.4May17.pair_python_long.g++.4 new file mode 100644 index 0000000000..35347da713 --- /dev/null +++ b/examples/python/log.4May17.pair_python_long.g++.4 @@ -0,0 +1,146 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style python 12.0 +pair_coeff * * py_pot.LJCutSPCE OW HW + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +# create only lj/cut table for the oxygen atoms from python +shell rm -f spce.table +WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +WARNING: Shell command 'rm' failed with error 'No such file or directory' (../input.cpp:1285) +pair_write 1 1 2000 rsq 0.1 12 spce.table OW-OW +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + +# switch to tabulated potential with long-range coulomb as overlay +pair_style hybrid/overlay coul/long 12.0 table linear 2000 +kspace_style pppm 1.0e-6 +pair_coeff * * coul/long +pair_coeff 1 1 table spce.table OW-OW + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 34263 16000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair table, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 13.45 | 13.45 | 13.45 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16690.032 0 -16690.032 -1268.9538 + 10 120.58553 -17767.504 0 -16689.536 -4063.8589 + 20 136.11736 -17882.557 0 -16665.742 -5124.6758 + 30 137.00764 -17872.318 0 -16647.545 -5337.2022 + 40 153.38868 -17999.269 0 -16628.059 -5213.6001 + 50 167.70342 -18103.06 0 -16603.883 -4460.6632 + 60 163.07134 -18034.856 0 -16577.088 -3285.0037 + 70 169.59286 -18064.636 0 -16548.57 -2606.407 + 80 182.92893 -18153.499 0 -16518.215 -2385.5152 + 90 191.2793 -18195.356 0 -16485.425 -2235.3701 + 100 194.68587 -18192.458 0 -16452.073 -1948.3746 +Loop time of 2.36748 on 4 procs for 100 steps with 4500 atoms + +Performance: 3.649 ns/day, 6.576 hours/ns, 42.239 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.5309 | 1.5977 | 1.6926 | 4.7 | 67.49 +Bond | 9.9182e-05 | 0.00012749 | 0.00016403 | 0.0 | 0.01 +Kspace | 0.52158 | 0.61232 | 0.67676 | 7.3 | 25.86 +Neigh | 0.066937 | 0.06702 | 0.067093 | 0.0 | 2.83 +Comm | 0.035882 | 0.039862 | 0.042244 | 1.2 | 1.68 +Output | 0.0004003 | 0.00044602 | 0.00057578 | 0.0 | 0.02 +Modify | 0.046088 | 0.046227 | 0.046315 | 0.0 | 1.95 +Other | | 0.003775 | | | 0.16 + +Nlocal: 1125 ave 1154 max 1092 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 12256.2 ave 12296 max 12213 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 650442 ave 678831 max 626373 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 2601769 +Ave neighs/atom = 578.171 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 + +shell rm spce.table + +Total wall time: 0:00:02 diff --git a/examples/python/log.4May17.pair_python_melt.g++.1 b/examples/python/log.4May17.pair_python_melt.g++.1 new file mode 100644 index 0000000000..d234ce93b5 --- /dev/null +++ b/examples/python/log.4May17.pair_python_melt.g++.1 @@ -0,0 +1,214 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6758903 -4.7955425 0 -2.2823355 5.670064 + 100 1.6458363 -4.7492704 0 -2.2811332 5.8691042 + 150 1.6324555 -4.7286791 0 -2.280608 5.9589514 + 200 1.6630725 -4.7750988 0 -2.2811136 5.7364886 + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 +Loop time of 20.9283 on 1 procs for 250 steps with 4000 atoms + +Performance: 5160.475 tau/day, 11.946 timesteps/s +98.6% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.809 | 20.809 | 20.809 | 0.0 | 99.43 +Neigh | 0.088638 | 0.088638 | 0.088638 | 0.0 | 0.42 +Comm | 0.013424 | 0.013424 | 0.013424 | 0.0 | 0.06 +Output | 0.0002737 | 0.0002737 | 0.0002737 | 0.0 | 0.00 +Modify | 0.014334 | 0.014334 | 0.014334 | 0.0 | 0.07 +Other | | 0.003089 | | | 0.01 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5499 ave 5499 max 5499 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151513 ave 151513 max 151513 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151513 +Ave neighs/atom = 37.8783 +Neighbor list builds = 12 +Dangerous builds not checked + +write_data melt.data +write_restart melt.restart + +clear + using 1 OpenMP thread(s) per MPI task + +read_restart melt.restart + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid + 4000 atoms + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.36 | 3.36 | 3.36 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 1.6275257 -4.7224992 0 -2.281821 5.9567365 + 300 1.645592 -4.7496711 0 -2.2819002 5.8734193 + 350 1.6514972 -4.7580756 0 -2.2814491 5.810167 + 400 1.6540555 -4.7622999 0 -2.281837 5.8200413 + 450 1.6264734 -4.7200865 0 -2.2809863 5.9546991 + 500 1.6366891 -4.7350979 0 -2.2806781 5.9369284 +Loop time of 21.1422 on 1 procs for 250 steps with 4000 atoms + +Performance: 5108.279 tau/day, 11.825 timesteps/s +98.5% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.925 | 20.925 | 20.925 | 0.0 | 98.97 +Neigh | 0.18452 | 0.18452 | 0.18452 | 0.0 | 0.87 +Comm | 0.014836 | 0.014836 | 0.014836 | 0.0 | 0.07 +Output | 0.00027108 | 0.00027108 | 0.00027108 | 0.0 | 0.00 +Modify | 0.01366 | 0.01366 | 0.01366 | 0.0 | 0.06 +Other | | 0.004355 | | | 0.02 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5472 ave 5472 max 5472 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151513 ave 151513 max 151513 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151513 +Ave neighs/atom = 37.8783 +Neighbor list builds = 25 +Dangerous builds = 25 + +clear + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style atomic + +read_data melt.data + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4000 atoms + reading velocities ... + 4000 velocities + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.86 | 2.86 | 2.86 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.6275257 -4.7224992 0 -2.281821 5.9567365 + 50 1.6454666 -4.7497515 0 -2.2821686 5.8729175 + 100 1.6512008 -4.7582693 0 -2.2820874 5.8090548 + 150 1.6537193 -4.7627023 0 -2.2827434 5.8177704 + 200 1.6258731 -4.7205017 0 -2.2823017 5.952511 + 250 1.6370862 -4.7373176 0 -2.2823022 5.925807 +Loop time of 21.1026 on 1 procs for 250 steps with 4000 atoms + +Performance: 5117.845 tau/day, 11.847 timesteps/s +98.7% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 20.984 | 20.984 | 20.984 | 0.0 | 99.44 +Neigh | 0.088639 | 0.088639 | 0.088639 | 0.0 | 0.42 +Comm | 0.012881 | 0.012881 | 0.012881 | 0.0 | 0.06 +Output | 0.00028563 | 0.00028563 | 0.00028563 | 0.0 | 0.00 +Modify | 0.013523 | 0.013523 | 0.013523 | 0.0 | 0.06 +Other | | 0.003033 | | | 0.01 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5487 ave 5487 max 5487 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151490 ave 151490 max 151490 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151490 +Ave neighs/atom = 37.8725 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm melt.data melt.restart +Total wall time: 0:01:05 diff --git a/examples/python/log.4May17.pair_python_melt.g++.4 b/examples/python/log.4May17.pair_python_melt.g++.4 new file mode 100644 index 0000000000..58dae340bd --- /dev/null +++ b/examples/python/log.4May17.pair_python_melt.g++.4 @@ -0,0 +1,214 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733681 0 -2.2744931 -3.7033504 + 50 1.6754119 -4.7947589 0 -2.2822693 5.6615925 + 100 1.6503357 -4.756014 0 -2.2811293 5.8050524 + 150 1.6596605 -4.7699432 0 -2.2810749 5.7830138 + 200 1.6371874 -4.7365462 0 -2.2813789 5.9246674 + 250 1.6323462 -4.7292021 0 -2.2812949 5.9762238 +Loop time of 5.65922 on 4 procs for 250 steps with 4000 atoms + +Performance: 19083.895 tau/day, 44.176 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.4529 | 5.5207 | 5.5575 | 1.7 | 97.55 +Neigh | 0.023164 | 0.023376 | 0.023883 | 0.2 | 0.41 +Comm | 0.073318 | 0.1099 | 0.17804 | 12.2 | 1.94 +Output | 0.00023365 | 0.00026143 | 0.00030684 | 0.0 | 0.00 +Modify | 0.0036483 | 0.0037143 | 0.003896 | 0.2 | 0.07 +Other | | 0.001274 | | | 0.02 + +Nlocal: 1000 ave 1010 max 982 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703.75 ave 2713 max 2689 min +Histogram: 1 0 0 0 0 0 0 2 0 1 +Neighs: 37915.5 ave 39239 max 36193 min +Histogram: 1 0 0 0 0 1 1 0 0 1 + +Total # of neighbors = 151662 +Ave neighs/atom = 37.9155 +Neighbor list builds = 12 +Dangerous builds not checked + +write_data melt.data +write_restart melt.restart + +clear + using 1 OpenMP thread(s) per MPI task + +read_restart melt.restart + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid + 4000 atoms + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.815 | 2.816 | 2.816 Mbytes +Step Temp E_pair E_mol TotEng Press + 250 1.6323462 -4.7292062 0 -2.2812991 5.9762168 + 300 1.6451788 -4.7488091 0 -2.2816578 5.8375485 + 350 1.6171909 -4.7064928 0 -2.2813129 6.0094235 + 400 1.6388136 -4.7387093 0 -2.2811035 5.9331084 + 450 1.6431295 -4.7452215 0 -2.2811435 5.8929898 + 500 1.643316 -4.7454222 0 -2.2810644 5.8454817 +Loop time of 5.70169 on 4 procs for 250 steps with 4000 atoms + +Performance: 18941.760 tau/day, 43.847 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.3919 | 5.4905 | 5.6136 | 3.7 | 96.30 +Neigh | 0.046791 | 0.047817 | 0.048795 | 0.3 | 0.84 +Comm | 0.034221 | 0.1575 | 0.25635 | 22.1 | 2.76 +Output | 0.00020409 | 0.00023448 | 0.00026131 | 0.0 | 0.00 +Modify | 0.0035028 | 0.0035674 | 0.0036926 | 0.1 | 0.06 +Other | | 0.002079 | | | 0.04 + +Nlocal: 1000 ave 1012 max 983 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Nghost: 2699 ave 2706 max 2693 min +Histogram: 1 1 0 0 0 0 1 0 0 1 +Neighs: 37930.8 ave 39292 max 36264 min +Histogram: 1 0 0 0 1 0 0 1 0 1 + +Total # of neighbors = 151723 +Ave neighs/atom = 37.9308 +Neighbor list builds = 25 +Dangerous builds = 25 + +clear + using 1 OpenMP thread(s) per MPI task + +units lj +atom_style atomic + +read_data melt.data + orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid + reading atoms ... + 4000 atoms + reading velocities ... + 4000 velocities + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.315 | 2.316 | 2.316 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 1.6323462 -4.7292062 0 -2.2812991 5.9762168 + 50 1.6450626 -4.7488948 0 -2.2819177 5.8370409 + 100 1.6169004 -4.7066969 0 -2.2819526 6.0082546 + 150 1.6384234 -4.7389689 0 -2.2819482 5.9315273 + 200 1.6428814 -4.7460743 0 -2.2823683 5.8888228 + 250 1.6432631 -4.7466603 0 -2.2823818 5.8398819 +Loop time of 5.69568 on 4 procs for 250 steps with 4000 atoms + +Performance: 18961.751 tau/day, 43.893 timesteps/s +98.3% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.4041 | 5.5245 | 5.6139 | 3.2 | 96.99 +Neigh | 0.022658 | 0.022986 | 0.023398 | 0.2 | 0.40 +Comm | 0.053521 | 0.14309 | 0.26385 | 20.2 | 2.51 +Output | 0.00027037 | 0.00029504 | 0.00033665 | 0.0 | 0.01 +Modify | 0.0035288 | 0.0035585 | 0.0035827 | 0.0 | 0.06 +Other | | 0.001275 | | | 0.02 + +Nlocal: 1000 ave 1013 max 989 min +Histogram: 1 0 0 1 0 1 0 0 0 1 +Nghost: 2695.5 ave 2706 max 2682 min +Histogram: 1 0 0 0 0 0 2 0 0 1 +Neighs: 37927.2 ave 39002 max 36400 min +Histogram: 1 0 0 0 1 0 0 0 0 2 + +Total # of neighbors = 151709 +Ave neighs/atom = 37.9273 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm melt.data melt.restart +Total wall time: 0:00:17 diff --git a/examples/python/log.4May17.pair_python_spce.g++.1 b/examples/python/log.4May17.pair_python_spce.g++.1 new file mode 100644 index 0000000000..540c06853f --- /dev/null +++ b/examples/python/log.4May17.pair_python_spce.g++.1 @@ -0,0 +1,122 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 1 by 1 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/long 12.0 python 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 103823 64000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 41.05 | 41.05 | 41.05 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.369 0 -16692.369 -1289.222 + 10 120.56861 -17769.719 0 -16691.902 -4082.7098 + 20 136.08014 -17884.591 0 -16668.109 -5140.7824 + 30 136.97316 -17874.351 0 -16649.887 -5351.3571 + 40 153.37285 -18001.493 0 -16630.424 -5227.0601 + 50 167.70414 -18105.435 0 -16606.252 -4473.2089 + 60 163.08253 -18037.29 0 -16579.422 -3295.8963 + 70 169.60395 -18067.078 0 -16550.912 -2615.7026 + 80 182.94811 -18155.978 0 -16520.523 -2393.3156 + 90 191.29902 -18197.887 0 -16487.779 -2242.7104 + 100 194.70949 -18195.021 0 -16454.425 -1955.2916 +Loop time of 23.5385 on 1 procs for 100 steps with 4500 atoms + +Performance: 0.367 ns/day, 65.385 hours/ns, 4.248 timesteps/s +98.9% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 21.642 | 21.642 | 21.642 | 0.0 | 91.94 +Bond | 0.00021696 | 0.00021696 | 0.00021696 | 0.0 | 0.00 +Kspace | 1.5436 | 1.5436 | 1.5436 | 0.0 | 6.56 +Neigh | 0.25623 | 0.25623 | 0.25623 | 0.0 | 1.09 +Comm | 0.024325 | 0.024325 | 0.024325 | 0.0 | 0.10 +Output | 0.00064301 | 0.00064301 | 0.00064301 | 0.0 | 0.00 +Modify | 0.065919 | 0.065919 | 0.065919 | 0.0 | 0.28 +Other | | 0.005401 | | | 0.02 + +Nlocal: 4500 ave 4500 max 4500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 21216 ave 21216 max 21216 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 2.60176e+06 ave 2.60176e+06 max 2.60176e+06 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 2601762 +Ave neighs/atom = 578.169 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:24 diff --git a/examples/python/log.4May17.pair_python_spce.g++.4 b/examples/python/log.4May17.pair_python_spce.g++.4 new file mode 100644 index 0000000000..332c079ec1 --- /dev/null +++ b/examples/python/log.4May17.pair_python_spce.g++.4 @@ -0,0 +1,122 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +units real +atom_style full + +read_data data.spce + orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736) + 2 by 2 by 1 MPI processor grid + reading atoms ... + 4500 atoms + scanning bonds ... + 2 = max bonds/atom + scanning angles ... + 1 = max angles/atom + reading bonds ... + 3000 bonds + reading angles ... + 1500 angles + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 1 = max # of 1-4 neighbors + 2 = max # of special neighbors + +pair_style hybrid/overlay coul/long 12.0 python 12.0 +kspace_style pppm 1.0e-6 + +pair_coeff * * coul/long +pair_coeff * * python py_pot.LJCutSPCE OW NULL + +bond_style harmonic +angle_style harmonic +dihedral_style none +improper_style none + +bond_coeff 1 1000.00 1.000 +angle_coeff 1 100.0 109.47 + +special_bonds lj/coul 0.0 0.0 1.0 + 2 = max # of 1-2 neighbors + 1 = max # of 1-3 neighbors + 2 = max # of special neighbors + +neighbor 2.0 bin + +fix 1 all shake 0.0001 20 0 b 1 a 1 + 0 = # of size 2 clusters + 0 = # of size 3 clusters + 0 = # of size 4 clusters + 1500 = # of frozen angles +fix 2 all nvt temp 300.0 300.0 100.0 + +thermo 10 +run 100 +PPPM initialization ... +WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:321) + G vector (1/distance) = 0.279652 + grid = 40 40 40 + stencil order = 5 + estimated absolute RMS force accuracy = 0.000394674 + estimated relative force accuracy = 1.18855e-06 + using double precision FFTs + 3d grid and FFT values/proc = 34263 16000 +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 14 + ghost atom cutoff = 14 + binsize = 7, bins = 6 6 6 + 2 neighbor lists, perpetual/occasional/extra = 2 0 0 + (1) pair coul/long, perpetual + attributes: half, newton on + pair build: half/bin/newton + stencil: half/bin/3d/newton + bin: standard + (2) pair python, perpetual, skip from (1) + attributes: half, newton on + pair build: skip + stencil: none + bin: none +Per MPI rank memory allocation (min/avg/max) = 14.59 | 14.59 | 14.59 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 0 -16692.369 0 -16692.369 -1289.222 + 10 120.56861 -17769.719 0 -16691.902 -4082.7098 + 20 136.08014 -17884.591 0 -16668.109 -5140.7824 + 30 136.97316 -17874.351 0 -16649.887 -5351.3571 + 40 153.37285 -18001.493 0 -16630.424 -5227.0601 + 50 167.70414 -18105.435 0 -16606.252 -4473.2089 + 60 163.08253 -18037.29 0 -16579.422 -3295.8963 + 70 169.60395 -18067.078 0 -16550.912 -2615.7026 + 80 182.94811 -18155.978 0 -16520.523 -2393.3156 + 90 191.29902 -18197.887 0 -16487.779 -2242.7104 + 100 194.70949 -18195.021 0 -16454.425 -1955.2916 +Loop time of 6.4942 on 4 procs for 100 steps with 4500 atoms + +Performance: 1.330 ns/day, 18.039 hours/ns, 15.398 timesteps/s +98.7% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.4084 | 5.572 | 5.8013 | 7.2 | 85.80 +Bond | 0.00012994 | 0.0001421 | 0.00016356 | 0.0 | 0.00 +Kspace | 0.52942 | 0.75773 | 0.92078 | 19.5 | 11.67 +Neigh | 0.071055 | 0.07116 | 0.071278 | 0.0 | 1.10 +Comm | 0.040311 | 0.041255 | 0.041817 | 0.3 | 0.64 +Output | 0.00040603 | 0.00048071 | 0.00058675 | 0.0 | 0.01 +Modify | 0.047507 | 0.047629 | 0.047772 | 0.1 | 0.73 +Other | | 0.003771 | | | 0.06 + +Nlocal: 1125 ave 1154 max 1092 min +Histogram: 1 0 0 0 1 0 0 1 0 1 +Nghost: 12256.2 ave 12296 max 12213 min +Histogram: 1 0 1 0 0 0 0 0 1 1 +Neighs: 650440 ave 678828 max 626375 min +Histogram: 1 0 0 0 2 0 0 0 0 1 + +Total # of neighbors = 2601762 +Ave neighs/atom = 578.169 +Ave special neighs/atom = 2 +Neighbor list builds = 3 +Dangerous builds = 0 +Total wall time: 0:00:06 diff --git a/examples/python/log.4May17.pair_python_table.g++.1 b/examples/python/log.4May17.pair_python_table.g++.1 new file mode 100644 index 0000000000..c594a8e90a --- /dev/null +++ b/examples/python/log.4May17.pair_python_table.g++.1 @@ -0,0 +1,99 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 1 by 1 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + +pair_style table linear 2000 +pair_coeff 1 1 lj_1_1.table LJ +WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:476) + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 3.184 | 3.184 | 3.184 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733629 0 -2.2744879 -3.7032813 + 50 1.6758731 -4.7953067 0 -2.2821255 5.6706553 + 100 1.6458118 -4.7490281 0 -2.2809276 5.8697466 + 150 1.632425 -4.7284533 0 -2.2804279 5.9595684 + 200 1.6631578 -4.7749889 0 -2.2808759 5.7365839 + 250 1.6277062 -4.7224727 0 -2.2815238 5.9572913 +Loop time of 0.996739 on 1 procs for 250 steps with 4000 atoms + +Performance: 108353.298 tau/day, 250.818 timesteps/s +99.8% CPU use with 1 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.87985 | 0.87985 | 0.87985 | 0.0 | 88.27 +Neigh | 0.08799 | 0.08799 | 0.08799 | 0.0 | 8.83 +Comm | 0.012301 | 0.012301 | 0.012301 | 0.0 | 1.23 +Output | 0.00013161 | 0.00013161 | 0.00013161 | 0.0 | 0.01 +Modify | 0.013656 | 0.013656 | 0.013656 | 0.0 | 1.37 +Other | | 0.002808 | | | 0.28 + +Nlocal: 4000 ave 4000 max 4000 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Nghost: 5500 ave 5500 max 5500 min +Histogram: 1 0 0 0 0 0 0 0 0 0 +Neighs: 151496 ave 151496 max 151496 min +Histogram: 1 0 0 0 0 0 0 0 0 0 + +Total # of neighbors = 151496 +Ave neighs/atom = 37.874 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm lj_1_1.table + +Total wall time: 0:00:01 diff --git a/examples/python/log.4May17.pair_python_table.g++.4 b/examples/python/log.4May17.pair_python_table.g++.4 new file mode 100644 index 0000000000..e509fc7f6a --- /dev/null +++ b/examples/python/log.4May17.pair_python_table.g++.4 @@ -0,0 +1,99 @@ +LAMMPS (4 May 2017) + using 1 OpenMP thread(s) per MPI task +# 3d Lennard-Jones melt + +units lj +atom_style atomic + +lattice fcc 0.8442 +Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 +region box block 0 10 0 10 0 10 +create_box 1 box +Created orthogonal box = (0 0 0) to (16.796 16.796 16.796) + 1 by 2 by 2 MPI processor grid +create_atoms 1 box +Created 4000 atoms +mass * 1.0 + +velocity all create 3.0 87287 + +pair_style python 2.5 +pair_coeff * * py_pot.LJCutMelt lj + +# generate tabulated potential from python variant +pair_write 1 1 2000 rsq 0.01 2.5 lj_1_1.table LJ +Neighbor list info ... + update every 1 steps, delay 10 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair python, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard + +pair_style table linear 2000 +pair_coeff 1 1 lj_1_1.table LJ +WARNING: 2 of 2000 force values in table are inconsistent with -dE/dr. + Should only be flagged at inflection points (../pair_table.cpp:476) + +neighbor 0.3 bin +neigh_modify every 20 delay 0 check no + +fix 1 all nve + +thermo 50 +run 250 +Neighbor list info ... + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4, bins = 12 12 12 + 1 neighbor lists, perpetual/occasional/extra = 1 0 0 + (1) pair table, perpetual + attributes: half, newton on + pair build: half/bin/atomonly/newton + stencil: half/bin/3d/newton + bin: standard +Per MPI rank memory allocation (min/avg/max) = 2.69 | 2.69 | 2.69 Mbytes +Step Temp E_pair E_mol TotEng Press + 0 3 -6.7733629 0 -2.2744879 -3.7032813 + 50 1.675395 -4.7945736 0 -2.2821094 5.6620623 + 100 1.6503067 -4.7558145 0 -2.2809733 5.8055967 + 150 1.6595852 -4.7697199 0 -2.2809644 5.7837898 + 200 1.6371471 -4.7363942 0 -2.2812874 5.924977 + 250 1.6315623 -4.7278268 0 -2.2810951 5.9807196 +Loop time of 0.291846 on 4 procs for 250 steps with 4000 atoms + +Performance: 370058.286 tau/day, 856.616 timesteps/s +99.4% CPU use with 4 MPI tasks x 1 OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.22586 | 0.23364 | 0.24085 | 1.3 | 80.06 +Neigh | 0.022808 | 0.023235 | 0.023602 | 0.2 | 7.96 +Comm | 0.022573 | 0.030065 | 0.038092 | 3.9 | 10.30 +Output | 0.00013423 | 0.00014067 | 0.00015759 | 0.0 | 0.05 +Modify | 0.0035079 | 0.0035501 | 0.0036008 | 0.1 | 1.22 +Other | | 0.001211 | | | 0.42 + +Nlocal: 1000 ave 1010 max 981 min +Histogram: 1 0 0 0 0 0 1 0 0 2 +Nghost: 2703 ave 2715 max 2688 min +Histogram: 1 0 0 0 0 1 1 0 0 1 +Neighs: 37915.2 ave 39191 max 36151 min +Histogram: 1 0 0 0 0 1 0 1 0 1 + +Total # of neighbors = 151661 +Ave neighs/atom = 37.9153 +Neighbor list builds = 12 +Dangerous builds not checked + +shell rm lj_1_1.table + +Total wall time: 0:00:00 diff --git a/examples/python/py_pot.py b/examples/python/py_pot.py new file mode 100644 index 0000000000..5699bd082c --- /dev/null +++ b/examples/python/py_pot.py @@ -0,0 +1,65 @@ +from __future__ import print_function + +class LAMMPSPairPotential(object): + def __init__(self): + self.pmap=dict() + self.units='lj' + def map_coeff(self,name,ltype): + self.pmap[ltype]=name + def check_units(self,units): + if (units != self.units): + raise Exception("Conflicting units: %s vs. %s" % (self.units,units)) + +class LJCutMelt(LAMMPSPairPotential): + def __init__(self): + super(LJCutMelt,self).__init__() + # set coeffs: 48*eps*sig**12, 24*eps*sig**6, + # 4*eps*sig**12, 4*eps*sig**6 + self.units = 'lj' + self.coeff = {'lj' : {'lj' : (48.0,24.0,4.0,4.0)}} + + def compute_force(self,rsq,itype,jtype): + coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj1 = coeff[0] + lj2 = coeff[1] + return (r6inv * (lj1*r6inv - lj2))*r2inv + + def compute_energy(self,rsq,itype,jtype): + coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj3 = coeff[2] + lj4 = coeff[3] + return (r6inv * (lj3*r6inv - lj4)) + + +class LJCutSPCE(LAMMPSPairPotential): + def __init__(self): + super(LJCutSPCE,self).__init__() + self.units='real' + # SPCE oxygen LJ parameters in real units + eps=0.15535 + sig=3.166 + self.coeff = {'OW' : {'OW' : (48.0*eps*sig**12,24.0*eps*sig**6, + 4.0*eps*sig**12, 4.0*eps*sig**6), + 'HW' : (0.0,0.0, 0.0,0.0)}, + 'HW' : {'OW' : (0.0,0.0, 0.0,0.0), + 'HW' : (0.0,0.0, 0.0,0.0)}} + + def compute_force(self,rsq,itype,jtype): + coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj1 = coeff[0] + lj2 = coeff[1] + return (r6inv * (lj1*r6inv - lj2))*r2inv + + def compute_energy(self,rsq,itype,jtype): + coeff = self.coeff[self.pmap[itype]][self.pmap[jtype]] + r2inv = 1.0/rsq + r6inv = r2inv*r2inv*r2inv + lj3 = coeff[2] + lj4 = coeff[3] + return (r6inv * (lj3*r6inv - lj4)) diff --git a/examples/snap/Ta06A.snapparam b/examples/snap/Ta06A.snapparam index 7b30312f59..283629d658 100644 --- a/examples/snap/Ta06A.snapparam +++ b/examples/snap/Ta06A.snapparam @@ -8,8 +8,8 @@ twojmax 6 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 bzeroflag 0 +quadraticflag 0 diff --git a/examples/snap/W_2940_2017_2.snap b/examples/snap/W_2940_2017_2.snap index 51eee41a0a..04b8d58094 100644 --- a/examples/snap/W_2940_2017_2.snap +++ b/examples/snap/W_2940_2017_2.snap @@ -5,7 +5,7 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay & zbl ${zblcutinner} ${zblcutouter} & diff --git a/examples/snap/W_2940_2017_2.snapparam b/examples/snap/W_2940_2017_2.snapparam index f17961bdd7..27ab61a266 100644 --- a/examples/snap/W_2940_2017_2.snapparam +++ b/examples/snap/W_2940_2017_2.snapparam @@ -6,8 +6,8 @@ twojmax 8 # optional -gamma 1 rfac0 0.99363 rmin0 0 diagonalstyle 3 bzeroflag 0 +quadraticflag 0 diff --git a/examples/snap/W_2940_2017_2_He_JW2013.snap b/examples/snap/W_2940_2017_2_He_JW2013.snap index 45a31955b3..cb70916ec4 100644 --- a/examples/snap/W_2940_2017_2_He_JW2013.snap +++ b/examples/snap/W_2940_2017_2_He_JW2013.snap @@ -5,7 +5,7 @@ variable zblcutinner equal 4 variable zblcutouter equal 4.8 variable zblz equal 74 -# Specify hybrid with SNAP, ZBL, and long-range Coulomb +# Specify hybrid with SNAP and ZBL pair_style hybrid/overlay zbl ${zblcutinner} ${zblcutouter} snap table spline 10000 table spline 10000 pair_coeff 1 1 zbl ${zblz} ${zblz} diff --git a/lib/gpu/Makefile.linux.mixed b/lib/gpu/Makefile.linux.mixed index 42fc8e9740..6289163ac8 100644 --- a/lib/gpu/Makefile.linux.mixed +++ b/lib/gpu/Makefile.linux.mixed @@ -8,7 +8,6 @@ EXTRAMAKE = Makefile.lammps.standard CUDA_HOME = /usr/local/cuda -CUDA_HOME = /home/projects/openmpi/1.8.1/intel/13.1.SP1.106/cuda/6.0.37 NVCC = nvcc # Kepler CUDA diff --git a/lib/gpu/Nvidia.makefile b/lib/gpu/Nvidia.makefile index 660544cfaa..ee2eb72632 100644 --- a/lib/gpu/Nvidia.makefile +++ b/lib/gpu/Nvidia.makefile @@ -63,6 +63,7 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \ $(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \ $(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \ $(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \ + $(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \ $(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \ $(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \ $(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \ @@ -117,6 +118,7 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \ $(OBJ_DIR)/lj_coul_debye.cubin $(OBJ_DIR)/lj_coul_debye_cubin.h \ $(OBJ_DIR)/coul_dsf.cubin $(OBJ_DIR)/coul_dsf_cubin.h \ $(OBJ_DIR)/sw.cubin $(OBJ_DIR)/sw_cubin.h \ + $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta_cubin.h \ $(OBJ_DIR)/beck.cubin $(OBJ_DIR)/beck_cubin.h \ $(OBJ_DIR)/mie.cubin $(OBJ_DIR)/mie_cubin.h \ $(OBJ_DIR)/soft.cubin $(OBJ_DIR)/soft_cubin.h \ @@ -613,6 +615,18 @@ $(OBJ_DIR)/lal_coul_dsf.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf.cpp $(OBJ_DIR)/c $(OBJ_DIR)/lal_coul_dsf_ext.o: $(ALL_H) lal_coul_dsf.h lal_coul_dsf_ext.cpp lal_base_charge.h $(CUDR) -o $@ -c lal_coul_dsf_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/vashishta.cubin: lal_vashishta.cu lal_precision.h lal_preprocessor.h + $(CUDA) --cubin -DNV_KERNEL -o $@ lal_vashishta.cu + +$(OBJ_DIR)/vashishta_cubin.h: $(OBJ_DIR)/vashishta.cubin $(OBJ_DIR)/vashishta.cubin + $(BIN2C) -c -n vashishta $(OBJ_DIR)/vashishta.cubin > $(OBJ_DIR)/vashishta_cubin.h + +$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cubin.h $(OBJ_DIR)/lal_base_three.o + $(CUDR) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h + $(CUDR) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR) + $(OBJ_DIR)/sw.cubin: lal_sw.cu lal_precision.h lal_preprocessor.h $(CUDA) --cubin -DNV_KERNEL -o $@ lal_sw.cu diff --git a/lib/gpu/Opencl.makefile b/lib/gpu/Opencl.makefile index 4a59595313..f116508ae5 100644 --- a/lib/gpu/Opencl.makefile +++ b/lib/gpu/Opencl.makefile @@ -52,6 +52,7 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_answer.o \ $(OBJ_DIR)/lal_lj_coul_debye.o $(OBJ_DIR)/lal_lj_coul_debye_ext.o \ $(OBJ_DIR)/lal_coul_dsf.o $(OBJ_DIR)/lal_coul_dsf_ext.o \ $(OBJ_DIR)/lal_sw.o $(OBJ_DIR)/lal_sw_ext.o \ + $(OBJ_DIR)/lal_vashishta.o $(OBJ_DIR)/lal_vashishta_ext.o \ $(OBJ_DIR)/lal_beck.o $(OBJ_DIR)/lal_beck_ext.o \ $(OBJ_DIR)/lal_mie.o $(OBJ_DIR)/lal_mie_ext.o \ $(OBJ_DIR)/lal_soft.o $(OBJ_DIR)/lal_soft_ext.o \ @@ -92,7 +93,7 @@ KERS = $(OBJ_DIR)/device_cl.h $(OBJ_DIR)/atom_cl.h \ $(OBJ_DIR)/tersoff_cl.h $(OBJ_DIR)/tersoff_zbl_cl.h \ $(OBJ_DIR)/tersoff_mod_cl.h $(OBJ_DIR)/coul_cl.h \ $(OBJ_DIR)/coul_debye_cl.h $(OBJ_DIR)/zbl_cl.h \ - $(OBJ_DIR)/lj_cubic_cl.h + $(OBJ_DIR)/lj_cubic_cl.h $(OBJ_DIR)/vashishta_cl.h OCL_EXECS = $(BIN_DIR)/ocl_get_devices @@ -450,6 +451,15 @@ $(OBJ_DIR)/lal_sw.o: $(ALL_H) lal_sw.h lal_sw.cpp $(OBJ_DIR)/sw_cl.h $(OBJ_DIR) $(OBJ_DIR)/lal_sw_ext.o: $(ALL_H) lal_sw.h lal_sw_ext.cpp lal_base_three.h $(OCL) -o $@ -c lal_sw_ext.cpp -I$(OBJ_DIR) +$(OBJ_DIR)/vashishta_cl.h: lal_vashishta.cu $(PRE1_H) + $(BSH) ./geryon/file_to_cstr.sh vashishta $(PRE1_H) lal_vashishta.cu $(OBJ_DIR)/vashishta_cl.h; + +$(OBJ_DIR)/lal_vashishta.o: $(ALL_H) lal_vashishta.h lal_vashishta.cpp $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/vashishta_cl.h $(OBJ_DIR)/lal_base_three.o + $(OCL) -o $@ -c lal_vashishta.cpp -I$(OBJ_DIR) + +$(OBJ_DIR)/lal_vashishta_ext.o: $(ALL_H) lal_vashishta.h lal_vashishta_ext.cpp lal_base_three.h + $(OCL) -o $@ -c lal_vashishta_ext.cpp -I$(OBJ_DIR) + $(OBJ_DIR)/beck_cl.h: lal_beck.cu $(PRE1_H) $(BSH) ./geryon/file_to_cstr.sh beck $(PRE1_H) lal_beck.cu $(OBJ_DIR)/beck_cl.h; diff --git a/lib/gpu/lal_vashishta.cpp b/lib/gpu/lal_vashishta.cpp new file mode 100644 index 0000000000..96537e65d3 --- /dev/null +++ b/lib/gpu/lal_vashishta.cpp @@ -0,0 +1,283 @@ +/*************************************************************************** + vashishta.cpp + ------------------- + Anders Hafreager (UiO) + + Class for acceleration of the vashishta pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : Mon June 12, 2017 + email : andershaf@gmail.com + ***************************************************************************/ + +#if defined(USE_OPENCL) +#include "vashishta_cl.h" +#elif defined(USE_CUDART) +const char *vashishta=0; +#else +#include "vashishta_cubin.h" +#endif + +#include "lal_vashishta.h" +#include +using namespace LAMMPS_AL; +#define VashishtaT Vashishta + +extern Device device; + +template +VashishtaT::Vashishta() : BaseThree(), _allocated(false) { +} + +template +VashishtaT::~Vashishta() { + clear(); +} + +template +int VashishtaT::bytes_per_atom(const int max_nbors) const { + return this->bytes_per_atom_atomic(max_nbors); +} + +template +int VashishtaT::init(const int ntypes, const int nlocal, const int nall, const int max_nbors, + const double cell_size, const double gpu_split, FILE *_screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc) +{ + int success; + success=this->init_three(nlocal,nall,max_nbors,0,cell_size,gpu_split, + _screen,vashishta,"k_vashishta","k_vashishta_three_center", + "k_vashishta_three_end"); + if (success!=0) + return success; + + // If atom type constants fit in shared memory use fast kernel + int lj_types=ntypes; + shared_types=false; + int max_shared_types=this->device->max_shared_types(); + if (lj_types<=max_shared_types && this->_block_size>=max_shared_types) { + lj_types=max_shared_types; + shared_types=true; + } + _lj_types=lj_types; + + _nparams = nparams; + _nelements = nelements; + + UCL_H_Vec dview(nparams,*(this->ucl_device), + UCL_WRITE_ONLY); + + for (int i=0; iucl_device),UCL_READ_ONLY); + + for (int i=0; i(eta[i]); + dview[i].y=static_cast(lam1inv[i]); + dview[i].z=static_cast(lam4inv[i]); + dview[i].w=static_cast(zizj[i]); + } + + ucl_copy(param1,dview,false); + param1_tex.get_texture(*(this->pair_program),"param1_tex"); + param1_tex.bind_float(param1,4); + + param2.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(mbigd[i]); + dview[i].y=static_cast(dvrc[i]); + dview[i].z=static_cast(big6w[i]); + dview[i].w=static_cast(heta[i]); + } + + ucl_copy(param2,dview,false); + param2_tex.get_texture(*(this->pair_program),"param2_tex"); + param2_tex.bind_float(param2,4); + + param3.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(bigh[i]); + dview[i].y=static_cast(bigw[i]); + dview[i].z=static_cast(dvrc[i]); + dview[i].w=static_cast(c0[i]); + } + + ucl_copy(param3,dview,false); + param3_tex.get_texture(*(this->pair_program),"param3_tex"); + param3_tex.bind_float(param3,4); + + param4.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(r0sq); + dview[i].y=static_cast(gamma[i]); + dview[i].z=static_cast(cutsq[i]); + dview[i].w=static_cast(r0[i]); + } + + ucl_copy(param4,dview,false); + param4_tex.get_texture(*(this->pair_program),"param4_tex"); + param4_tex.bind_float(param4,4); + + param5.alloc(nparams,*(this->ucl_device),UCL_READ_ONLY); + + for (int i=0; i(bigc[i]); + dview[i].y=static_cast(costheta[i]); + dview[i].z=static_cast(bigb[i]); + dview[i].w=static_cast(big2b[i]); + } + + ucl_copy(param5,dview,false); + param5_tex.get_texture(*(this->pair_program),"param5_tex"); + param5_tex.bind_float(param5,4); + + UCL_H_Vec dview_elem2param(nelements*nelements*nelements, + *(this->ucl_device), UCL_WRITE_ONLY); + + elem2param.alloc(nelements*nelements*nelements,*(this->ucl_device), + UCL_READ_ONLY); + + for (int i = 0; i < nelements; i++) + for (int j = 0; j < nelements; j++) + for (int k = 0; k < nelements; k++) { + int idx = i*nelements*nelements+j*nelements+k; + dview_elem2param[idx] = host_elem2param[i][j][k]; + } + + ucl_copy(elem2param,dview_elem2param,false); + + UCL_H_Vec dview_map(lj_types, *(this->ucl_device), UCL_WRITE_ONLY); + for (int i = 0; i < ntypes; i++) + dview_map[i] = host_map[i]; + + map.alloc(lj_types,*(this->ucl_device), UCL_READ_ONLY); + ucl_copy(map,dview_map,false); + + _allocated=true; + this->_max_bytes=param1.row_bytes()+param2.row_bytes()+param3.row_bytes()+param4.row_bytes()+param5.row_bytes()+ + map.row_bytes()+elem2param.row_bytes(); + return 0; +} + +template +void VashishtaT::clear() { + if (!_allocated) + return; + _allocated=false; + + param1.clear(); + param2.clear(); + param3.clear(); + param4.clear(); + param5.clear(); + map.clear(); + elem2param.clear(); + this->clear_atomic(); +} + +template +double VashishtaT::host_memory_usage() const { + return this->host_memory_usage_atomic()+sizeof(Vashishta); +} + +#define KTHREADS this->_threads_per_atom +#define JTHREADS this->_threads_per_atom +// --------------------------------------------------------------------------- +// Calculate energies, forces, and torques +// --------------------------------------------------------------------------- +template +void VashishtaT::loop(const bool _eflag, const bool _vflag, const int evatom) { + // Compute the block size and grid size to keep all cores busy + int BX=this->block_pair(); + int eflag, vflag; + if (_eflag) + eflag=1; + else + eflag=0; + + if (_vflag) + vflag=1; + else + vflag=0; + + int GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/this->_threads_per_atom))); + + // this->_nbor_data == nbor->dev_packed for gpu_nbor == 0 and tpa > 1 + // this->_nbor_data == nbor->dev_nbor for gpu_nbor == 1 or tpa == 1 + int ainum=this->ans->inum(); + int nbor_pitch=this->nbor->nbor_pitch(); + this->time_pair.start(); + + this->k_pair.set_size(GX,BX); + this->k_pair.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, + &eflag, &vflag, &ainum, &nbor_pitch, + &this->_threads_per_atom); + + BX=this->block_size(); + GX=static_cast(ceil(static_cast(this->ans->inum())/ + (BX/(KTHREADS*JTHREADS)))); + + this->k_three_center.set_size(GX,BX); + this->k_three_center.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->ans->force, &this->ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &evatom); + Answer *end_ans; + #ifdef THREE_CONCURRENT + end_ans=this->ans2; + #else + end_ans=this->ans; + #endif + if (evatom!=0) { + + this->k_three_end_vatom.set_size(GX,BX); + this->k_three_end_vatom.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->nbor->dev_acc, + &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); + } else { + + this->k_three_end.set_size(GX,BX); + this->k_three_end.run(&this->atom->x, ¶m1, ¶m2, ¶m3, ¶m4, ¶m5, + &map, &elem2param, &_nelements, + &this->nbor->dev_nbor, &this->_nbor_data->begin(), + &this->nbor->dev_acc, + &end_ans->force, &end_ans->engv, &eflag, &vflag, &ainum, + &nbor_pitch, &this->_threads_per_atom, &this->_gpu_nbor); + } + + this->time_pair.stop(); +} + +template class Vashishta; + diff --git a/lib/gpu/lal_vashishta.cu b/lib/gpu/lal_vashishta.cu new file mode 100644 index 0000000000..caa3c03613 --- /dev/null +++ b/lib/gpu/lal_vashishta.cu @@ -0,0 +1,744 @@ +// ************************************************************************** +// vashishta.cu +// ------------------- +// Anders Hafreager (UiO) +// +// Device code for acceleration of the vashishta pair style +// +// __________________________________________________________________________ +// This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) +// __________________________________________________________________________ +// +// begin : Mon June 12, 2017 +// email : andershaf@gmail.com +// ***************************************************************************/ + +#ifdef NV_KERNEL +#include "lal_aux_fun1.h" + +#ifndef _DOUBLE_DOUBLE +texture pos_tex; +texture param1_tex; +texture param2_tex; +texture param3_tex; +texture param4_tex; +texture param5_tex; +#else +texture pos_tex; +texture param1_tex; +texture param2_tex; +texture param3_tex; +texture param4_tex; +texture param5_tex; +#endif + +#else +#define pos_tex x_ +#define param1_tex param1 +#define param2_tex param2 +#define param3_tex param3 +#define param4_tex param4 +#define param5_tex param5 +#endif + +#define THIRD (numtyp)0.66666666666666666667 + +//#define THREE_CONCURRENT + +#if (ARCH < 300) + +#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \ + eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + __local acctyp red_acc[6][BLOCK_ELLIPSE]; \ + red_acc[0][tid]=f.x; \ + red_acc[1][tid]=f.y; \ + red_acc[2][tid]=f.z; \ + red_acc[3][tid]=energy; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<4; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + f.x=red_acc[0][tid]; \ + f.y=red_acc[1][tid]; \ + f.z=red_acc[2][tid]; \ + energy=red_acc[3][tid]; \ + if (vflag>0) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid]=virial[r]; \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + if (offset < s) { \ + for (int r=0; r<6; r++) \ + red_acc[r][tid] += red_acc[r][tid+s]; \ + } \ + } \ + for (int r=0; r<6; r++) \ + virial[r]=red_acc[r][tid]; \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]+=energy*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]+=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + acctyp4 old=ans[ii]; \ + old.x+=f.x; \ + old.y+=f.y; \ + old.z+=f.z; \ + ans[ii]=old; \ + } + +#else + +#define store_answers_p(f, energy, virial, ii, inum, tid, t_per_atom, offset, \ + eflag, vflag, ans, engv) \ + if (t_per_atom>1) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + f.x += shfl_xor(f.x, s, t_per_atom); \ + f.y += shfl_xor(f.y, s, t_per_atom); \ + f.z += shfl_xor(f.z, s, t_per_atom); \ + energy += shfl_xor(energy, s, t_per_atom); \ + } \ + if (vflag>0) { \ + for (unsigned int s=t_per_atom/2; s>0; s>>=1) { \ + for (int r=0; r<6; r++) \ + virial[r] += shfl_xor(virial[r], s, t_per_atom); \ + } \ + } \ + } \ + if (offset==0) { \ + int ei=ii; \ + if (eflag>0) { \ + engv[ei]+=energy*(acctyp)0.5; \ + ei+=inum; \ + } \ + if (vflag>0) { \ + for (int i=0; i<6; i++) { \ + engv[ei]+=virial[i]*(acctyp)0.5; \ + ei+=inum; \ + } \ + } \ + acctyp4 old=ans[ii]; \ + old.x+=f.x; \ + old.y+=f.y; \ + old.z+=f.z; \ + ans[ii]=old; \ + } + +#endif + + +__kernel void k_vashishta(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict param1, + const __global numtyp4 *restrict param2, + const __global numtyp4 *restrict param3, + const __global numtyp4 *restrict param4, + const __global numtyp4 *restrict param5, + const __global int *restrict map, + const __global int *restrict elem2param, + const int nelements, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, const int inum, + const int nbor_pitch, const int t_per_atom) { + __local int n_stride; + int tid, ii, offset; + atom_info(t_per_atom,ii,tid,offset); + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii0) + energy += (param3_bigh*reta+vc2-vc3-param3_bigw*r6inv-r*param3_dvrc+param3_c0); + + if (vflag>0) { + virial[0] += delx*delx*force; + virial[1] += dely*dely*force; + virial[2] += delz*delz*force; + virial[3] += delx*dely*force; + virial[4] += delx*delz*force; + virial[5] += dely*delz*force; + } + } + } // for nbor + + store_answers(f,energy,virial,ii,inum,tid,t_per_atom,offset,eflag,vflag, + ans,engv); + } // if ii + +} + +#define threebody(delr1x, delr1y, delr1z, eflag, energy) \ +{ \ + numtyp r1 = ucl_sqrt(rsq1); \ + numtyp rinvsq1 = ucl_recip(rsq1); \ + numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \ + numtyp gsrainv1 = param_gamma_ij * rainv1; \ + numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \ + numtyp expgsrainv1 = ucl_exp(gsrainv1); \ + \ + numtyp r2 = ucl_sqrt(rsq2); \ + numtyp rinvsq2 = ucl_recip(rsq2); \ + numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \ + numtyp gsrainv2 = param_gamma_ik * rainv2; \ + numtyp gsrainvsq2 = gsrainv2*rainv2/r2; \ + numtyp expgsrainv2 = ucl_exp(gsrainv2); \ + \ + numtyp rinv12 = ucl_recip(r1*r2); \ + numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \ + numtyp delcs = cs - param_costheta_ijk; \ + numtyp delcssq = delcs*delcs; \ + numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \ + numtyp pcsinvsq = pcsinv*pcsinv; \ + numtyp pcs = delcssq/pcsinv; \ + \ + numtyp facexp = expgsrainv1*expgsrainv2; \ + \ + numtyp facrad = param_bigb_ijk * facexp*pcs; \ + numtyp frad1 = facrad*gsrainvsq1; \ + numtyp frad2 = facrad*gsrainvsq2; \ + numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \ + numtyp facang12 = rinv12*facang; \ + numtyp csfacang = cs*facang; \ + numtyp csfac1 = rinvsq1*csfacang; \ + \ + fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \ + fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \ + fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \ + \ + numtyp csfac2 = rinvsq2*csfacang; \ + \ + fkx = delr2x*(frad2+csfac2)-delr1x*facang12; \ + fky = delr2y*(frad2+csfac2)-delr1y*facang12; \ + fkz = delr2z*(frad2+csfac2)-delr1z*facang12; \ + \ + if (eflag>0) \ + energy+=facrad; \ + if (vflag>0) { \ + virial[0] += delr1x*fjx + delr2x*fkx; \ + virial[1] += delr1y*fjy + delr2y*fky; \ + virial[2] += delr1z*fjz + delr2z*fkz; \ + virial[3] += delr1x*fjy + delr2x*fky; \ + virial[4] += delr1x*fjz + delr2x*fkz; \ + virial[5] += delr1y*fjz + delr2y*fkz; \ + } \ +} + +#define threebody_half(delr1x, delr1y, delr1z) \ +{ \ + numtyp r1 = ucl_sqrt(rsq1); \ + numtyp rinvsq1 = ucl_recip(rsq1); \ + numtyp rainv1 = ucl_recip(r1 - param_r0_ij); \ + numtyp gsrainv1 = param_gamma_ij * rainv1; \ + numtyp gsrainvsq1 = gsrainv1*rainv1/r1; \ + numtyp expgsrainv1 = ucl_exp(gsrainv1); \ + \ + numtyp r2 = ucl_sqrt(rsq2); \ + numtyp rainv2 = ucl_recip(r2 - param_r0_ik); \ + numtyp gsrainv2 = param_gamma_ik * rainv2; \ + numtyp expgsrainv2 = ucl_exp(gsrainv2); \ + \ + numtyp rinv12 = ucl_recip(r1*r2); \ + numtyp cs = (delr1x*delr2x + delr1y*delr2y + delr1z*delr2z) * rinv12; \ + numtyp delcs = cs - param_costheta_ijk; \ + numtyp delcssq = delcs*delcs; \ + numtyp pcsinv = param_bigc_ijk*delcssq+1.0; \ + numtyp pcsinvsq = pcsinv*pcsinv; \ + numtyp pcs = delcssq/pcsinv; \ + \ + numtyp facexp = expgsrainv1*expgsrainv2; \ + \ + numtyp facrad = param_bigb_ijk * facexp*pcs; \ + numtyp frad1 = facrad*gsrainvsq1; \ + numtyp facang = param_big2b_ijk * facexp*delcs/pcsinvsq; \ + numtyp facang12 = rinv12*facang; \ + numtyp csfacang = cs*facang; \ + numtyp csfac1 = rinvsq1*csfacang; \ + \ + fjx = delr1x*(frad1+csfac1)-delr2x*facang12; \ + fjy = delr1y*(frad1+csfac1)-delr2y*facang12; \ + fjz = delr1z*(frad1+csfac1)-delr2z*facang12; \ +} + +__kernel void k_vashishta_three_center(const __global numtyp4 *restrict x_, + const __global numtyp4 *restrict param1, + const __global numtyp4 *restrict param2, + const __global numtyp4 *restrict param3, + const __global numtyp4 *restrict param4, + const __global numtyp4 *restrict param5, + const __global int *restrict map, + const __global int *restrict elem2param, + const int nelements, + const __global int * dev_nbor, + const __global int * dev_packed, + __global acctyp4 *restrict ans, + __global acctyp *restrict engv, + const int eflag, const int vflag, + const int inum, const int nbor_pitch, + const int t_per_atom, const int evatom) { + __local int tpa_sq, n_stride; + tpa_sq=fast_mul(t_per_atom,t_per_atom); + numtyp param_gamma_ij, param_r0sq_ij, param_r0_ij, param_gamma_ik, param_r0sq_ik, param_r0_ik; + numtyp param_costheta_ijk, param_bigc_ijk, param_bigb_ijk, param_big2b_ijk; + + int tid, ii, offset; + atom_info(tpa_sq,ii,tid,offset); + + acctyp energy=(acctyp)0; + acctyp4 f; + f.x=(acctyp)0; f.y=(acctyp)0; f.z=(acctyp)0; + acctyp virial[6]; + for (int i=0; i<6; i++) + virial[i]=(acctyp)0; + + __syncthreads(); + + if (ii param_r0sq_ij) continue; + param_gamma_ij=param4_ijparam.y; + param_r0_ij=param4_ijparam.w; + + int nbor_k=nbor_j-offset_j+offset_k; + if (nbor_k<=nbor_j) + nbor_k+=n_stride; + + for ( ; nbor_k param_r0sq_ij) continue; + + param_gamma_ij=param4_ijparam.y; + param_r0_ij = param4_ijparam.w; + + int nbor_k,numk; + if (dev_nbor==dev_packed) { + if (gpu_nbor) nbor_k=j+nbor_pitch; + else nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); + k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); + nbor_k+=offset_k; + } else { + nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch; + nbor_k=dev_nbor[nbor_k]; + k_end=nbor_k+numk; + nbor_k+=offset_k; + } + + for ( ; nbor_k param_r0sq_ij) continue; + + param_gamma_ij=param4_ijparam.y; + param_r0_ij=param4_ijparam.w; + + int nbor_k,numk; + if (dev_nbor==dev_packed) { + if (gpu_nbor) nbor_k=j+nbor_pitch; + else nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch+fast_mul(j,t_per_atom-1); + k_end=nbor_k+fast_mul(numk/t_per_atom,n_stride)+(numk & (t_per_atom-1)); + nbor_k+=offset_k; + } else { + nbor_k=dev_acc[j]+nbor_pitch; + numk=dev_nbor[nbor_k]; + nbor_k+=nbor_pitch; + nbor_k=dev_nbor[nbor_k]; + k_end=nbor_k+numk; + nbor_k+=offset_k; + } + + for ( ; nbor_k +class Vashishta : public BaseThree { + public: + Vashishta(); + ~Vashishta(); + + /// Clear any previous data and set up for a new LAMMPS run + /** \param max_nbors initial number of rows in the neighbor matrix + * \param cell_size cutoff + skin + * \param gpu_split fraction of particles handled by device + * + * Returns: + * - 0 if successfull + * - -1 if fix gpu not found + * - -3 if there is an out of memory error + * - -4 if the GPU library was not compiled for GPU + * - -5 Double precision is not supported on card **/ + int init(const int ntypes, const int nlocal, const int nall, const int max_nbors, + const double cell_size, const double gpu_split, FILE *screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc); + + /// Clear all host and device data + /** \note This is called at the beginning of the init() routine **/ + void clear(); + + /// Returns memory usage on device per atom + int bytes_per_atom(const int max_nbors) const; + + /// Total host memory used by library for pair style + double host_memory_usage() const; + + // --------------------------- TYPE DATA -------------------------- + + /// If atom type constants fit in shared memory, use fast kernels + bool shared_types; + + /// Number of atom types + int _lj_types; + + /// param1.x = eta, param1.y = lam1inv, param1.z = lam4inv, param1.w = zizj + UCL_D_Vec param1; + /// param2.x = mbigd, param2.y = dvrc, param2.z = big6w, param2.w = heta + UCL_D_Vec param2; + /// param3.x = bigh, param3.y = bigw, param3.z = dvrc, param3.w = c0 + UCL_D_Vec param3; + /// param4.x = r0sq, param4.y = gamma, param4.z = cutsq, param4.w = r0 + UCL_D_Vec param4; + /// param5.x = bigc, param5.y = costheta, param5.z = bigb, param5.w = big2b + UCL_D_Vec param5; + + UCL_D_Vec elem2param; + UCL_D_Vec map; + int _nparams,_nelements; + + UCL_Texture param1_tex, param2_tex, param3_tex, param4_tex, param5_tex; + + private: + bool _allocated; + void loop(const bool _eflag, const bool _vflag, const int evatom); + +}; + +} + +#endif + diff --git a/lib/gpu/lal_vashishta_ext.cpp b/lib/gpu/lal_vashishta_ext.cpp new file mode 100644 index 0000000000..22f530a7ed --- /dev/null +++ b/lib/gpu/lal_vashishta_ext.cpp @@ -0,0 +1,134 @@ +/*************************************************************************** + vashishta_ext.cpp + ------------------- + Anders Hafreager (UiO) + + Class for acceleration of the vashishta pair style. + + __________________________________________________________________________ + This file is part of the LAMMPS Accelerator Library (LAMMPS_AL) + __________________________________________________________________________ + + begin : Mon June 12, 2017 + email : andershaf@gmail.com + ***************************************************************************/ + +#include +#include +#include + +#include "lal_vashishta.h" +using namespace LAMMPS_AL; + +static Vashishta VashishtaMF; + +// --------------------------------------------------------------------------- +// Allocate memory on host and device and copy constants to device +// --------------------------------------------------------------------------- +int vashishta_gpu_init(const int ntypes, const int inum, const int nall, const int max_nbors, + const double cell_size, int &gpu_mode, FILE *screen, + int* host_map, const int nelements, int*** host_elem2param, const int nparams, + const double* cutsq, const double* r0, + const double* gamma, const double* eta, + const double* lam1inv, const double* lam4inv, + const double* zizj, const double* mbigd, + const double* dvrc, const double* big6w, + const double* heta, const double* bigh, + const double* bigw, const double* c0, + const double* costheta, const double* bigb, + const double* big2b, const double* bigc) { + VashishtaMF.clear(); + gpu_mode=VashishtaMF.device->gpu_mode(); + double gpu_split=VashishtaMF.device->particle_split(); + int first_gpu=VashishtaMF.device->first_device(); + int last_gpu=VashishtaMF.device->last_device(); + int world_me=VashishtaMF.device->world_me(); + int gpu_rank=VashishtaMF.device->gpu_rank(); + int procs_per_gpu=VashishtaMF.device->procs_per_gpu(); + + // disable host/device split for now + if (gpu_split != 1.0) + return -8; + + VashishtaMF.device->init_message(screen,"vashishta/gpu",first_gpu,last_gpu); + + bool message=false; + if (VashishtaMF.device->replica_me()==0 && screen) + message=true; + + if (message) { + fprintf(screen,"Initializing Device and compiling on process 0..."); + fflush(screen); + } + + int init_ok=0; + if (world_me==0) + init_ok=VashishtaMF.init(ntypes, inum, nall, 500, cell_size, gpu_split, screen, + host_map, nelements, host_elem2param, nparams, + cutsq, r0, gamma, eta, lam1inv, + lam4inv, zizj, mbigd, dvrc, big6w, heta, bigh, bigw, + c0, costheta, bigb, big2b, bigc); + + VashishtaMF.device->world_barrier(); + if (message) + fprintf(screen,"Done.\n"); + + for (int i=0; igpu_barrier(); + if (message) + fprintf(screen,"Done.\n"); + } + if (message) + fprintf(screen,"\n"); + + if (init_ok==0) + VashishtaMF.estimate_gpu_overhead(); + + return init_ok; +} + +void vashishta_gpu_clear() { + VashishtaMF.clear(); +} + +int ** vashishta_gpu_compute_n(const int ago, const int inum_full, + const int nall, double **host_x, int *host_type, + double *sublo, double *subhi, tagint *tag, int **nspecial, + tagint **special, const bool eflag, const bool vflag, + const bool eatom, const bool vatom, int &host_start, + int **ilist, int **jnum, const double cpu_time, + bool &success) { + return VashishtaMF.compute(ago, inum_full, nall, host_x, host_type, sublo, + subhi, tag, nspecial, special, eflag, vflag, eatom, + vatom, host_start, ilist, jnum, cpu_time, success); +} + +void vashishta_gpu_compute(const int ago, const int nlocal, const int nall, + const int nlist, double **host_x, int *host_type, + int *ilist, int *numj, int **firstneigh, const bool eflag, + const bool vflag, const bool eatom, const bool vatom, + int &host_start, const double cpu_time, bool &success) { + VashishtaMF.compute(ago,nlocal,nall,nlist,host_x,host_type,ilist,numj, + firstneigh,eflag,vflag,eatom,vatom,host_start,cpu_time,success); +} + +double vashishta_gpu_bytes() { + return VashishtaMF.host_memory_usage(); +} + + diff --git a/lib/kokkos/CHANGELOG.md b/lib/kokkos/CHANGELOG.md index c6fe991b97..acb54ff22f 100644 --- a/lib/kokkos/CHANGELOG.md +++ b/lib/kokkos/CHANGELOG.md @@ -1,5 +1,53 @@ # Change Log + +## [2.03.05](https://github.com/kokkos/kokkos/tree/2.03.05) (2017-05-27) +[Full Changelog](https://github.com/kokkos/kokkos/compare/2.03.00...2.03.05) + +**Implemented enhancements:** + +- Harmonize Custom Reductions over nesting levels [\#802](https://github.com/kokkos/kokkos/issues/802) +- Prevent users directly including KokkosCore\_config.h [\#815](https://github.com/kokkos/kokkos/issues/815) +- DualView aborts on concurrent host/device modify \(in debug mode\) [\#814](https://github.com/kokkos/kokkos/issues/814) +- Abort when running on a NVIDIA CC5.0 or higher architecture with code compiled for CC \< 5.0 [\#813](https://github.com/kokkos/kokkos/issues/813) +- Add "name" function to ExecSpaces [\#806](https://github.com/kokkos/kokkos/issues/806) +- Allow null Future in task spawn dependences [\#795](https://github.com/kokkos/kokkos/issues/795) +- Add Unit Tests for Kokkos::complex [\#785](https://github.com/kokkos/kokkos/issues/785) +- Add pow function for Kokkos::complex [\#784](https://github.com/kokkos/kokkos/issues/784) +- Square root of a complex [\#729](https://github.com/kokkos/kokkos/issues/729) +- Command line processing of --threads argument prevents users from having any commandline arguments starting with --threads [\#760](https://github.com/kokkos/kokkos/issues/760) +- Protected deprecated API with appropriate macro [\#756](https://github.com/kokkos/kokkos/issues/756) +- Allow task scheduler memory pool to be used by tasks [\#747](https://github.com/kokkos/kokkos/issues/747) +- View bounds checking on host-side performance: constructing a std::string [\#723](https://github.com/kokkos/kokkos/issues/723) +- Add check for AppleClang as compiler distinct from check for Clang. [\#705](https://github.com/kokkos/kokkos/issues/705) +- Uninclude source files for specific configurations to prevent link warning. [\#701](https://github.com/kokkos/kokkos/issues/701) +- Add --small option to snapshot script [\#697](https://github.com/kokkos/kokkos/issues/697) +- CMake Standalone Support [\#674](https://github.com/kokkos/kokkos/issues/674) +- CMake build unit test and install [\#808](https://github.com/kokkos/kokkos/issues/808) +- CMake: Fix having kokkos as a subdirectory in a pure cmake project [\#629](https://github.com/kokkos/kokkos/issues/629) +- Tribits macro assumes build directory is in top level source directory [\#654](https://github.com/kokkos/kokkos/issues/654) +- Use bin/nvcc\_wrapper, not config/nvcc\_wrapper [\#562](https://github.com/kokkos/kokkos/issues/562) +- Allow MemoryPool::allocate\(\) to be called from multiple threads per warp. [\#487](https://github.com/kokkos/kokkos/issues/487) +- Allow MemoryPool::allocate\\(\\) to be called from multiple threads per warp. [\#487](https://github.com/kokkos/kokkos/issues/487) +- Move OpenMP 4.5 OpenMPTarget backend into Develop [\#456](https://github.com/kokkos/kokkos/issues/456) +- Testing on ARM testbed [\#288](https://github.com/kokkos/kokkos/issues/288) + +**Fixed bugs:** + +- Fix label in OpenMP parallel\_reduce verify\_initialized [\#834](https://github.com/kokkos/kokkos/issues/834) +- TeamScratch Level 1 on Cuda hangs [\#820](https://github.com/kokkos/kokkos/issues/820) +- \[bug\] memory pool. [\#786](https://github.com/kokkos/kokkos/issues/786) +- Some Reduction Tests fail on Intel 18 with aggressive vectorization on [\#774](https://github.com/kokkos/kokkos/issues/774) +- Error copying dynamic view on copy of memory pool [\#773](https://github.com/kokkos/kokkos/issues/773) +- CUDA stack overflow with TaskDAG test [\#758](https://github.com/kokkos/kokkos/issues/758) +- ThreadVectorRange Customized Reduction Bug [\#739](https://github.com/kokkos/kokkos/issues/739) +- set\_scratch\_size overflows [\#726](https://github.com/kokkos/kokkos/issues/726) +- Get wrong results for compiler checks in Makefile on OS X. [\#706](https://github.com/kokkos/kokkos/issues/706) +- Fix check if multiple host architectures enabled. [\#702](https://github.com/kokkos/kokkos/issues/702) +- Threads Backend Does not Pass on Cray Compilers [\#609](https://github.com/kokkos/kokkos/issues/609) +- Rare bug in memory pool where allocation can finish on superblock in empty state [\#452](https://github.com/kokkos/kokkos/issues/452) +- LDFLAGS in core/unit\_test/Makefile: potential "undefined reference" to pthread lib [\#148](https://github.com/kokkos/kokkos/issues/148) + ## [2.03.00](https://github.com/kokkos/kokkos/tree/2.03.00) (2017-04-25) [Full Changelog](https://github.com/kokkos/kokkos/compare/2.02.15...2.03.00) diff --git a/lib/kokkos/CMakeLists.txt b/lib/kokkos/CMakeLists.txt index 1c820660ae..b2771ed527 100644 --- a/lib/kokkos/CMakeLists.txt +++ b/lib/kokkos/CMakeLists.txt @@ -5,11 +5,12 @@ ELSE() ENDIF() IF(NOT KOKKOS_HAS_TRILINOS) - CMAKE_MINIMUM_REQUIRED(VERSION 2.8.11 FATAL_ERROR) - INCLUDE(cmake/tribits.cmake) - SET(CMAKE_CXX_STANDARD 11) -ENDIF() + cmake_minimum_required(VERSION 3.1 FATAL_ERROR) + project(Kokkos CXX) + INCLUDE(cmake/kokkos.cmake) +ELSE() +#------------------------------------------------------------------------------ # # A) Forward delcare the package so that certain options are also defined for # subpackages @@ -17,14 +18,13 @@ ENDIF() TRIBITS_PACKAGE_DECL(Kokkos) # ENABLE_SHADOWING_WARNINGS) + #------------------------------------------------------------------------------ # # B) Define the common options for Kokkos first so they can be used by # subpackages as well. # - - # mfh 01 Aug 2016: See Issue #61: # # https://github.com/kokkos/kokkos/issues/61 @@ -83,10 +83,10 @@ TRIBITS_ADD_OPTION_AND_DEFINE( ) ASSERT_DEFINED(TPL_ENABLE_Pthread) -IF (Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread) +IF(Kokkos_ENABLE_Pthread AND NOT TPL_ENABLE_Pthread) MESSAGE(FATAL_ERROR "You set Kokkos_ENABLE_Pthread=ON, but Trilinos' support for Pthread(s) is not enabled (TPL_ENABLE_Pthread=OFF). This is not allowed. Please enable Pthreads in Trilinos before attempting to enable Kokkos' support for Pthreads.") -ENDIF () -IF (NOT TPL_ENABLE_Pthread) +ENDIF() +IF(NOT TPL_ENABLE_Pthread) ADD_DEFINITIONS(-DGTEST_HAS_PTHREAD=0) ENDIF() @@ -98,12 +98,13 @@ TRIBITS_ADD_OPTION_AND_DEFINE( ) TRIBITS_ADD_OPTION_AND_DEFINE( - Kokkos_ENABLE_Qthreads + Kokkos_ENABLE_QTHREAD KOKKOS_HAVE_QTHREADS "Enable Qthreads support in Kokkos." - "${TPL_ENABLE_QTHREADS}" + "${TPL_ENABLE_QTHREAD}" ) +# TODO: No longer an option in Kokkos. Needs to be removed. TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_CXX11 KOKKOS_HAVE_CXX11 @@ -118,6 +119,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${TPL_ENABLE_HWLOC}" ) +# TODO: This is currently not used in Kokkos. Should it be removed? TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_MPI KOKKOS_HAVE_MPI @@ -154,13 +156,27 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${Kokkos_ENABLE_Debug_Bounds_Check_DEFAULT}" ) +TRIBITS_ADD_OPTION_AND_DEFINE( + Kokkos_ENABLE_Debug_DualView_Modify_Check + KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + "Enable abort when Kokkos::DualView modified on host and device without sync." + "${Kokkos_ENABLE_DEBUG}" + ) + TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_Profiling - KOKKOS_ENABLE_PROFILING_INTERNAL + KOKKOS_ENABLE_PROFILING "Enable KokkosP profiling support for kernel data collections." "${TPL_ENABLE_DLlib}" ) +TRIBITS_ADD_OPTION_AND_DEFINE( + Kokkos_ENABLE_Profiling_Load_Print + KOKKOS_ENABLE_PROFILING_LOAD_PRINT + "Print to standard output which profiling library was loaded." + OFF + ) + # placeholder for future device... TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_ENABLE_Winthread @@ -169,6 +185,7 @@ TRIBITS_ADD_OPTION_AND_DEFINE( "${TPL_ENABLE_Winthread}" ) +# TODO: No longer an option in Kokkos. Needs to be removed. # use new/old View TRIBITS_ADD_OPTION_AND_DEFINE( Kokkos_USING_DEPRECATED_VIEW @@ -177,12 +194,12 @@ TRIBITS_ADD_OPTION_AND_DEFINE( OFF ) + #------------------------------------------------------------------------------ # # C) Install Kokkos' executable scripts # - # nvcc_wrapper is Kokkos' wrapper for NVIDIA's NVCC CUDA compiler. # Kokkos needs nvcc_wrapper in order to build. Other libraries and # executables also need nvcc_wrapper. Thus, we need to install it. @@ -199,6 +216,8 @@ INSTALL(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/bin/nvcc_wrapper DESTINATION bin) TRIBITS_PROCESS_SUBPACKAGES() + +#------------------------------------------------------------------------------ # # E) If Kokkos itself is enabled, process the Kokkos package # @@ -213,3 +232,4 @@ TRIBITS_EXCLUDE_FILES( ) TRIBITS_PACKAGE_POSTPROCESS() +ENDIF() diff --git a/lib/kokkos/Makefile.kokkos b/lib/kokkos/Makefile.kokkos index 5b094dba8c..24cd772e00 100644 --- a/lib/kokkos/Makefile.kokkos +++ b/lib/kokkos/Makefile.kokkos @@ -35,23 +35,26 @@ KOKKOS_INTERNAL_USE_MEMKIND := $(strip $(shell echo $(KOKKOS_USE_TPLS) | grep "e # Check for advanced settings. KOKKOS_INTERNAL_OPT_RANGE_AGGRESSIVE_VECTORIZATION := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "aggressive_vectorization" | wc -l)) KOKKOS_INTERNAL_DISABLE_PROFILING := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_profiling" | wc -l)) +KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "disable_dualview_modify_check" | wc -l)) +KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT := $(strip $(shell echo $(KOKKOS_OPTIONS) | grep "enable_profile_load_print" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_LDG := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "use_ldg" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_UVM := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "force_uvm" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_RELOC := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "rdc" | wc -l)) KOKKOS_INTERNAL_CUDA_USE_LAMBDA := $(strip $(shell echo $(KOKKOS_CUDA_OPTIONS) | grep "enable_lambda" | wc -l)) # Check for Kokkos Host Execution Spaces one of which must be on. -KOKKOS_INTERNAL_USE_OPENMP := $(strip $(shell echo $(KOKKOS_DEVICES) | grep OpenMP | wc -l)) +KOKKOS_INTERNAL_USE_OPENMPTARGET := $(strip $(shell echo $(KOKKOS_DEVICES) | grep OpenMPTarget | wc -l)) +KOKKOS_INTERNAL_USE_OPENMP := $(strip $(shell echo $(subst OpenMPTarget,,$(KOKKOS_DEVICES)) | grep OpenMP | wc -l)) KOKKOS_INTERNAL_USE_PTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Pthread | wc -l)) KOKKOS_INTERNAL_USE_QTHREADS := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Qthreads | wc -l)) KOKKOS_INTERNAL_USE_SERIAL := $(strip $(shell echo $(KOKKOS_DEVICES) | grep Serial | wc -l)) ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 0) -ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 0) -ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 0) - KOKKOS_INTERNAL_USE_SERIAL := 1 -endif -endif + ifeq ($(KOKKOS_INTERNAL_USE_PTHREADS), 0) + ifeq ($(KOKKOS_INTERNAL_USE_QTHREADS), 0) + KOKKOS_INTERNAL_USE_SERIAL := 1 + endif + endif endif # Check for other Execution Spaces. @@ -64,24 +67,25 @@ ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) endif # Check OS. -KOKKOS_OS := $(shell uname -s) -KOKKOS_INTERNAL_OS_CYGWIN := $(shell uname -s | grep CYGWIN | wc -l) -KOKKOS_INTERNAL_OS_LINUX := $(shell uname -s | grep Linux | wc -l) -KOKKOS_INTERNAL_OS_DARWIN := $(shell uname -s | grep Darwin | wc -l) +KOKKOS_OS := $(strip $(shell uname -s)) +KOKKOS_INTERNAL_OS_CYGWIN := $(strip $(shell uname -s | grep CYGWIN | wc -l)) +KOKKOS_INTERNAL_OS_LINUX := $(strip $(shell uname -s | grep Linux | wc -l)) +KOKKOS_INTERNAL_OS_DARWIN := $(strip $(shell uname -s | grep Darwin | wc -l)) # Check compiler. -KOKKOS_INTERNAL_COMPILER_INTEL := $(shell $(CXX) --version 2>&1 | grep "Intel Corporation" | wc -l) -KOKKOS_INTERNAL_COMPILER_PGI := $(shell $(CXX) --version 2>&1 | grep PGI | wc -l) -KOKKOS_INTERNAL_COMPILER_XL := $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l) -KOKKOS_INTERNAL_COMPILER_CRAY := $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l) -KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(CXX) --version 2>&1 | grep "nvcc" | wc -l) +KOKKOS_INTERNAL_COMPILER_INTEL := $(strip $(shell $(CXX) --version 2>&1 | grep "Intel Corporation" | wc -l)) +KOKKOS_INTERNAL_COMPILER_PGI := $(strip $(shell $(CXX) --version 2>&1 | grep PGI | wc -l)) +KOKKOS_INTERNAL_COMPILER_XL := $(strip $(shell $(CXX) -qversion 2>&1 | grep XL | wc -l)) +KOKKOS_INTERNAL_COMPILER_CRAY := $(strip $(shell $(CXX) -craype-verbose 2>&1 | grep "CC-" | wc -l)) +KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(CXX) --version 2>&1 | grep nvcc | wc -l)) +KOKKOS_INTERNAL_COMPILER_CLANG := $(strip $(shell $(CXX) --version 2>&1 | grep clang | wc -l)) +KOKKOS_INTERNAL_COMPILER_APPLE_CLANG := $(strip $(shell $(CXX) --version 2>&1 | grep "apple-darwin" | wc -l)) ifneq ($(OMPI_CXX),) - KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(OMPI_CXX) --version 2>&1 | grep "nvcc" | wc -l) + KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(OMPI_CXX) --version 2>&1 | grep "nvcc" | wc -l)) endif ifneq ($(MPICH_CXX),) - KOKKOS_INTERNAL_COMPILER_NVCC := $(shell $(MPICH_CXX) --version 2>&1 | grep "nvcc" | wc -l) + KOKKOS_INTERNAL_COMPILER_NVCC := $(strip $(shell $(MPICH_CXX) --version 2>&1 | grep "nvcc" | wc -l)) endif -KOKKOS_INTERNAL_COMPILER_CLANG := $(shell $(CXX) --version 2>&1 | grep "clang" | wc -l) ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 2) KOKKOS_INTERNAL_COMPILER_CLANG = 1 @@ -90,6 +94,11 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 2) KOKKOS_INTERNAL_COMPILER_XL = 1 endif +# Apple Clang passes both clang and apple clang tests, so turn off clang. +ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1) + KOKKOS_INTERNAL_COMPILER_CLANG = 0 +endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_COMPILER_CLANG_VERSION := $(shell clang --version | grep version | cut -d ' ' -f3 | tr -d '.') @@ -97,29 +106,43 @@ ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_CLANG_VERSION) -lt 400; echo $$?),0) $(error Compiling Cuda code directly with Clang requires version 4.0.0 or higher) endif + KOKKOS_INTERNAL_CUDA_USE_LAMBDA := 1 endif endif +# Set OpenMP flags. ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -mp else ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp else - ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) - KOKKOS_INTERNAL_OPENMP_FLAG := -qsmp=omp + ifeq ($(KOKKOS_INTERNAL_COMPILER_APPLE_CLANG), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp=libomp else - ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) - # OpenMP is turned on by default in Cray compiler environment. - KOKKOS_INTERNAL_OPENMP_FLAG := + ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) + KOKKOS_INTERNAL_OPENMP_FLAG := -qsmp=omp else - KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) + # OpenMP is turned on by default in Cray compiler environment. + KOKKOS_INTERNAL_OPENMP_FLAG := + else + KOKKOS_INTERNAL_OPENMP_FLAG := -fopenmp + endif endif endif endif endif +ifeq ($(KOKKOS_INTERNAL_COMPILER_XL), 1) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := -DKOKKOS_IBM_XL_OMP45_WORKAROUND -qsmp=omp -qoffload -qnoeh +else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := -DKOKKOS_BUG_WORKAROUND_IBM_CLANG_OMP45_VIEW_INIT -fopenmp-implicit-declare-target -fopenmp-targets=nvptx64-nvidia-cuda -fopenmp -fopenmp=libomp + endif +endif +# Set C++11 flags. ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) KOKKOS_INTERNAL_CXX11_FLAG := --c++11 else @@ -146,7 +169,7 @@ KOKKOS_INTERNAL_USE_ARCH_SKX := $(strip $(shell echo $(KOKKOS_ARCH) | grep SKX | KOKKOS_INTERNAL_USE_ARCH_KNL := $(strip $(shell echo $(KOKKOS_ARCH) | grep KNL | wc -l)) # NVIDIA based. -NVCC_WRAPPER := $(KOKKOS_PATH)/config/nvcc_wrapper +NVCC_WRAPPER := $(KOKKOS_PATH)/bin/nvcc_wrapper KOKKOS_INTERNAL_USE_ARCH_KEPLER30 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler30 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_KEPLER32 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler32 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_KEPLER35 := $(strip $(shell echo $(KOKKOS_ARCH) | grep Kepler35 | wc -l)) @@ -180,10 +203,20 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + $(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53) | bc)) endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 1) + ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_NVCC_PATH := $(shell which nvcc) + CUDA_PATH ?= $(KOKKOS_INTERNAL_NVCC_PATH:/bin/nvcc=) + KOKKOS_INTERNAL_OPENMPTARGET_FLAG := $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) --cuda-path=$(CUDA_PATH) + endif + endif +endif # ARM based. KOKKOS_INTERNAL_USE_ARCH_ARMV80 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv80 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_ARMV81 := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv81 | wc -l)) KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX := $(strip $(shell echo $(KOKKOS_ARCH) | grep ARMv8-ThunderX | wc -l)) +KOKKOS_INTERNAL_USE_ARCH_ARM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX) | bc)) # IBM based. KOKKOS_INTERNAL_USE_ARCH_BGQ := $(strip $(shell echo $(KOKKOS_ARCH) | grep BGQ | wc -l)) @@ -206,8 +239,11 @@ KOKKOS_INTERNAL_USE_ISA_X86_64 := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ KOKKOS_INTERNAL_USE_ISA_KNC := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_KNC) | bc )) KOKKOS_INTERNAL_USE_ISA_POWERPCLE := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_POWER8)+$(KOKKOS_INTERNAL_USE_ARCH_POWER9) | bc )) +# Decide whether we can support transactional memory +KOKKOS_INTERNAL_USE_TM := $(strip $(shell echo $(KOKKOS_INTERNAL_USE_ARCH_BDW)+$(KOKKOS_INTERNAL_USE_ARCH_SKX) | bc )) + # Incompatible flags? -KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_AMDAVX)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV80)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV81)+$(KOKKOS_INTERNAL_USE_ARCH_ARMV8_THUNDERX)>1" | bc )) +KOKKOS_INTERNAL_USE_ARCH_MULTIHOST := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_AVX)+$(KOKKOS_INTERNAL_USE_ARCH_AVX2)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC)+$(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON)+$(KOKKOS_INTERNAL_USE_ARCH_KNC)+$(KOKKOS_INTERNAL_USE_ARCH_IBM)+$(KOKKOS_INTERNAL_USE_ARCH_ARM)>1" | bc )) KOKKOS_INTERNAL_USE_ARCH_MULTIGPU := $(strip $(shell echo "$(KOKKOS_INTERNAL_USE_ARCH_NVIDIA)>1" | bc)) ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MULTIHOST), 1) @@ -240,12 +276,22 @@ tmp := $(shell echo "Makefile constructed configuration:" >> KokkosCore_config.t tmp := $(shell date >> KokkosCore_config.tmp) tmp := $(shell echo "----------------------------------------------*/" >> KokkosCore_config.tmp) +tmp := $(shell echo '\#if !defined(KOKKOS_MACROS_HPP) || defined(KOKKOS_CORE_CONFIG_H)' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#error "Do not include KokkosCore_config.h directly; include Kokkos_Macros.hpp instead."' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#else' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#define KOKKOS_CORE_CONFIG_H' >> KokkosCore_config.tmp) +tmp := $(shell echo '\#endif' >> KokkosCore_config.tmp) + tmp := $(shell echo "/* Execution Spaces */" >> KokkosCore_config.tmp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_CUDA 1" >> KokkosCore_config.tmp ) endif +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + tmp := $(shell echo '\#define KOKKOS_ENABLE_OPENMPTARGET 1' >> KokkosCore_config.tmp) +endif + ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) tmp := $(shell echo '\#define KOKKOS_HAVE_OPENMP 1' >> KokkosCore_config.tmp) endif @@ -262,6 +308,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_SERIAL 1" >> KokkosCore_config.tmp ) endif +ifeq ($(KOKKOS_INTERNAL_USE_TM), 1) + tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ENABLE_TM" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#endif" >> KokkosCore_config.tmp ) +endif + ifeq ($(KOKKOS_INTERNAL_USE_ISA_X86_64), 1) tmp := $(shell echo "\#ifndef __CUDA_ARCH__" >> KokkosCore_config.tmp ) tmp := $(shell echo "\#define KOKKOS_USE_ISA_X86_64" >> KokkosCore_config.tmp ) @@ -293,13 +345,21 @@ ifeq ($(KOKKOS_INTERNAL_ENABLE_CXX1Z), 1) endif ifeq ($(KOKKOS_INTERNAL_ENABLE_DEBUG), 1) -ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_CXXFLAGS += -lineinfo -endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_CXXFLAGS += -lineinfo + endif + KOKKOS_CXXFLAGS += -g KOKKOS_LDFLAGS += -g -ldl tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK 1" >> KokkosCore_config.tmp ) tmp := $(shell echo "\#define KOKKOS_HAVE_DEBUG 1" >> KokkosCore_config.tmp ) + ifeq ($(KOKKOS_INTERNAL_DISABLE_DUALVIEW_MODIFY_CHECK), 0) + tmp := $(shell echo "\#define KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK 1" >> KokkosCore_config.tmp ) + endif +endif + +ifeq ($(KOKKOS_INTERNAL_ENABLE_PROFILING_LOAD_PRINT), 1) + tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING_LOAD_PRINT 1" >> KokkosCore_config.tmp ) endif ifeq ($(KOKKOS_INTERNAL_USE_HWLOC), 1) @@ -311,8 +371,6 @@ endif ifeq ($(KOKKOS_INTERNAL_USE_LIBRT), 1) tmp := $(shell echo "\#define KOKKOS_USE_LIBRT 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define PREC_TIMER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOSP_ENABLE_RTLIB 1" >> KokkosCore_config.tmp ) KOKKOS_LIBS += -lrt endif @@ -323,8 +381,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) tmp := $(shell echo "\#define KOKKOS_HAVE_HBWSPACE 1" >> KokkosCore_config.tmp ) endif -ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 1) - tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING 0" >> KokkosCore_config.tmp ) +ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 0) + tmp := $(shell echo "\#define KOKKOS_ENABLE_PROFILING" >> KokkosCore_config.tmp ) endif tmp := $(shell echo "/* Optimization Settings */" >> KokkosCore_config.tmp) @@ -336,39 +394,44 @@ endif tmp := $(shell echo "/* Cuda Settings */" >> KokkosCore_config.tmp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) + endif + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LDG), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LDG_INTRINSIC 1" >> KokkosCore_config.tmp ) -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_UVM 1" >> KokkosCore_config.tmp ) + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_UVM), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_UVM 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_USE_CUDA_UVM 1" >> KokkosCore_config.tmp ) -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE 1" >> KokkosCore_config.tmp ) + KOKKOS_CXXFLAGS += --relocatable-device-code=true + KOKKOS_LDFLAGS += --relocatable-device-code=true + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_RELOC), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_RELOCATABLE_DEVICE_CODE 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += --relocatable-device-code=true - KOKKOS_LDFLAGS += --relocatable-device-code=true -endif + ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0) + tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) + KOKKOS_CXXFLAGS += -expt-extended-lambda + else + $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.) + endif + endif -ifeq ($(KOKKOS_INTERNAL_CUDA_USE_LAMBDA), 1) - ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - ifeq ($(shell test $(KOKKOS_INTERNAL_COMPILER_NVCC_VERSION) -gt 70; echo $$?),0) + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += -expt-extended-lambda - else - $(warning Warning: Cuda Lambda support was requested but NVCC version is too low. This requires NVCC for Cuda version 7.5 or higher. Disabling Lambda support now.) endif endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - tmp := $(shell echo "\#define KOKKOS_CUDA_USE_LAMBDA 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_CUDA_CLANG_WORKAROUND" >> KokkosCore_config.tmp ) endif endif -endif - # Add Architecture flags. ifeq ($(KOKKOS_INTERNAL_USE_ARCH_ARMV80), 1) @@ -469,7 +532,7 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_POWER9), 1) endif endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1) +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_HSW), 1) tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp ) ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) @@ -491,6 +554,28 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX2), 1) endif endif +ifeq ($(KOKKOS_INTERNAL_USE_ARCH_BDW), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_AVX2 1" >> KokkosCore_config.tmp ) + + ifeq ($(KOKKOS_INTERNAL_COMPILER_INTEL), 1) + KOKKOS_CXXFLAGS += -xCORE-AVX2 + KOKKOS_LDFLAGS += -xCORE-AVX2 + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) + + else + ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) + KOKKOS_CXXFLAGS += -tp=haswell + KOKKOS_LDFLAGS += -tp=haswell + else + # Assume that this is a really a GNU compiler. + KOKKOS_CXXFLAGS += -march=core-avx2 -mtune=core-avx2 -mrtm + KOKKOS_LDFLAGS += -march=core-avx2 -mtune=core-avx2 -mrtm + endif + endif + endif +endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1) tmp := $(shell echo "\#define KOKKOS_ARCH_AVX512MIC 1" >> KokkosCore_config.tmp ) @@ -501,12 +586,12 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512MIC), 1) ifeq ($(KOKKOS_INTERNAL_COMPILER_CRAY), 1) else - ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_PGI), 1) else # Asssume that this is really a GNU compiler. - KOKKOS_CXXFLAGS += -march=knl - KOKKOS_LDFLAGS += -march=knl + KOKKOS_CXXFLAGS += -march=knl -mtune=knl + KOKKOS_LDFLAGS += -march=knl -mtune=knl endif endif endif @@ -526,8 +611,8 @@ ifeq ($(KOKKOS_INTERNAL_USE_ARCH_AVX512XEON), 1) else # Nothing here yet. - KOKKOS_CXXFLAGS += -march=skylake-avx512 - KOKKOS_LDFLAGS += -march=skylake-avx512 + KOKKOS_CXXFLAGS += -march=skylake-avx512 -mtune=skylake-avx512 -mrtm + KOKKOS_LDFLAGS += -march=skylake-avx512 -mtune=skylake-avx512 -mrtm endif endif endif @@ -541,70 +626,67 @@ endif # Figure out the architecture flag for Cuda. ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG=-arch + endif + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG=--cuda-gpu-arch + KOKKOS_CXXFLAGS += -x cuda + endif -ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) - KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG=-arch -endif -ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) - KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG=--cuda-gpu-arch - KOKKOS_CXXFLAGS += -x cuda -endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER30 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_30 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER32 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_32 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER35 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_35 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER37 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_37 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL50 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_50 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL52 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_52 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_53 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL60 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_60 + endif + ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) + tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp ) + KOKKOS_INTERNAL_CUDA_ARCH_FLAG := $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG)=sm_61 + endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER30), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER30 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_30 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_30 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER32), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER32 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_32 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_32 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER35), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER35 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_35 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_35 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_KEPLER37), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_KEPLER37 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_37 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_37 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL50), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL50 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_50 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_50 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL52), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL52 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_52 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_52 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_MAXWELL53), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_MAXWELL53 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_53 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_53 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL61), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL61 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_61 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_61 -endif -ifeq ($(KOKKOS_INTERNAL_USE_ARCH_PASCAL60), 1) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL 1" >> KokkosCore_config.tmp ) - tmp := $(shell echo "\#define KOKKOS_ARCH_PASCAL60 1" >> KokkosCore_config.tmp ) - KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_60 - KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_COMPILER_CUDA_ARCH_FLAG)=sm_60 -endif + ifneq ($(KOKKOS_INTERNAL_USE_ARCH_NVIDIA), 0) + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) + ifeq ($(KOKKOS_INTERNAL_COMPILER_NVCC), 1) + KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_CUDA_ARCH_FLAG) + endif + endif endif KOKKOS_INTERNAL_LS_CONFIG := $(shell ls KokkosCore_config.h) @@ -630,9 +712,24 @@ KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/containers/src/impl/*.cpp) ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) KOKKOS_SRC += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.cpp) KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/Cuda/*.hpp) - KOKKOS_CXXFLAGS += -I$(CUDA_PATH)/include + KOKKOS_CPPFLAGS += -I$(CUDA_PATH)/include KOKKOS_LDFLAGS += -L$(CUDA_PATH)/lib64 KOKKOS_LIBS += -lcudart -lcuda + + ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) + KOKKOS_CXXFLAGS += --cuda-path=$(CUDA_PATH) + endif +endif + +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) + KOKKOS_SRC += $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp + KOKKOS_HEADERS += $(wildcard $(KOKKOS_PATH)/core/src/OpenMPTarget/*.hpp) + ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) + KOKKOS_CXXFLAGS += -Xcompiler $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) + else + KOKKOS_CXXFLAGS += $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) + endif + KOKKOS_LDFLAGS += $(KOKKOS_INTERNAL_OPENMPTARGET_FLAG) endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) @@ -666,10 +763,27 @@ endif ifeq ($(KOKKOS_INTERNAL_COMPILER_CLANG), 1) KOKKOS_INTERNAL_GCC_PATH = $(shell which g++) KOKKOS_INTERNAL_GCC_TOOLCHAIN = $(KOKKOS_INTERNAL_GCC_PATH:/bin/g++=) - KOKKOS_CXXFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) -DKOKKOS_CUDA_CLANG_WORKAROUND -DKOKKOS_CUDA_USE_LDG_INTRINSIC + KOKKOS_CXXFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) KOKKOS_LDFLAGS += --gcc-toolchain=$(KOKKOS_INTERNAL_GCC_TOOLCHAIN) endif +# Don't include Kokkos_HBWSpace.cpp if not using MEMKIND to avoid a link warning. +ifneq ($(KOKKOS_INTERNAL_USE_MEMKIND), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp,$(KOKKOS_SRC)) +endif + +# Don't include Kokkos_Profiling_Interface.cpp if not using profiling to avoid a link warning. +ifeq ($(KOKKOS_INTERNAL_DISABLE_PROFILING), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Profiling_Interface.cpp,$(KOKKOS_SRC)) +endif + +# Don't include Kokkos_Serial.cpp or Kokkos_Serial_Task.cpp if not using Serial +# device to avoid a link warning. +ifneq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial.cpp,$(KOKKOS_SRC)) + KOKKOS_SRC := $(filter-out $(KOKKOS_PATH)/core/src/impl/Kokkos_Serial_Task.cpp,$(KOKKOS_SRC)) +endif + # With Cygwin functions such as fdopen and fileno are not defined # when strict ansi is enabled. strict ansi gets enabled with --std=c++11 # though. So we hard undefine it here. Not sure if that has any bad side effects diff --git a/lib/kokkos/Makefile.targets b/lib/kokkos/Makefile.targets index 54cacb741b..3cb52a04cd 100644 --- a/lib/kokkos/Makefile.targets +++ b/lib/kokkos/Makefile.targets @@ -53,11 +53,20 @@ Kokkos_Qthreads_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/Qthreads/K endif ifeq ($(KOKKOS_INTERNAL_USE_OPENMP), 1) -Kokkos_OpenMPexec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp - $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMPexec.cpp +Kokkos_OpenMP_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Exec.cpp Kokkos_OpenMP_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMP/Kokkos_OpenMP_Task.cpp endif +ifeq ($(KOKKOS_INTERNAL_USE_OPENMPTARGET), 1) +Kokkos_OpenMPTarget_Exec.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Exec.cpp +Kokkos_OpenMPTargetSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp + $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTargetSpace.cpp +#Kokkos_OpenMPTarget_Task.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Task.cpp +# $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/OpenMPTarget/Kokkos_OpenMPTarget_Task.cpp +endif + Kokkos_HBWSpace.o: $(KOKKOS_CPP_DEPENDS) $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) -c $(KOKKOS_PATH)/core/src/impl/Kokkos_HBWSpace.cpp diff --git a/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp b/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp index e69de29bb2..9c08a088b0 100644 --- a/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp +++ b/lib/kokkos/algorithms/src/KokkosAlgorithms_dummy.cpp @@ -0,0 +1 @@ +void KOKKOS_ALGORITHMS_SRC_DUMMY_PREVENT_LINK_ERROR() {} diff --git a/lib/kokkos/algorithms/src/Kokkos_Random.hpp b/lib/kokkos/algorithms/src/Kokkos_Random.hpp index bd73582362..42c115b7a5 100644 --- a/lib/kokkos/algorithms/src/Kokkos_Random.hpp +++ b/lib/kokkos/algorithms/src/Kokkos_Random.hpp @@ -674,7 +674,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION @@ -917,7 +917,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION @@ -1171,7 +1171,7 @@ namespace Kokkos { const double V = 2.0*drand() - 1.0; S = U*U+V*V; } - return U*sqrt(-2.0*log(S)/S); + return U*std::sqrt(-2.0*log(S)/S); } KOKKOS_INLINE_FUNCTION diff --git a/lib/kokkos/algorithms/unit_tests/Makefile b/lib/kokkos/algorithms/unit_tests/Makefile index 3027c6a94b..b74192ef18 100644 --- a/lib/kokkos/algorithms/unit_tests/Makefile +++ b/lib/kokkos/algorithms/unit_tests/Makefile @@ -8,7 +8,7 @@ default: build_all echo "End Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) - CXX = $(KOKKOS_PATH)/config/nvcc_wrapper + CXX = $(KOKKOS_PATH)/bin/nvcc_wrapper else CXX = g++ endif @@ -21,8 +21,8 @@ include $(KOKKOS_PATH)/Makefile.kokkos KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/algorithms/unit_tests -TEST_TARGETS = -TARGETS = +TEST_TARGETS = +TARGETS = ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o UnitTestMain.o gtest-all.o @@ -49,16 +49,16 @@ ifeq ($(KOKKOS_INTERNAL_USE_SERIAL), 1) endif KokkosAlgorithms_UnitTest_Cuda: $(OBJ_CUDA) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Cuda + $(LINK) $(EXTRA_PATH) $(OBJ_CUDA) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Cuda KokkosAlgorithms_UnitTest_Threads: $(OBJ_THREADS) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Threads + $(LINK) $(EXTRA_PATH) $(OBJ_THREADS) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Threads KokkosAlgorithms_UnitTest_OpenMP: $(OBJ_OPENMP) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_OPENMP) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_OpenMP + $(LINK) $(EXTRA_PATH) $(OBJ_OPENMP) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_OpenMP KokkosAlgorithms_UnitTest_Serial: $(OBJ_SERIAL) $(KOKKOS_LINK_DEPENDS) - $(LINK) $(KOKKOS_LDFLAGS) $(LDFLAGS) $(EXTRA_PATH) $(OBJ_SERIAL) $(KOKKOS_LIBS) $(LIB) -o KokkosAlgorithms_UnitTest_Serial + $(LINK) $(EXTRA_PATH) $(OBJ_SERIAL) $(KOKKOS_LIBS) $(LIB) $(KOKKOS_LDFLAGS) $(LDFLAGS) -o KokkosAlgorithms_UnitTest_Serial test-cuda: KokkosAlgorithms_UnitTest_Cuda ./KokkosAlgorithms_UnitTest_Cuda @@ -76,7 +76,7 @@ build_all: $(TARGETS) test: $(TEST_TARGETS) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o $(TARGETS) # Compilation rules @@ -84,6 +84,5 @@ clean: kokkos-clean %.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc +gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $(GTEST_PATH)/gtest/gtest-all.cc - diff --git a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp index ba3938f497..710eeb8ada 100644 --- a/lib/kokkos/algorithms/unit_tests/TestCuda.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestCuda.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,12 +36,15 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#ifdef KOKKOS_ENABLE_CUDA + +#include #include #include @@ -49,8 +52,6 @@ #include -#ifdef KOKKOS_ENABLE_CUDA - #include #include @@ -105,6 +106,7 @@ CUDA_SORT_UNSIGNED(171) #undef CUDA_RANDOM_XORSHIFT1024 #undef CUDA_SORT_UNSIGNED } - +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTCUDA_PREVENT_LINK_ERROR() {} #endif /* #ifdef KOKKOS_ENABLE_CUDA */ diff --git a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp index f4d582d0bb..1e7ee68549 100644 --- a/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestOpenMP.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,13 +36,16 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#ifdef KOKKOS_ENABLE_OPENMP + +#include #include //---------------------------------------------------------------------------- @@ -52,7 +55,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_OPENMP class openmp : public ::testing::Test { protected: static void SetUpTestCase() @@ -97,6 +99,8 @@ OPENMP_SORT_UNSIGNED(171) #undef OPENMP_RANDOM_XORSHIFT64 #undef OPENMP_RANDOM_XORSHIFT1024 #undef OPENMP_SORT_UNSIGNED -#endif } // namespace test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTOPENMP_PREVENT_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp index c906b9f2cd..9cf02f74b4 100644 --- a/lib/kokkos/algorithms/unit_tests/TestRandom.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestRandom.hpp @@ -295,7 +295,7 @@ struct test_random_scalar { parallel_reduce (num_draws/1024, functor_type (pool, density_1d, density_3d), result); //printf("Result: %lf %lf %lf\n",result.mean/num_draws/3,result.variance/num_draws/3,result.covariance/num_draws/2); - double tolerance = 1.6*sqrt(1.0/num_draws); + double tolerance = 1.6*std::sqrt(1.0/num_draws); double mean_expect = 0.5*Kokkos::rand::max(); double variance_expect = 1.0/3.0*mean_expect*mean_expect; double mean_eps = mean_expect/(result.mean/num_draws/3)-1.0; @@ -321,7 +321,7 @@ struct test_random_scalar { typedef test_histogram1d_functor functor_type; parallel_reduce (HIST_DIM1D, functor_type (density_1d, num_draws), result); - double tolerance = 6*sqrt(1.0/HIST_DIM1D); + double tolerance = 6*std::sqrt(1.0/HIST_DIM1D); double mean_expect = 1.0*num_draws*3/HIST_DIM1D; double variance_expect = 1.0*num_draws*3/HIST_DIM1D*(1.0-1.0/HIST_DIM1D); double covariance_expect = -1.0*num_draws*3/HIST_DIM1D/HIST_DIM1D; @@ -354,7 +354,7 @@ struct test_random_scalar { typedef test_histogram3d_functor functor_type; parallel_reduce (HIST_DIM1D, functor_type (density_3d, num_draws), result); - double tolerance = 6*sqrt(1.0/HIST_DIM1D); + double tolerance = 6*std::sqrt(1.0/HIST_DIM1D); double mean_expect = 1.0*num_draws/HIST_DIM1D; double variance_expect = 1.0*num_draws/HIST_DIM1D*(1.0-1.0/HIST_DIM1D); double covariance_expect = -1.0*num_draws/HIST_DIM1D/HIST_DIM1D; diff --git a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp index 6ac80cf73a..a1df93e07b 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSerial.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestSerial.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#ifdef KOKKOS_ENABLE_SERIAL + #include #include @@ -55,7 +58,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_SERIAL class serial : public ::testing::Test { protected: static void SetUpTestCase() @@ -93,7 +95,9 @@ SERIAL_SORT_UNSIGNED(171) #undef SERIAL_RANDOM_XORSHIFT1024 #undef SERIAL_SORT_UNSIGNED -#endif // KOKKOS_ENABLE_SERIAL } // namespace Test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTSERIAL_PREVENT_LINK_ERROR() {} +#endif // KOKKOS_ENABLE_SERIAL diff --git a/lib/kokkos/algorithms/unit_tests/TestSort.hpp b/lib/kokkos/algorithms/unit_tests/TestSort.hpp index 61ffa6f43a..04be98f1cc 100644 --- a/lib/kokkos/algorithms/unit_tests/TestSort.hpp +++ b/lib/kokkos/algorithms/unit_tests/TestSort.hpp @@ -1,12 +1,12 @@ //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -35,12 +35,12 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER -#ifndef TESTSORT_HPP_ -#define TESTSORT_HPP_ +#ifndef KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP +#define KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP #include #include @@ -212,7 +212,12 @@ void test_dynamic_view_sort(unsigned int n ) const size_t upper_bound = 2 * n ; typename KeyDynamicViewType::memory_pool - pool( memory_space() , 2 * n * sizeof(KeyType) ); + pool( memory_space() + , n * sizeof(KeyType) * 1.2 + , 500 /* min block size in bytes */ + , 30000 /* max block size in bytes */ + , 1000000 /* min superblock size in bytes */ + ); KeyDynamicViewType keys("Keys",pool,upper_bound); @@ -272,4 +277,4 @@ void test_sort(unsigned int N) } } -#endif /* TESTSORT_HPP_ */ +#endif /* KOKKOS_ALGORITHMS_UNITTESTS_TESTSORT_HPP */ diff --git a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp index 36d438b643..08749779ff 100644 --- a/lib/kokkos/algorithms/unit_tests/TestThreads.cpp +++ b/lib/kokkos/algorithms/unit_tests/TestThreads.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#ifdef KOKKOS_ENABLE_THREADS + #include #include @@ -55,7 +58,6 @@ namespace Test { -#ifdef KOKKOS_ENABLE_PTHREAD class threads : public ::testing::Test { protected: static void SetUpTestCase() @@ -107,7 +109,9 @@ THREADS_SORT_UNSIGNED(171) #undef THREADS_RANDOM_XORSHIFT1024 #undef THREADS_SORT_UNSIGNED -#endif } // namespace Test +#else +void KOKKOS_ALGORITHMS_UNITTESTS_TESTTHREADS_PREVENT_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/benchmarks/bytes_and_flops/Makefile b/lib/kokkos/benchmarks/bytes_and_flops/Makefile index 6a1917a523..5ddf78f28e 100644 --- a/lib/kokkos/benchmarks/bytes_and_flops/Makefile +++ b/lib/kokkos/benchmarks/bytes_and_flops/Makefile @@ -7,7 +7,7 @@ default: build echo "Start Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) -CXX = ${KOKKOS_PATH}/config/nvcc_wrapper +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper EXE = bytes_and_flops.cuda KOKKOS_DEVICES = "Cuda,OpenMP" KOKKOS_ARCH = "SNB,Kepler35" @@ -22,7 +22,7 @@ CXXFLAGS = -O3 -g DEPFLAGS = -M LINK = ${CXX} -LINKFLAGS = +LINKFLAGS = OBJ = $(SRC:.cpp=.o) LIB = @@ -34,7 +34,7 @@ build: $(EXE) $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o *.cuda *.host # Compilation rules diff --git a/lib/kokkos/benchmarks/gather/Makefile b/lib/kokkos/benchmarks/gather/Makefile index fd1feab6fa..0ea9fb1dd2 100644 --- a/lib/kokkos/benchmarks/gather/Makefile +++ b/lib/kokkos/benchmarks/gather/Makefile @@ -7,7 +7,7 @@ default: build echo "Start Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) -CXX = ${KOKKOS_PATH}/config/nvcc_wrapper +CXX = ${KOKKOS_PATH}/bin/nvcc_wrapper EXE = gather.cuda KOKKOS_DEVICES = "Cuda,OpenMP" KOKKOS_ARCH = "SNB,Kepler35" @@ -22,7 +22,7 @@ CXXFLAGS = -O3 -g DEPFLAGS = -M LINK = ${CXX} -LINKFLAGS = +LINKFLAGS = OBJ = $(SRC:.cpp=.o) LIB = @@ -35,10 +35,10 @@ build: $(EXE) $(EXE): $(OBJ) $(KOKKOS_LINK_DEPENDS) $(LINK) $(KOKKOS_LDFLAGS) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(KOKKOS_LIBS) $(LIB) -o $(EXE) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o *.cuda *.host # Compilation rules -%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp +%.o:%.cpp $(KOKKOS_CPP_DEPENDS) gather_unroll.hpp gather.hpp $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< diff --git a/lib/kokkos/cmake/KokkosConfig.cmake.in b/lib/kokkos/cmake/KokkosConfig.cmake.in new file mode 100644 index 0000000000..fc099a494c --- /dev/null +++ b/lib/kokkos/cmake/KokkosConfig.cmake.in @@ -0,0 +1,18 @@ +# - Config file for the Kokkos package +# It defines the following variables +# Kokkos_INCLUDE_DIRS - include directories for Kokkos +# Kokkos_LIBRARIES - libraries to link against + +# Compute paths +GET_FILENAME_COMPONENT(Kokkos_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +SET(Kokkos_INCLUDE_DIRS "@CONF_INCLUDE_DIRS@") + +# Our library dependencies (contains definitions for IMPORTED targets) +IF(NOT TARGET kokkos AND NOT Kokkos_BINARY_DIR) + INCLUDE("${Kokkos_CMAKE_DIR}/KokkosTargets.cmake") +ENDIF() + +# These are IMPORTED targets created by KokkosTargets.cmake +SET(Kokkos_LIBRARY_DIRS @INSTALL_LIB_DIR@) +SET(Kokkos_LIBRARIES @Kokkos_LIBRARIES_NAMES@) +SET(Kokkos_TPL_LIBRARIES @KOKKOS_LIBS@) diff --git a/lib/kokkos/cmake/Modules/FindHWLOC.cmake b/lib/kokkos/cmake/Modules/FindHWLOC.cmake new file mode 100644 index 0000000000..273dcb5c8a --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindHWLOC.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindHWLOC +# ---------- +# +# Try to find HWLOC. +# +# The following variables are defined: +# +# HWLOC_FOUND - System has HWLOC +# HWLOC_INCLUDE_DIR - HWLOC include directory +# HWLOC_LIBRARIES - Libraries needed to use HWLOC + +find_path(HWLOC_INCLUDE_DIR hwloc.h) +find_library(HWLOC_LIBRARIES hwloc) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(HWLOC DEFAULT_MSG + HWLOC_INCLUDE_DIR HWLOC_LIBRARIES) + +mark_as_advanced(HWLOC_INCLUDE_DIR HWLOC_LIBRARIES) diff --git a/lib/kokkos/cmake/Modules/FindMemkind.cmake b/lib/kokkos/cmake/Modules/FindMemkind.cmake new file mode 100644 index 0000000000..245fb44c19 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindMemkind.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindMemkind +# ---------- +# +# Try to find Memkind. +# +# The following variables are defined: +# +# MEMKIND_FOUND - System has Memkind +# MEMKIND_INCLUDE_DIR - Memkind include directory +# MEMKIND_LIBRARIES - Libraries needed to use Memkind + +find_path(MEMKIND_INCLUDE_DIR memkind.h) +find_library(MEMKIND_LIBRARIES memkind) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(Memkind DEFAULT_MSG + MEMKIND_INCLUDE_DIR MEMKIND_LIBRARIES) + +mark_as_advanced(MEMKIND_INCLUDE_DIR MEMKIND_LIBRARIES) diff --git a/lib/kokkos/cmake/Modules/FindQthreads.cmake b/lib/kokkos/cmake/Modules/FindQthreads.cmake new file mode 100644 index 0000000000..a254b0e996 --- /dev/null +++ b/lib/kokkos/cmake/Modules/FindQthreads.cmake @@ -0,0 +1,20 @@ +#.rst: +# FindQthreads +# ---------- +# +# Try to find Qthreads. +# +# The following variables are defined: +# +# QTHREADS_FOUND - System has Qthreads +# QTHREADS_INCLUDE_DIR - Qthreads include directory +# QTHREADS_LIBRARIES - Libraries needed to use Qthreads + +find_path(QTHREADS_INCLUDE_DIR qthread.h) +find_library(QTHREADS_LIBRARIES qthread) + +include(FindPackageHandleStandardArgs) +find_package_handle_standard_args(Qthreads DEFAULT_MSG + QTHREADS_INCLUDE_DIR QTHREADS_LIBRARIES) + +mark_as_advanced(QTHREADS_INCLUDE_DIR QTHREADS_LIBRARIES) diff --git a/lib/kokkos/cmake/kokkos.cmake b/lib/kokkos/cmake/kokkos.cmake new file mode 100644 index 0000000000..235b7eaba4 --- /dev/null +++ b/lib/kokkos/cmake/kokkos.cmake @@ -0,0 +1,1198 @@ + + +# Set which Kokkos backend to use. +set(KOKKOS_ENABLE_CUDA OFF CACHE BOOL "Use Kokkos CUDA backend") +set(KOKKOS_ENABLE_OPENMP ON CACHE BOOL "Use Kokkos OpenMP backend") +set(KOKKOS_ENABLE_PTHREAD OFF CACHE BOOL "Use Kokkos Pthreads backend") +set(KOKKOS_ENABLE_QTHREADS OFF CACHE BOOL "Use Kokkos Qthreads backend") +set(KOKKOS_ENABLE_SERIAL ON CACHE BOOL "Use Kokkos Serial backend") + +# List of possible host architectures. +list(APPEND KOKKOS_HOST_ARCH_LIST + None # No architecture optimization + AMDAVX # AMD chip + ARMv80 # ARMv8.0 Compatible CPU + ARMv81 # ARMv8.1 Compatible CPU + ARMv8-ThunderX # ARMv8 Cavium ThunderX CPU + SNB # Intel Sandy/Ivy Bridge CPUs + HSW # Intel Haswell CPUs + BDW # Intel Broadwell Xeon E-class CPUs + SKX # Intel Sky Lake Xeon E-class HPC CPUs (AVX512) + KNC # Intel Knights Corner Xeon Phi + KNL # Intel Knights Landing Xeon Phi + BGQ # IBM Blue Gene Q + Power7 # IBM POWER7 CPUs + Power8 # IBM POWER8 CPUs + Power9 # IBM POWER9 CPUs + ) + +# Setting this variable to a value other than "None" can improve host +# performance by turning on architecture specific code. +set(KOKKOS_HOST_ARCH "None" CACHE STRING "Optimize for specific host architecture.") +set_property(CACHE KOKKOS_HOST_ARCH PROPERTY STRINGS ${KOKKOS_HOST_ARCH_LIST}) + +# List of possible GPU architectures. +list(APPEND KOKKOS_GPU_ARCH_LIST + None # No architecture optimization + Kepler # NVIDIA Kepler default (generation CC 3.5) + Kepler30 # NVIDIA Kepler generation CC 3.0 + Kepler32 # NVIDIA Kepler generation CC 3.2 + Kepler35 # NVIDIA Kepler generation CC 3.5 + Kepler37 # NVIDIA Kepler generation CC 3.7 + Maxwell # NVIDIA Maxwell default (generation CC 5.0) + Maxwell50 # NVIDIA Maxwell generation CC 5.0 + Maxwell52 # NVIDIA Maxwell generation CC 5.2 + Maxwell53 # NVIDIA Maxwell generation CC 5.3 + Pascal60 # NVIDIA Pascal generation CC 6.0 + Pascal61 # NVIDIA Pascal generation CC 6.1 + ) + +# Setting this variable to a value other than "None" can improve GPU +# performance by turning on architecture specific code. +set(KOKKOS_GPU_ARCH "None" CACHE STRING "Optimize for specific GPU architecture.") +set_property(CACHE KOKKOS_GPU_ARCH PROPERTY STRINGS ${KOKKOS_GPU_ARCH_LIST}) + +set(KOKKOS_SEPARATE_LIBS OFF CACHE BOOL "OFF = kokkos. ON = kokkoscore, kokkoscontainers, and kokkosalgorithms.") + +# Enable hwloc library. +set(KOKKOS_ENABLE_HWLOC OFF CACHE BOOL "Enable hwloc for better process placement.") +set(KOKKOS_HWLOC_DIR "" CACHE PATH "Location of hwloc library.") + +# Enable memkind library. +set(KOKKOS_ENABLE_MEMKIND OFF CACHE BOOL "Enable memkind.") +set(KOKKOS_MEMKIND_DIR "" CACHE PATH "Location of memkind library.") + +set(KOKKOS_ENABLE_LIBRT OFF CACHE BOOL "Enable librt for more precise timer.") + +# Enable debugging. +set(KOKKOS_DEBUG OFF CACHE BOOL "Enable debugging in Kokkos.") + +# Enable profiling. +set(KOKKOS_ENABLE_PROFILING ON CACHE BOOL "Enable profiling.") + +# Enable aggressive vectorization. +set(KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION OFF CACHE BOOL "Enable aggressive vectorization.") + +# Qthreads options. +set(KOKKOS_QTHREADS_DIR "" CACHE PATH "Location of Qthreads library.") + +# CUDA options. +set(KOKKOS_CUDA_DIR "" CACHE PATH "Location of CUDA library. Defaults to where nvcc installed.") +set(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC OFF CACHE BOOL "Enable CUDA LDG.") +set(KOKKOS_ENABLE_CUDA_UVM OFF CACHE BOOL "Enable CUDA unified virtual memory.") +set(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE OFF CACHE BOOL "Enable relocatable device code for CUDA.") +set(KOKKOS_ENABLE_CUDA_LAMBDA ON CACHE BOOL "Enable lambdas for CUDA.") + +################################### FUNCTIONS ################################## + +# Sets the following compiler variables that are analogous to the CMAKE_* +# versions. We add the ability to detect NVCC (really nvcc_wrapper). +# KOKKOS_CXX_COMPILER +# KOKKOS_CXX_COMPILER_ID +# KOKKOS_CXX_COMPILER_VERSION +# +# Also verifies the compiler version meets the minimum required by Kokkos. +function(set_kokkos_cxx_compiler) + # Since CMake doesn't recognize the nvcc compiler until 3.8, we use our own + # version of the CMake variables and detect nvcc ourselves. Initially set to + # the CMake variable values. + set(INTERNAL_CXX_COMPILER ${CMAKE_CXX_COMPILER}) + set(INTERNAL_CXX_COMPILER_ID ${CMAKE_CXX_COMPILER_ID}) + set(INTERNAL_CXX_COMPILER_VERSION ${CMAKE_CXX_COMPILER_VERSION}) + + # Check if the compiler is nvcc (which really means nvcc_wrapper). + execute_process(COMMAND ${INTERNAL_CXX_COMPILER} --version + COMMAND grep nvcc + COMMAND wc -l + OUTPUT_VARIABLE INTERNAL_HAVE_COMPILER_NVCC + OUTPUT_STRIP_TRAILING_WHITESPACE) + + string(REGEX REPLACE "^ +" "" + INTERNAL_HAVE_COMPILER_NVCC ${INTERNAL_HAVE_COMPILER_NVCC}) + + if(INTERNAL_HAVE_COMPILER_NVCC) + # Set the compiler id to nvcc. We use the value used by CMake 3.8. + set(INTERNAL_CXX_COMPILER_ID NVIDIA) + + # Set nvcc's compiler version. + execute_process(COMMAND ${INTERNAL_CXX_COMPILER} --version + COMMAND grep release + OUTPUT_VARIABLE INTERNAL_CXX_COMPILER_VERSION + OUTPUT_STRIP_TRAILING_WHITESPACE) + + string(REGEX MATCH "[0-9]+\.[0-9]+\.[0-9]+$" + INTERNAL_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION}) + endif() + + # Enforce the minimum compilers supported by Kokkos. + set(KOKKOS_MESSAGE_TEXT "Compiler not supported by Kokkos. Required compiler versions:") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Clang 3.5.2 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n GCC 4.7.2 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Intel 14.0.4 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n NVCC 7.0.28 or higher") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n PGI 17.1 or higher\n") + + if(INTERNAL_CXX_COMPILER_ID STREQUAL Clang) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 3.5.2) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL GNU) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 4.7.2) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL Intel) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 14.0.4) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 7.0.28) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + elseif(INTERNAL_CXX_COMPILER_ID STREQUAL PGI) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 17.1) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") + endif() + endif() + + # Enforce that extensions are turned off for nvcc_wrapper. + if(INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + if(NOT DEFINED CMAKE_CXX_EXTENSIONS OR CMAKE_CXX_EXTENSIONS STREQUAL ON) + message(FATAL_ERROR "NVCC doesn't support C++ extensions. Set CMAKE_CXX_EXTENSIONS to OFF in your CMakeLists.txt.") + endif() + endif() + + if(KOKKOS_ENABLE_CUDA) + # Enforce that the compiler can compile CUDA code. + if(INTERNAL_CXX_COMPILER_ID STREQUAL Clang) + if(INTERNAL_CXX_COMPILER_VERSION VERSION_LESS 4.0.0) + message(FATAL_ERROR "Compiling CUDA code directly with Clang requires version 4.0.0 or higher.") + endif() + elseif(NOT INTERNAL_CXX_COMPILER_ID STREQUAL NVIDIA) + message(FATAL_ERROR "Invalid compiler for CUDA. The compiler must be nvcc_wrapper or Clang.") + endif() + endif() + + set(KOKKOS_CXX_COMPILER ${INTERNAL_CXX_COMPILER} PARENT_SCOPE) + set(KOKKOS_CXX_COMPILER_ID ${INTERNAL_CXX_COMPILER_ID} PARENT_SCOPE) + set(KOKKOS_CXX_COMPILER_VERSION ${INTERNAL_CXX_COMPILER_VERSION} PARENT_SCOPE) +endfunction() + +# Transitively enforces that the appropriate CXX standard compile flags (C++11 +# or above) are added to targets that use the Kokkos library. Compile features +# are used if possible. Otherwise, the appropriate flags are added to +# KOKKOS_CXX_FLAGS. Values set by the user to CMAKE_CXX_STANDARD and +# CMAKE_CXX_EXTENSIONS are honored. +function(set_kokkos_compiler_standard) + # The following table lists the versions of CMake that supports CXX_STANDARD + # and the CXX compile features for different compilers. The versions are + # based on CMake documentation, looking at CMake code, and verifying by + # testing with specific CMake versions. + # + # COMPILER CXX_STANDARD Compile Features + # --------------------------------------------------------------- + # Clang 3.1 3.1 + # GNU 3.1 3.2 + # AppleClang 3.2 3.2 + # Intel 3.6 3.6 + # Cray No No + # PGI No No + # XL No No + # + # For compiling CUDA code using nvcc_wrapper, we will use the host compiler's + # flags for turning on C++11. Since for compiler ID and versioning purposes + # CMake recognizes the host compiler when calling nvcc_wrapper, this just + # works. Both NVCC and nvcc_wrapper only recognize '-std=c++11' which means + # that we can only use host compilers for CUDA builds that use those flags. + # It also means that extensions (gnu++11) can't be turned on for CUDA builds. + + # Check if we can use compile features. + if(NOT KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + if(CMAKE_CXX_COMPILER_ID STREQUAL Clang) + if(NOT CMAKE_VERSION VERSION_LESS 3.1) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL AppleClang OR CMAKE_CXX_COMPILER_ID STREQUAL GNU) + if(NOT CMAKE_VERSION VERSION_LESS 3.2) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Intel) + if(NOT CMAKE_VERSION VERSION_LESS 3.6) + set(INTERNAL_USE_COMPILE_FEATURES ON) + endif() + endif() + endif() + + if(INTERNAL_USE_COMPILE_FEATURES) + # Use the compile features aspect of CMake to transitively cause C++ flags + # to populate to user code. + + # I'm using a hack by requiring features that I know force the lowest version + # of the compilers we want to support. Clang 3.3 and later support all of + # the C++11 standard. With CMake 3.8 and higher, we could switch to using + # cxx_std_11. + set(KOKKOS_CXX11_FEATURES + cxx_nonstatic_member_init # Forces GCC 4.7 or later and Intel 14.0 or later. + PARENT_SCOPE + ) + else() + # CXX compile features are not yet implemented for this combination of + # compiler and version of CMake. + + if(CMAKE_CXX_COMPILER_ID STREQUAL AppleClang) + # Versions of CMAKE before 3.2 don't support CXX_STANDARD or C++ compile + # features for the AppleClang compiler. Set compiler flags transitively + # here such that they trickle down to a call to target_compile_options(). + + # The following two blocks of code were copied from + # /Modules/Compiler/AppleClang-CXX.cmake from CMake 3.7.2 and then + # modified. + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.0) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-std=gnu++11") + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 6.1) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++14") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=gnu++14") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.1) + # AppleClang 5.0 knows this flag, but does not set a __cplusplus macro + # greater than 201103L. + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++1y") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=gnu++1y") + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Intel) + # Versions of CMAKE before 3.6 don't support CXX_STANDARD or C++ compile + # features for the Intel compiler. Set compiler flags transitively here + # such that they trickle down to a call to target_compile_options(). + + # The following three blocks of code were copied from + # /Modules/Compiler/Intel-CXX.cmake from CMake 3.7.2 and then modified. + if("x${CMAKE_CXX_SIMULATE_ID}" STREQUAL "xMSVC") + set(_std -Qstd) + set(_ext c++) + else() + set(_std -std) + set(_ext gnu++) + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.0.2) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "${_std}=c++14") + # TODO: There is no gnu++14 value supported; figure out what to do. + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "${_std}=c++14") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.0.0) + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "${_std}=c++1y") + # TODO: There is no gnu++14 value supported; figure out what to do. + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "${_std}=c++1y") + endif() + + if(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 13.0) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "${_std}=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "${_std}=${_ext}11") + elseif(NOT CMAKE_CXX_COMPILER_VERSION VERSION_LESS 12.1) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "${_std}=c++0x") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "${_std}=${_ext}0x") + endif() + elseif(CMAKE_CXX_COMPILER_ID STREQUAL Cray) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the Cray + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-hstd=c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-hstd=c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL PGI) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the PGI + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "--c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "--c++11") + elseif(CMAKE_CXX_COMPILER_ID STREQUAL XL) + # CMAKE doesn't support CXX_STANDARD or C++ compile features for the XL + # compiler. Set compiler options transitively here such that they trickle + # down to a call to target_compile_options(). + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX14_STANDARD_COMPILE_OPTION "-std=c++11") + set(INTERNAL_CXX14_EXTENSION_COMPILE_OPTION "-std=c++11") + else() + # Assume GNU. CMAKE_CXX_STANDARD is handled correctly by CMake 3.1 and + # above for this compiler. If the user explicitly requests a C++ + # standard, CMake takes care of it. If not, transitively require C++11. + if(NOT CMAKE_CXX_STANDARD) + set(INTERNAL_CXX11_STANDARD_COMPILE_OPTION ${CMAKE_CXX11_STANDARD_COMPILE_OPTION}) + set(INTERNAL_CXX11_EXTENSION_COMPILE_OPTION ${CMAKE_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + endif() + + # Set the C++ standard info for Kokkos respecting user set values for + # CMAKE_CXX_STANDARD and CMAKE_CXX_EXTENSIONS. + if(CMAKE_CXX_STANDARD EQUAL 14) + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX14_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX14_EXTENSION_COMPILE_OPTION}) + endif() + elseif(CMAKE_CXX_STANDARD EQUAL 11) + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + else() + # The user didn't explicitly request a standard, transitively require + # C++11 respecting CMAKE_CXX_EXTENSIONS. + if(DEFINED CMAKE_CXX_EXTENSIONS AND CMAKE_CXX_EXTENSIONS STREQUAL OFF) + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_STANDARD_COMPILE_OPTION}) + else() + set(INTERNAL_CXX_FLAGS ${INTERNAL_CXX11_EXTENSION_COMPILE_OPTION}) + endif() + endif() + + set(KOKKOS_CXX_FLAGS ${INTERNAL_CXX_FLAGS} PARENT_SCOPE) + endif() +endfunction() + +########################## COMPILER AND FEATURE CHECKS ######################### + +# TODO: We are assuming that nvcc_wrapper is using g++ as the host compiler. +# Should we allow the user the option to change this? The host compiler +# for nvcc_wrapper can be set via the NVCC_WRAPPER_DEFAULT_COMPILER +# environment variable or by passing a different host compiler with the +# -ccbin flag. + +# TODO: Fully add CUDA support for Clang. +set_kokkos_cxx_compiler() + +set_kokkos_compiler_standard() + +######################### INITIALIZE INTERNAL VARIABLES ######################## + +# Add Kokkos' modules to CMake's module path. +set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${Kokkos_SOURCE_DIR}/cmake/Modules/") + +# Start with all global variables set to false. This guarantees correct +# results with changes and multiple configures. +set(KOKKOS_HAVE_CUDA OFF CACHE INTERNAL "") +set(KOKKOS_USE_CUDA_UVM OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_CUDA_RDC OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_CUDA_LAMBDA OFF CACHE INTERNAL "") +set(KOKKOS_CUDA_CLANG_WORKAROUND OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_OPENMP OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_PTHREAD OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_QTHREADS OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_SERIAL OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_HWLOC OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_HBWSPACE OFF CACHE INTERNAL "") +set(KOKKOS_HAVE_DEBUG OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_X86_64 OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_KNC OFF CACHE INTERNAL "") +set(KOKKOS_ENABLE_ISA_POWERPCLE OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV80 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV81 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_ARMV8_THUNDERX OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX2 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX512MIC OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_AVX512XEON OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KNC OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_POWER8 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_POWER9 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER30 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER32 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER35 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_KEPLER37 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL50 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL52 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_MAXWELL53 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL60 OFF CACHE INTERNAL "") +set(KOKKOS_ARCH_PASCAL61 OFF CACHE INTERNAL "") + +############################## SET BACKEND OPTIONS ############################# + +# Make sure at least one backend is selected. +if(NOT KOKKOS_ENABLE_CUDA AND NOT KOKKOS_ENABLE_OPENMP AND NOT KOKKOS_ENABLE_PTHREAD AND NOT KOKKOS_ENABLE_QTHREADS AND NOT KOKKOS_ENABLE_SERIAL) + message(FATAL_ERROR "Must set one of KOKKOS_ENABLE_CUDA, KOKKOS_ENABLE_OPENMP, KOKKOS_ENABLE_PTHREAD, KOKKOS_ENABLE_QTHREADS, or KOKKOS_ENABLE_SERIAL") +endif() + +# Only one of OpenMP, Pthreads, and Qthreads can be set. +set(KOKKOS_MESSAGE_TEXT "Only one of KOKKOS_ENABLE_OPENMP, KOKKOS_ENABLE_PTHREAD, and KOKKOS_ENABLE_QTHREADS can be selected") +if(KOKKOS_ENABLE_OPENMP AND KOKKOS_ENABLE_PTHREAD) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +elseif(KOKKOS_ENABLE_OPENMP AND KOKKOS_ENABLE_QTHREADS) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +elseif(KOKKOS_ENABLE_PTHREAD AND KOKKOS_ENABLE_QTHREADS) + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Get source files. +file(GLOB KOKKOS_CORE_SRCS core/src/impl/*.cpp) +file(GLOB KOKKOS_CONTAINERS_SRCS containers/src/impl/*.cpp) + +# Set options if using CUDA backend. +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_CUDA_DIR) + set(CUDA_TOOLKIT_ROOT_DIR ${KOKKOS_CUDA_DIR}) + endif() + + find_package(CUDA) + + if(NOT CUDA_FOUND) + if(KOKKOS_CUDA_DIR) + message(FATAL_ERROR "Couldn't find CUDA in default locations, and KOKKOS_CUDA_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find CUDA in default locations. Set KOKKOS_CUDA_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${CUDA_INCLUDE_DIRS}) + list(APPEND KOKKOS_LD_FLAGS -L${CUDA_TOOLKIT_ROOT_DIR}/lib64) + list(APPEND KOKKOS_LIBS cudart cuda) + + set(KOKKOS_HAVE_CUDA ON CACHE INTERNAL "") + file(GLOB KOKKOS_CUDA_SRCS core/src/Cuda/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_CUDA_SRCS}) + + # Set CUDA UVM if requested. + if(KOKKOS_ENABLE_CUDA_UVM) + set(KOKKOS_USE_CUDA_UVM ON CACHE INTERNAL "") + endif() + + # Set CUDA relocatable device code if requested. + if(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) + set(KOKKOS_HAVE_CUDA_RDC ON CACHE INTERNAL "") + list(APPEND KOKKOS_CXX_FLAGS --relocatable-device-code=true) + list(APPEND KOKKOS_LD_FLAGS --relocatable-device-code=true) + endif() + + # Set CUDA lambda if requested. + if(KOKKOS_ENABLE_CUDA_LAMBDA) + set(KOKKOS_HAVE_CUDA_LAMBDA ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + if(KOKKOS_CXX_COMPILER_VERSION VERSION_LESS 7.5) + message(FATAL_ERROR "CUDA lambda support requires CUDA 7.5 or higher. Disable it or use a 7.5 or later compiler.") + else() + list(APPEND KOKKOS_CXX_FLAGS -expt-extended-lambda) + endif() + endif() + endif() + + # Set Clang specific options. + if(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) + list(APPEND KOKKOS_CXX_FLAGS --cuda-path=${CUDA_TOOLKIT_ROOT_DIR}) + + set(KOKKOS_CUDA_CLANG_WORKAROUND ON CACHE INTERNAL "") + + # Force CUDA_LDG_INTRINSIC on when using Clang. + set(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC ON CACHE BOOL "Enable CUDA LDG." FORCE) + endif() +endif() + +# Set options if using OpenMP backend. +if(KOKKOS_ENABLE_OPENMP) + find_package(OpenMP REQUIRED) + + if(OPENMP_FOUND) + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + list(APPEND KOKKOS_CXX_FLAGS -Xcompiler) + endif() + + list(APPEND KOKKOS_CXX_FLAGS ${OpenMP_CXX_FLAGS}) + list(APPEND KOKKOS_LD_FLAGS ${OpenMP_CXX_FLAGS}) + endif() + + set(KOKKOS_HAVE_OPENMP ON CACHE INTERNAL "") + file(GLOB KOKKOS_OPENMP_SRCS core/src/OpenMP/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_OPENMP_SRCS}) +endif() + +# Set options if using Pthreads backend. +if(KOKKOS_ENABLE_PTHREAD) + find_package(Threads REQUIRED) + + list(APPEND KOKKOS_LIBS Threads::Threads) + + set(KOKKOS_HAVE_PTHREAD ON CACHE INTERNAL "") + file(GLOB KOKKOS_PTHREAD_SRCS core/src/Threads/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_PTHREAD_SRCS}) +endif() + +# Set options if using Qthreads backend. +if(KOKKOS_ENABLE_QTHREADS) + if(KOKKOS_QTHREADS_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_QTHREADS_DIR}) + endif() + + find_package(Qthreads) + + if(NOT QTHREADS_FOUND) + if(KOKKOS_QTHREADS_DIR) + message(FATAL_ERROR "Couldn't find Qthreads in default locations, and KOKKOS_QTHREADS_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find Qthreads in default locations. Set KOKKOS_QTHREADS_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${QTHREADS_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${QTHREADS_LIBRARIES}) + + set(KOKKOS_HAVE_QTHREADS ON CACHE INTERNAL "") + file(GLOB KOKKOS_QTHREADS_SRCS core/src/Threads/*.cpp) + list(APPEND KOKKOS_CORE_SRCS ${KOKKOS_QTHREADS_SRCS}) + + if(KOKKOS_QTHREADS_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +endif() + +# Set options if using Serial backend. +if(KOKKOS_ENABLE_SERIAL) + set(KOKKOS_HAVE_SERIAL ON CACHE INTERNAL "") +else() + # Remove serial source files. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Serial.cpp" + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Serial_Task.cpp") +endif() + +########################### SET ARCHITECTURE OPTIONS ########################### + +# Make sure the host architecture option is valid. Need to verify in case user +# passes the option via the command line. +list(FIND KOKKOS_HOST_ARCH_LIST "${KOKKOS_HOST_ARCH}" KOKKOS_VALID_HOST_ARCH) +if(KOKKOS_VALID_HOST_ARCH EQUAL -1) + set(KOKKOS_ARCH_TEXT "\n ${KOKKOS_HOST_ARCH_LIST}") + string(REPLACE ";" "\n " KOKKOS_ARCH_TEXT "${KOKKOS_ARCH_TEXT}") + set(KOKKOS_MESSAGE_TEXT "Invalid architecture for KOKKOS_HOST_ARCH: '${KOKKOS_HOST_ARCH}'") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Choices:${KOKKOS_ARCH_TEXT}\n") + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Make sure the GPU architecture option is valid. Need to verify in case user +# passes the option via the command line. +list(FIND KOKKOS_GPU_ARCH_LIST "${KOKKOS_GPU_ARCH}" KOKKOS_VALID_GPU_ARCH) +if(KOKKOS_VALID_GPU_ARCH EQUAL -1) + set(KOKKOS_ARCH_TEXT "\n ${KOKKOS_GPU_ARCH_LIST}") + string(REPLACE ";" "\n " KOKKOS_ARCH_TEXT "${KOKKOS_ARCH_TEXT}") + set(KOKKOS_MESSAGE_TEXT "Invalid architecture for KOKKOS_GPU_ARCH: '${KOKKOS_GPU_ARCH}'") + set(KOKKOS_MESSAGE_TEXT "${KOKKOS_MESSAGE_TEXT}\n Choices:${KOKKOS_ARCH_TEXT}\n") + message(FATAL_ERROR "${KOKKOS_MESSAGE_TEXT}") +endif() + +# Decide what ISA level we are able to support. +if(KOKKOS_HOST_ARCH STREQUAL SNB OR KOKKOS_HOST_ARCH STREQUAL HSW OR KOKKOS_HOST_ARCH STREQUAL BDW OR + KOKKOS_HOST_ARCH STREQUAL SKX OR KOKKOS_HOST_ARCH STREQUAL KNL) + set(KOKKOS_ENABLE_ISA_X86_64 ON CACHE INTERNAL "") +endif() + +if(KOKKOS_HOST_ARCH STREQUAL KNC) + set(KOKKOS_ENABLE_ISA_KNC ON CACHE INTERNAL "") +endif() + +if(KOKKOS_HOST_ARCH STREQUAL Power8 OR KOKKOS_HOST_ARCH STREQUAL Power9) + set(KOKKOS_ENABLE_ISA_POWERPCLE ON CACHE INTERNAL "") +endif() + +# Add host architecture options. +if(KOKKOS_HOST_ARCH STREQUAL ARMv80) + set(KOKKOS_ARCH_ARMV80 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8-a) + list(APPEND KOKKOS_LD_FLAGS -march=armv8-a) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL ARMv81) + set(KOKKOS_ARCH_ARMV81 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8.1-a) + list(APPEND KOKKOS_LD_FLAGS -march=armv8.1-a) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL ARMv8-ThunderX) + set(KOKKOS_ARCH_ARMV80 ON CACHE INTERNAL "") + set(KOKKOS_ARCH_ARMV8_THUNDERX ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=armv8-a -mtune=thunderx) + list(APPEND KOKKOS_LD_FLAGS -march=armv8-a -mtune=thunderx) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL SNB OR KOKKOS_HOST_ARCH STREQUAL AMDAVX) + set(KOKKOS_ARCH_AVX ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -mavx) + list(APPEND KOKKOS_LD_FLAGS -mavx) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + list(APPEND KOKKOS_CXX_FLAGS -tp=sandybridge) + list(APPEND KOKKOS_LD_FLAGS -tp=sandybridge) + else() + list(APPEND KOKKOS_CXX_FLAGS -mavx) + list(APPEND KOKKOS_LD_FLAGS -mavx) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL HSW OR KOKKOS_HOST_ARCH STREQUAL BDW) + set(KOKKOS_ARCH_AVX2 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xCORE-AVX2) + list(APPEND KOKKOS_LD_FLAGS -xCORE-AVX2) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + list(APPEND KOKKOS_CXX_FLAGS -tp=haswell) + list(APPEND KOKKOS_LD_FLAGS -tp=haswell) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=core-avx2 -mtune=core-avx2) + list(APPEND KOKKOS_LD_FLAGS -march=core-avx2 -mtune=core-avx2) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL KNL) + set(KOKKOS_ARCH_AVX512MIC ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xMIC-AVX512) + list(APPEND KOKKOS_LD_FLAGS -xMIC-AVX512) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=knl) + list(APPEND KOKKOS_LD_FLAGS -march=knl) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL SKX) + set(KOKKOS_ARCH_AVX512XEON ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL Intel) + list(APPEND KOKKOS_CXX_FLAGS -xCORE-AVX512) + list(APPEND KOKKOS_LD_FLAGS -xCORE-AVX512) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Cray) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -march=skylake-avx512) + list(APPEND KOKKOS_LD_FLAGS -march=skylake-avx512) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL KNC) + set(KOKKOS_ARCH_KNC ON CACHE INTERNAL "") + list(APPEND KOKKOS_CXX_FLAGS -mmic) + list(APPEND KOKKOS_LD_FLAGS -mmic) +elseif(KOKKOS_HOST_ARCH STREQUAL Power8) + set(KOKKOS_ARCH_POWER8 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -mcpu=power8 -mtune=power8) + list(APPEND KOKKOS_LD_FLAGS -mcpu=power8 -mtune=power8) + endif() +elseif(KOKKOS_HOST_ARCH STREQUAL Power9) + set(KOKKOS_ARCH_POWER9 ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COMPILER_ID STREQUAL PGI) + else() + list(APPEND KOKKOS_CXX_FLAGS -mcpu=power9 -mtune=power9) + list(APPEND KOKKOS_LD_FLAGS -mcpu=power9 -mtune=power9) + endif() +endif() + +# Add GPU architecture options. +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + set(KOKKOS_GPU_ARCH_FLAG -arch) + elseif(KOKKOS_CXX_COMPILER_ID STREQUAL Clang) + list(APPEND KOKKOS_CXX_FLAGS -x cuda) + set(KOKKOS_GPU_ARCH_FLAG --cuda-gpu-arch) + endif() + + if(KOKKOS_GPU_ARCH STREQUAL Kepler30) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER30 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_30) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler32) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER32 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_32) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler35 OR KOKKOS_GPU_ARCH STREQUAL Kepler) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER35 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_35) + elseif(KOKKOS_GPU_ARCH STREQUAL Kepler37) + set(KOKKOS_ARCH_KEPLER ON CACHE INTERNAL "") + set(KOKKOS_ARCH_KEPLER37 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_37) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell50 OR KOKKOS_GPU_ARCH STREQUAL Maxwell) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL50 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_50) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell52) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL52 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_52) + elseif(KOKKOS_GPU_ARCH STREQUAL Maxwell53) + set(KOKKOS_ARCH_MAXWELL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_MAXWELL53 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_53) + elseif(KOKKOS_GPU_ARCH STREQUAL Pascal60) + set(KOKKOS_ARCH_PASCAL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_PASCAL60 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_60) + elseif(KOKKOS_GPU_ARCH STREQUAL Pascal61) + set(KOKKOS_ARCH_PASCAL ON CACHE INTERNAL "") + set(KOKKOS_ARCH_PASCAL61 ON CACHE INTERNAL "") + set(KOKKOS_GPU_ARCH_FLAG ${KOKKOS_GPU_ARCH_FLAG}=sm_61) + endif() + + if(NOT KOKKOS_GPU_ARCH STREQUAL None) + list(APPEND KOKKOS_CXX_FLAGS ${KOKKOS_GPU_ARCH_FLAG}) + + if(KOKKOS_CXX_COMPILER_ID STREQUAL NVIDIA) + list(APPEND KOKKOS_LD_FLAGS ${KOKKOS_GPU_ARCH_FLAG}) + endif() + endif() +endif() + +############################### SET OTHER OPTIONS ############################## + +# Set options if using hwloc. +if(KOKKOS_ENABLE_HWLOC) + if(KOKKOS_HWLOC_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_HWLOC_DIR}) + endif() + + find_package(HWLOC) + + if(NOT HWLOC_FOUND) + if(KOKKOS_HWLOC_DIR) + message(FATAL_ERROR "Couldn't find HWLOC in default locations, and KOKKOS_HWLOC_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find HWLOC in default locations. Set KOKKOS_HWLOC_DIR.") + endif() + endif() + + list(APPEND KOKKOS_INCLUDE_DIRS ${HWLOC_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${HWLOC_LIBRARIES}) + + set(KOKKOS_HAVE_HWLOC ON CACHE INTERNAL "") + + if(KOKKOS_HWLOC_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +endif() + +# Set options if using memkind. +if(KOKKOS_ENABLE_MEMKIND) + if(KOKKOS_MEMKIND_DIR) + list(APPEND CMAKE_PREFIX_PATH ${KOKKOS_MEMKIND_DIR}) + endif() + + find_package(Memkind) + + if(NOT MEMKIND_FOUND) + if(KOKKOS_MEMKIND_DIR) + message(FATAL_ERROR "Couldn't find Memkind in default locations, and KOKKOS_MEMKIND_DIR points to an invalid installation.") + else() + message(FATAL_ERROR "Couldn't find Memkind in default locations. Set KOKKOS_MEMKIND_DIR.") + endif() + endif() + + set(KOKKOS_ENABLE_HBWSPACE ON CACHE INTERNAL "") + list(APPEND KOKKOS_INCLUDE_DIRS ${MEMKIND_INCLUDE_DIR}) + list(APPEND KOKKOS_LIBS ${MEMKIND_LIBRARIES}) + + if(KOKKOS_MEMKIND_DIR) + list(REMOVE_AT CMAKE_PREFIX_PATH -1) + endif() +else() + # Remove HBW source file. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_HBWSpace.cpp") +endif() + +# Set options if using librt. +if(KOKKOS_ENABLE_LIBRT) + list(APPEND KOKKOS_LIBS rt) +endif() + +# Set debugging if requested. +if(KOKKOS_DEBUG) + set(KOKKOS_HAVE_DEBUG ON CACHE INTERNAL "") + set(KOKKOS_ENABLE_DEBUG_BOUNDS_CHECK ON CACHE INTERNAL "") + + if(KOKKOS_CXX_COVIDIA) + list(APPEND KOKKOS_CXX_FLAGS -lineinfo) + endif() + + list(APPEND KOKKOS_CXX_FLAGS -g) + list(APPEND KOKKOS_LD_FLAGS -g) +endif() + +# Set profiling if requested. +if(KOKKOS_ENABLE_PROFILING) + list(APPEND KOKKOS_LIBS dl) +else() + # Remove profiling source file. + list(REMOVE_ITEM KOKKOS_CORE_SRCS + "${Kokkos_SOURCE_DIR}/core/src/impl/Kokkos_Profiling_Interface.cpp") +endif() + +# Use GCC toolchain with Clang. +if(KOKKOS_CXX_COMPILER_ID STREQUAL Clang AND NOT APPLE) + find_program(KOKKOS_GCC_PATH g++) + if(NOT KOKKOS_GCC_PATH) + message(FATAL_ERROR "Can't find GCC path to get toolchain for Clang.") + endif() + string(REPLACE "/bin/g++" "" KOKKOS_GCC_PATH ${KOKKOS_GCC_PATH}) + + list(APPEND KOKKOS_CXX_FLAGS --gcc-toolchain=${KOKKOS_GCC_PATH}) + list(APPEND KOKKOS_LD_FLAGS --gcc-toolchain=${KOKKOS_GCC_PATH}) +endif() + +############################ Detect if submodule ############################### +# +# With thanks to StackOverflow: +# http://stackoverflow.com/questions/25199677/how-to-detect-if-current-scope-has-a-parent-in-cmake +# +get_directory_property(HAS_PARENT PARENT_DIRECTORY) +if(HAS_PARENT) + message(STATUS "Submodule build") + SET(KOKKOS_HEADER_DIR "include/kokkos") +else() + message(STATUS "Standalone build") + SET(KOKKOS_HEADER_DIR "include") +endif() + +############################ PRINT CONFIGURE STATUS ############################ + +message(STATUS "") +message(STATUS "****************** Kokkos Settings ******************") +message(STATUS "Execution Spaces") + +if(KOKKOS_ENABLE_CUDA) + message(STATUS " Device Parallel: Cuda") +else() + message(STATUS " Device Parallel: None") +endif() + +if(KOKKOS_ENABLE_OPENMP) + message(STATUS " Host Parallel: OpenMP") +elseif(KOKKOS_ENABLE_PTHREAD) + message(STATUS " Host Parallel: Pthread") +elseif(KOKKOS_ENABLE_QTHREADS) + message(STATUS " Host Parallel: Qthreads") +else() + message(STATUS " Host Parallel: None") +endif() + +if(KOKKOS_ENABLE_SERIAL) + message(STATUS " Host Serial: Serial") +else() + message(STATUS " Host Serial: None") +endif() + +message(STATUS "") +message(STATUS "Architectures") +message(STATUS " Host Architecture: ${KOKKOS_HOST_ARCH}") +message(STATUS " Device Architecture: ${KOKKOS_GPU_ARCH}") + +message(STATUS "") +message(STATUS "Enabled options") + +if(KOKKOS_SEPARATE_LIBS) + message(STATUS " KOKKOS_SEPARATE_LIBS") +endif() + +if(KOKKOS_ENABLE_HWLOC) + message(STATUS " KOKKOS_ENABLE_HWLOC") +endif() + +if(KOKKOS_ENABLE_MEMKIND) + message(STATUS " KOKKOS_ENABLE_MEMKIND") +endif() + +if(KOKKOS_DEBUG) + message(STATUS " KOKKOS_DEBUG") +endif() + +if(KOKKOS_ENABLE_PROFILING) + message(STATUS " KOKKOS_ENABLE_PROFILING") +endif() + +if(KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION) + message(STATUS " KOKKOS_ENABLE_AGGRESSIVE_VECTORIZATION") +endif() + +if(KOKKOS_ENABLE_CUDA) + if(KOKKOS_ENABLE_CUDA_LDG_INTRINSIC) + message(STATUS " KOKKOS_ENABLE_CUDA_LDG_INTRINSIC") + endif() + + if(KOKKOS_ENABLE_CUDA_UVM) + message(STATUS " KOKKOS_ENABLE_CUDA_UVM") + endif() + + if(KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE) + message(STATUS " KOKKOS_ENABLE_CUDA_RELOCATABLE_DEVICE_CODE") + endif() + + if(KOKKOS_ENABLE_CUDA_LAMBDA) + message(STATUS " KOKKOS_ENABLE_CUDA_LAMBDA") + endif() + + if(KOKKOS_CUDA_DIR) + message(STATUS " KOKKOS_CUDA_DIR: ${KOKKOS_CUDA_DIR}") + endif() +endif() + +if(KOKKOS_QTHREADS_DIR) + message(STATUS " KOKKOS_QTHREADS_DIR: ${KOKKOS_QTHREADS_DIR}") +endif() + +if(KOKKOS_HWLOC_DIR) + message(STATUS " KOKKOS_HWLOC_DIR: ${KOKKOS_HWLOC_DIR}") +endif() + +if(KOKKOS_MEMKIND_DIR) + message(STATUS " KOKKOS_MEMKIND_DIR: ${KOKKOS_MEMKIND_DIR}") +endif() + +message(STATUS "*****************************************************") +message(STATUS "") + +################################ SET UP PROJECT ################################ + +configure_file( + ${Kokkos_SOURCE_DIR}/core/cmake/KokkosCore_config.h.in + ${Kokkos_BINARY_DIR}/KokkosCore_config.h +) + +SET(INSTALL_LIB_DIR lib CACHE PATH "Installation directory for libraries") +SET(INSTALL_BIN_DIR bin CACHE PATH "Installation directory for executables") +SET(INSTALL_INCLUDE_DIR ${KOKKOS_HEADER_DIR} CACHE PATH + "Installation directory for header files") +IF(WIN32 AND NOT CYGWIN) + SET(DEF_INSTALL_CMAKE_DIR CMake) +ELSE() + SET(DEF_INSTALL_CMAKE_DIR lib/CMake/Kokkos) +ENDIF() + +SET(INSTALL_CMAKE_DIR ${DEF_INSTALL_CMAKE_DIR} CACHE PATH + "Installation directory for CMake files") + +# Make relative paths absolute (needed later on) +FOREACH(p LIB BIN INCLUDE CMAKE) + SET(var INSTALL_${p}_DIR) + IF(NOT IS_ABSOLUTE "${${var}}") + SET(${var} "${CMAKE_INSTALL_PREFIX}/${${var}}") + ENDIF() +ENDFOREACH() + +# set up include-directories +SET (Kokkos_INCLUDE_DIRS + ${Kokkos_SOURCE_DIR}/core/src + ${Kokkos_SOURCE_DIR}/containers/src + ${Kokkos_SOURCE_DIR}/algorithms/src + ${Kokkos_BINARY_DIR} # to find KokkosCore_config.h +) + +INCLUDE_DIRECTORIES(${Kokkos_INCLUDE_DIRS}) + +IF(KOKKOS_SEPARATE_LIBS) + # kokkoscore + ADD_LIBRARY( + kokkoscore + ${KOKKOS_CORE_SRCS} + ) + + target_compile_options( + kokkoscore + PUBLIC ${KOKKOS_CXX_FLAGS} + ) + + target_compile_features( + kokkoscore + PUBLIC ${KOKKOS_CXX11_FEATURES} + ) + + # Install the kokkoscore library + INSTALL (TARGETS kokkoscore + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin + ) + + # Install the kokkoscore headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/core/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + # Install KokkosCore_config.h header + INSTALL (FILES + ${Kokkos_BINARY_DIR}/KokkosCore_config.h + DESTINATION ${KOKKOS_HEADER_DIR} + ) + + TARGET_LINK_LIBRARIES( + kokkoscore + ${KOKKOS_LD_FLAGS} + ${KOKKOS_LIBS} + ) + + # kokkoscontainers + ADD_LIBRARY( + kokkoscontainers + ${KOKKOS_CONTAINERS_SRCS} + ) + + TARGET_LINK_LIBRARIES( + kokkoscontainers + kokkoscore + ) + + # Install the kokkocontainers library + INSTALL (TARGETS kokkoscontainers + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + # Install the kokkoscontainers headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/containers/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + # kokkosalgorithms - Build as interface library since no source files. + ADD_LIBRARY( + kokkosalgorithms + INTERFACE + ) + + target_include_directories( + kokkosalgorithms + INTERFACE ${Kokkos_SOURCE_DIR}/algorithms/src + ) + + TARGET_LINK_LIBRARIES( + kokkosalgorithms + INTERFACE kokkoscore + ) + + # Install the kokkoalgorithms library + INSTALL (TARGETS kokkosalgorithms + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + # Install the kokkosalgorithms headers + INSTALL (DIRECTORY + ${Kokkos_SOURCE_DIR}/algorithms/src/ + DESTINATION ${KOKKOS_INSTALL_INDLUDE_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + SET (Kokkos_LIBRARIES_NAMES kokkoscore kokkoscontainers kokkosalgorithms) + +ELSE() + # kokkos + ADD_LIBRARY( + kokkos + ${KOKKOS_CORE_SRCS} + ${KOKKOS_CONTAINERS_SRCS} + ) + + target_compile_options( + kokkos + PUBLIC ${KOKKOS_CXX_FLAGS} + ) + + target_compile_features( + kokkos + PUBLIC ${KOKKOS_CXX11_FEATURES} + ) + + TARGET_LINK_LIBRARIES( + kokkos + ${KOKKOS_LD_FLAGS} + ${KOKKOS_LIBS} + ) + + # Install the kokkos library + INSTALL (TARGETS kokkos + EXPORT KokkosTargets + ARCHIVE DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + LIBRARY DESTINATION ${CMAKE_INSTALL_PREFIX}/lib + RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin) + + + # Install the kokkos headers + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/core/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/containers/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + INSTALL (DIRECTORY + EXPORT KokkosTargets + ${Kokkos_SOURCE_DIR}/algorithms/src/ + DESTINATION ${KOKKOS_HEADER_DIR} + FILES_MATCHING PATTERN "*.hpp" + ) + + INSTALL (FILES + ${Kokkos_BINARY_DIR}/KokkosCore_config.h + DESTINATION ${KOKKOS_HEADER_DIR} + ) + + include_directories(${Kokkos_BINARY_DIR}) + include_directories(${Kokkos_SOURCE_DIR}/core/src) + include_directories(${Kokkos_SOURCE_DIR}/containers/src) + include_directories(${Kokkos_SOURCE_DIR}/algorithms/src) + + + SET (Kokkos_LIBRARIES_NAMES kokkos) + +endif() + +# Add all targets to the build-tree export set +export(TARGETS ${Kokkos_LIBRARIES_NAMES} + FILE "${Kokkos_BINARY_DIR}/KokkosTargets.cmake") + +# Export the package for use from the build-tree +# (this registers the build-tree with a global CMake-registry) +export(PACKAGE Kokkos) + +# Create the KokkosConfig.cmake and KokkosConfigVersion files +file(RELATIVE_PATH REL_INCLUDE_DIR "${INSTALL_CMAKE_DIR}" + "${INSTALL_INCLUDE_DIR}") +# ... for the build tree +set(CONF_INCLUDE_DIRS "${Kokkos_SOURCE_DIR}" "${Kokkos_BINARY_DIR}") +configure_file(${Kokkos_SOURCE_DIR}/cmake/KokkosConfig.cmake.in + "${Kokkos_BINARY_DIR}/KokkosConfig.cmake" @ONLY) +# ... for the install tree +set(CONF_INCLUDE_DIRS "\${Kokkos_CMAKE_DIR}/${REL_INCLUDE_DIR}") +configure_file(${Kokkos_SOURCE_DIR}/cmake/KokkosConfig.cmake.in + "${Kokkos_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/KokkosConfig.cmake" @ONLY) + +# Install the KokkosConfig.cmake and KokkosConfigVersion.cmake +install(FILES + "${Kokkos_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/KokkosConfig.cmake" + DESTINATION "${INSTALL_CMAKE_DIR}") + +# Install the export set for use with the install-tree +INSTALL(EXPORT KokkosTargets DESTINATION + "${INSTALL_CMAKE_DIR}") diff --git a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt index 961e4186ec..0f24487814 100644 --- a/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt +++ b/lib/kokkos/config/kokkos-trilinos-integration-procedure.txt @@ -60,34 +60,12 @@ Step 2: // -------------------------------------------------------------------------------- // Step 3: - 3.1. Build and test Trilinos with 3 different configurations; a configure-all script is provided in Trilinos and should be modified to test each of the following 3 configurations with appropriate environment variable(s): + 3.1. Build and test Trilinos with 4 different configurations; Run scripts for white and shepard are provided in kokkos/config/trilinos-integration - - GCC/4.7.2-OpenMP/Complex - Run tests with the following environment variable: + Usually its a good idea to run those script via nohup. + You can run all four at the same time, use separate directories for each. - export OMP_NUM_THREADS=2 - - - - Intel/15.0.2-Serial/NoComplex - - - - GCC/4.8.4/CUDA/7.5.18-Cuda/Serial/NoComplex - Run tests with the following environment variables: - - export CUDA_LAUNCH_BLOCKING=1 - export CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 - - - mkdir Build - cd Build - cp TRILINOS_PATH/sampleScripts/Sandia-SEMS/configure-all ./ - ** Set the path to Trilinos appropriately within the configure-all script ** - source $SEMS_MODULE_ROOT/utils/sems-modules-init.sh kokkos - source configure-all - make -k (-k means "keep going" to get past build errors; -j12 can also be specified to build with 12 threads, for example) - ctest - - 3.2. Compare the failed test output to the test output on the dashboard ( testing.sandia.gov/cdash select Trilinos ); investigate and fix problems if new tests fail after the Kokkos snapshot + 3.2. Compare the failed test output between the pristine and the updated runs; investigate and fix problems if new tests fail after the Kokkos snapshot // -------------------------------------------------------------------------------- // @@ -134,7 +112,7 @@ Step 4: Once all Trilinos tests pass promote Kokkos develop branch to master on master: sha1 develop: sha1 - git push --follow-tags origin master + 4.4. Do NOT push yet // -------------------------------------------------------------------------------- // @@ -156,9 +134,15 @@ Step 5: python KOKKOS_PATH/config/snapshot.py KOKKOS_PATH TRILINOS_PATH/packages - 5.3. Push the updated develop branch of Trilinos to Github - congratulations!!! + 5.3. Run checkin-test to push to trilinos using the CI build modules (gcc/4.9.3) - (From Trilinos directory): - git push + The modules are listed in kokkos/config/trilinos-integration/checkin-test + Run checkin-test, forward dependencies and optional dependencies must be enabled + If push failed because someone else clearly broke something, push manually. + If push failed for unclear reasons, investigate, fix, and potentially start over from step 2 after reseting your local kokkos/master branch + +Step 6: Push Kokkos to master + + git push --follow-tags origin master // -------------------------------------------------------------------------------- // diff --git a/lib/kokkos/config/kokkos_dev/config-core-all.sh b/lib/kokkos/config/kokkos_dev/config-core-all.sh index d4fb25a8e1..1867de7204 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-all.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-all.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh index c2e17bb944..5a6cc1493e 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-cuda-omp-hwloc.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh b/lib/kokkos/config/kokkos_dev/config-core-cuda.sh index 39b72d5ce1..606755da81 100755 --- a/lib/kokkos/config/kokkos_dev/config-core-cuda.sh +++ b/lib/kokkos/config/kokkos_dev/config-core-cuda.sh @@ -13,7 +13,7 @@ # module load cmake/2.8.11.2 gcc/4.8.3 cuda/6.5.14 nvcc-wrapper/gnu # # The 'nvcc-wrapper' module should load a script that matches -# kokkos/config/nvcc_wrapper +# kokkos/bin/nvcc_wrapper # #----------------------------------------------------------------------------- # Source and installation directories: diff --git a/lib/kokkos/config/master_history.txt b/lib/kokkos/config/master_history.txt index 9eaecb5031..cc6f4c97d7 100644 --- a/lib/kokkos/config/master_history.txt +++ b/lib/kokkos/config/master_history.txt @@ -5,4 +5,5 @@ tag: 2.02.00 date: 10:30:2016 master: 6c90a581 develop: ca3dd56e tag: 2.02.01 date: 11:01:2016 master: 9c698c86 develop: b0072304 tag: 2.02.07 date: 12:16:2016 master: 4b4cc4ba develop: 382c0966 tag: 2.02.15 date: 02:10:2017 master: 8c64cd93 develop: 28dea8b6 -tag: 2.03.00 date: 04:25:2017 master: 120d9ce7 develop: 015ba641 +tag: 2.03.00 date: 04:25:2017 master: 120d9ce7 develop: 015ba641 +tag: 2.03.05 date: 05:27:2017 master: 36b92f43 develop: 79073186 diff --git a/lib/kokkos/config/snapshot.py b/lib/kokkos/config/snapshot.py index d816cd0c9c..bfa97bf48a 100755 --- a/lib/kokkos/config/snapshot.py +++ b/lib/kokkos/config/snapshot.py @@ -27,7 +27,7 @@ import subprocess, argparse, re, doctest, os, datetime, traceback def parse_cmdline(description): parser = argparse.ArgumentParser(usage="snapshot.py [options] source destination", description=description) - parser.add_argument("-n", "--no-comit", action="store_false", dest="create_commit", default=True, + parser.add_argument("-n", "--no-commit", action="store_false", dest="create_commit", default=True, help="Do not perform a commit or create a commit message.") parser.add_argument("-v", "--verbose", action="store_true", dest="verbose_mode", default=False, help="Enable verbose mode.") @@ -39,6 +39,8 @@ def parse_cmdline(description): help="Type of repository of the source, use none to skip all repository operations.") parser.add_argument("--dest-repo", choices=["git","none"], default="", help="Type of repository of the destination, use none to skip all repository operations.") + parser.add_argument("--small", action="store_true", dest="small_mode", + help="Don't include tests and other extra files when copying.") parser.add_argument("source", help="Source project to snapshot from.") parser.add_argument("destination", help="Destination to snapshot too.") @@ -58,9 +60,9 @@ def validate_options(options): options.source = os.path.abspath(options.source) options.destination = os.path.abspath(options.destination) - + if os.path.exists(options.source): - apparent_source_repo_type, source_root = deterimine_repo_type(options.source) + apparent_source_repo_type, source_root = determine_repo_type(options.source) else: raise RuntimeError("Could not find source directory of %s." % options.source) options.source_root = source_root @@ -69,7 +71,7 @@ def validate_options(options): print "Could not find destination directory of %s so it will be created." % options.destination os.makedirs(options.destination) - apparent_dest_repo_type, dest_root = deterimine_repo_type(options.destination) + apparent_dest_repo_type, dest_root = determine_repo_type(options.destination) options.dest_root = dest_root #error on svn repo types for now @@ -111,7 +113,7 @@ def run_cmd(cmd, options, working_dir="."): print "==== %s stderr ====" % cmd_str print proc_stderr print "==== %s stderr ====" % cmd_str - + if ret_val != 0: raise RuntimeError("Command '%s' failed with error code %d. Error message:%s%s%sstdout:%s" % \ (cmd_str, ret_val, os.linesep, proc_stderr, os.linesep, proc_stdout)) @@ -119,7 +121,7 @@ def run_cmd(cmd, options, working_dir="."): return proc_stdout, proc_stderr #end run_cmd -def deterimine_repo_type(location): +def determine_repo_type(location): apparent_repo_type = "none" while location != "": @@ -133,16 +135,32 @@ def deterimine_repo_type(location): location = location[:location.rfind(os.sep)] return apparent_repo_type, location - -#end deterimine_repo_type +#end determine_repo_type def rsync(source, dest, options): rsync_cmd = ["rsync", "-ar", "--delete"] if options.debug_mode: rsync_cmd.append("-v") + if options.small_mode or options.source_repo == "git": + rsync_cmd.append("--delete-excluded") + + if options.small_mode: + rsync_cmd.append("--include=config/master_history.txt") + rsync_cmd.append("--include=cmake/tpls") + rsync_cmd.append("--exclude=benchmarks/") + rsync_cmd.append("--exclude=config/*") + rsync_cmd.append("--exclude=doc/") + rsync_cmd.append("--exclude=example/") + rsync_cmd.append("--exclude=tpls/") + rsync_cmd.append("--exclude=HOW_TO_SNAPSHOT") + rsync_cmd.append("--exclude=unit_test") + rsync_cmd.append("--exclude=unit_tests") + rsync_cmd.append("--exclude=perf_test") + rsync_cmd.append("--exclude=performance_tests") + if options.source_repo == "git": - rsync_cmd.append("--exclude=.git") + rsync_cmd.append("--exclude=.git*") rsync_cmd.append(options.source) rsync_cmd.append(options.destination) @@ -171,28 +189,27 @@ def find_git_commit_information(options): ('sems', 'software.sandia.gov:/git/sems') """ git_log_cmd = ["git", "log", "-1"] - + output, error = run_cmd(git_log_cmd, options, options.source) - + commit_match = re.match("commit ([0-9a-fA-F]+)", output) commit_id = commit_match.group(1) commit_log = output - + git_remote_cmd = ["git", "remote", "-v"] output, error = run_cmd(git_remote_cmd, options, options.source) - + remote_match = re.search("origin\s([^ ]*/([^ ]+))", output, re.MULTILINE) if not remote_match: raise RuntimeError("Could not find origin of repo at %s. Consider using none for source repo type." % (options.source)) source_location = remote_match.group(1) source_name = remote_match.group(2).strip() - + if source_name[-1] == "/": source_name = source_name[:-1] return commit_id, commit_log, source_name, source_location - #end find_git_commit_information def do_git_commit(message, options): @@ -201,10 +218,10 @@ def do_git_commit(message, options): git_add_cmd = ["git", "add", "-A"] run_cmd(git_add_cmd, options, options.destination) - + git_commit_cmd = ["git", "commit", "-m%s" % message] run_cmd(git_commit_cmd, options, options.destination) - + git_log_cmd = ["git", "log", "--format=%h", "-1"] commit_sha1, error = run_cmd(git_log_cmd, options, options.destination) @@ -214,7 +231,7 @@ def do_git_commit(message, options): def verify_git_repo_clean(location, options): git_status_cmd = ["git", "status", "--porcelain"] output, error = run_cmd(git_status_cmd, options, location) - + if output != "": if options.no_validate_repo == False: raise RuntimeError("%s is not clean.%sPlease commit or stash all changes before running snapshot." @@ -223,7 +240,6 @@ def verify_git_repo_clean(location, options): print "WARNING: %s is not clean. Proceeding anyway." % location print "WARNING: This could lead to differences in the source and destination." print "WARNING: It could also lead to extra files being included in the snapshot commit." - #end verify_git_repo_clean def main(options): @@ -238,14 +254,14 @@ def main(options): commit_log = "Unknown commit from %s snapshotted at: %s" % (options.source, datetime.datetime.now()) repo_name = options.source repo_location = options.source - + commit_message = create_commit_message(commit_id, commit_log, repo_name, repo_location) + os.linesep*2 - + if options.dest_repo == "git": verify_git_repo_clean(options.destination, options) rsync(options.source, options.destination, options) - + if options.dest_repo == "git": do_git_commit(commit_message, options) elif options.dest_repo == "none": @@ -256,10 +272,6 @@ def main(options): cwd = os.getcwd() print "No commit done by request. Please use file at:" print "%s%sif you wish to commit this to a repo later." % (cwd+"/"+file_name, os.linesep) - - - - #end main if (__name__ == "__main__"): @@ -267,7 +279,7 @@ if (__name__ == "__main__"): doctest.testmod() sys.exit(0) - try: + try: options = parse_cmdline(__doc__) main(options) except RuntimeError, e: @@ -275,5 +287,5 @@ if (__name__ == "__main__"): if "--debug" in sys.argv: traceback.print_exc() sys.exit(1) - else: + else: sys.exit(0) diff --git a/lib/kokkos/config/test_all_sandia b/lib/kokkos/config/test_all_sandia index 6909606643..8e1246bf8b 100755 --- a/lib/kokkos/config/test_all_sandia +++ b/lib/kokkos/config/test_all_sandia @@ -24,6 +24,8 @@ elif [[ "$HOSTNAME" =~ node.* ]]; then # Warning: very generic name fi elif [[ "$HOSTNAME" =~ apollo ]]; then MACHINE=apollo +elif [[ "$HOSTNAME" =~ sullivan ]]; then + MACHINE=sullivan elif [ ! -z "$SEMS_MODULEFILES_ROOT" ]; then MACHINE=sems else @@ -152,7 +154,7 @@ if [ "$MACHINE" = "sems" ]; then "gcc/5.1.0 $BASE_MODULE_LIST "Serial" g++ $GCC_WARNING_FLAGS" "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" - "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA8_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else # Format: (compiler module-list build-list exe-name warning-flag) @@ -164,6 +166,7 @@ if [ "$MACHINE" = "sems" ]; then "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.7.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.8.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" + "clang/3.9.0 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" "cuda/8.0.44 $CUDA8_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" @@ -184,7 +187,7 @@ elif [ "$MACHINE" = "white" ]; then # Format: (compiler module-list build-list exe-name warning-flag) COMPILERS=("gcc/5.4.0 $BASE_MODULE_LIST $IBM_BUILD_LIST g++ $GCC_WARNING_FLAGS" "ibm/13.1.3 $IBM_MODULE_LIST $IBM_BUILD_LIST xlC $IBM_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA_MODULE_LIST $CUDA_IBM_BUILD_LIST ${KOKKOS_PATH}/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) if [ -z "$ARCH_FLAG" ]; then @@ -221,7 +224,7 @@ elif [ "$MACHINE" = "sullivan" ]; then BASE_MODULE_LIST="/" # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("gcc/5.3.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS") + COMPILERS=("gcc/6.1.0 $BASE_MODULE_LIST $ARM_GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS") if [ -z "$ARCH_FLAG" ]; then ARCH_FLAG="--arch=ARMv8-ThunderX" @@ -278,11 +281,11 @@ elif [ "$MACHINE" = "apollo" ]; then "intel/16.0.1 $BASE_MODULE_LIST "OpenMP" icpc $INTEL_WARNING_FLAGS" "clang/3.9.0 $BASE_MODULE_LIST "Pthread_Serial" clang++ $CLANG_WARNING_FLAGS" "clang/head $CLANG_MODULE_LIST "Cuda_Pthread" clang++ $CUDA_WARNING_FLAGS" - "cuda/8.0.44 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/8.0.44 $CUDA_MODULE_LIST "Cuda_OpenMP" $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) else # Format: (compiler module-list build-list exe-name warning-flag) - COMPILERS=("cuda/8.0.44 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + COMPILERS=("cuda/8.0.44 $CUDA8_MODULE_LIST $BUILD_LIST_CUDA_NVCC $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" "clang/head $CLANG_MODULE_LIST $BUILD_LIST_CUDA_CLANG clang++ $CUDA_WARNING_FLAGS" "clang/3.9.0 $CLANG_MODULE_LIST $BUILD_LIST_CLANG clang++ $CLANG_WARNING_FLAGS" "gcc/4.7.2 $BASE_MODULE_LIST $GCC_BUILD_LIST g++ $GCC_WARNING_FLAGS" @@ -295,8 +298,8 @@ elif [ "$MACHINE" = "apollo" ]; then "intel/16.0.1 $BASE_MODULE_LIST $INTEL_BUILD_LIST icpc $INTEL_WARNING_FLAGS" "clang/3.5.2 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" "clang/3.6.1 $BASE_MODULE_LIST $CLANG_BUILD_LIST clang++ $CLANG_WARNING_FLAGS" - "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" - "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/config/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.0.28 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" + "cuda/7.5.18 $CUDA_MODULE_LIST $CUDA_BUILD_LIST $KOKKOS_PATH/bin/nvcc_wrapper $CUDA_WARNING_FLAGS" ) fi diff --git a/lib/kokkos/config/testing_scripts/jenkins_test_driver b/lib/kokkos/config/testing_scripts/jenkins_test_driver index 9cba7fa518..f393940304 100755 --- a/lib/kokkos/config/testing_scripts/jenkins_test_driver +++ b/lib/kokkos/config/testing_scripts/jenkins_test_driver @@ -48,7 +48,7 @@ esac #nvcc wrapper and make the wrapper the compiler. if [ $cuda_compiler != "" ]; then export NVCC_WRAPPER_DEFAULT_COMPILER=$compiler - compiler=$kokkos_path/config/nvcc_wrapper + compiler=$kokkos_path/bin/nvcc_wrapper fi if [ $host_compiler_brand == "intel" -a $cuda_compiler != "" ]; then diff --git a/lib/kokkos/config/trilinos-integration/checkin-test b/lib/kokkos/config/trilinos-integration/checkin-test new file mode 100644 index 0000000000..92a1b1c068 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/checkin-test @@ -0,0 +1,4 @@ +module purge +module load sems-env sems-gcc/4.9.3 sems-openmpi/1.10.1 sems-hdf5/1.8.12/parallel sems-netcdf/4.3.2/parallel sems-python/2.7.9 sems-zlib/1.2.8/base sems-cmake/3.5.2 sems-parmetis/4.0.3/64bit_parallel sems-scotch/6.0.3/nopthread_64bit_parallel sems-boost/1.59.0/base + +#Run Trilinos CheckinTest diff --git a/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh b/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh index 2692f76038..b81a3b1566 100755 --- a/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh +++ b/lib/kokkos/config/trilinos-integration/prepare_trilinos_repos.sh @@ -1,5 +1,18 @@ #!/bin/bash -le +TRILINOS_UPDATE_BRANCH=$1 +TRILINOS_PRISTINE_BRANCH=$2 + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + export TRILINOS_UPDATED_PATH=${PWD}/trilinos-update export TRILINOS_PRISTINE_PATH=${PWD}/trilinos-pristine @@ -16,8 +29,8 @@ if [ ! -d "${TRILINOS_PRISTINE_PATH}" ]; then fi cd ${TRILINOS_UPDATED_PATH} -git checkout develop -git reset --hard origin/develop +git checkout $TRILINOS_UPDATE_BRANCH +git reset --hard origin/$TRILINOS_UPDATE_BRANCH git pull cd .. @@ -28,18 +41,14 @@ echo "" echo "" echo "Trilinos State:" git log --pretty=oneline --since=7.days -SHA=`git log --pretty=oneline --since=7.days | head -n 2 | tail -n 1 | awk '{print $1}'` cd .. cd ${TRILINOS_PRISTINE_PATH} git status -git log --pretty=oneline --since=7.days -echo "Checkout develop" -git checkout develop +echo "Checkout $TRILINOS_PRISTINE_BRANCH" +git checkout $TRILINOS_PRISTINE_BRANCH echo "Pull" git pull -echo "Checkout SHA" -git checkout ${SHA} cd .. cd ${TRILINOS_PRISTINE_PATH} diff --git a/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel new file mode 100755 index 0000000000..23968e8c0f --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_pthread_intel @@ -0,0 +1,60 @@ +#!/bin/bash -el +ulimit -c 0 +module load devpack/openmpi/1.10.0/intel/16.1.056/cuda/none + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=ON +export JENKINS_DO_SERIAL=OFF +export JENKINS_DO_COMPLEX=OFF + +export ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" +export ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" +export LAPACK_LIBRARIES=${BLAS_LIBRARIES} + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON +export JENKINS_DO_SHARED=OFF + +export QUEUE=haswell + + +module load python + + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_slurm ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} diff --git a/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel new file mode 100755 index 0000000000..964de3a002 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/shepard_jenkins_run_script_serial_intel @@ -0,0 +1,60 @@ +#!/bin/bash -el +ulimit -c 0 +module load devpack/openmpi/1.10.0/intel/16.1.056/cuda/none + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=ON +export JENKINS_DO_COMPLEX=ON + +export ARCH_CXX_FLAG="-xCORE-AVX2 -mkl" +export ARCH_C_FLAG="-xCORE-AVX2 -mkl" +export BLAS_LIBRARIES="-mkl;${MKLROOT}/lib/intel64/libmkl_intel_lp64.a;${MKLROOT}/lib/intel64/libmkl_intel_thread.a;${MKLROOT}/lib/intel64/libmkl_core.a" +export LAPACK_LIBRARIES=${BLAS_LIBRARIES} + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON +export JENKINS_DO_SHARED=OFF + +export QUEUE=haswell + + +module load python + + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_slurm ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} diff --git a/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda new file mode 100755 index 0000000000..52af024858 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_cuda @@ -0,0 +1,63 @@ +#!/bin/bash -el +ulimit -c 0 + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=ON +export JENKINS_DO_OPENMP=OFF +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=ON +export JENKINS_DO_COMPLEX=OFF + +export JENKINS_ARCH_CXX_FLAG="-mcpu=power8 -arch=sm_37" +export JENKINS_ARCH_C_FLAG="-mcpu=power8" +export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" +export LAPACK_LIBRARIES="${LAPACK_ROOT}/lib/liblapack.a;gfortran;gomp" + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON + +export QUEUE=rhel7F + +module load python + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +export OMPI_CXX=${KOKKOS_PATH}/bin/nvcc_wrapper + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +export CUDA_LAUNCH_BLOCKING=1 +export CUDA_MANAGED_FORCE_DEVICE_ALLOC=1 + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_lsf ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} + diff --git a/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp new file mode 100755 index 0000000000..452165eef2 --- /dev/null +++ b/lib/kokkos/config/trilinos-integration/white_run_jenkins_script_omp @@ -0,0 +1,58 @@ +#!/bin/bash -el +ulimit -c 0 + +KOKKOS_BRANCH=$1 +TRILINOS_UPDATE_BRANCH=$2 +TRILINOS_PRISTINE_BRANCH=$3 + +if [ -z $KOKKOS_BRANCH ] +then + KOKKOS_BRANCH=develop +fi + +if [ -z $TRILINOS_UPDATE_BRANCH ] +then + TRILINOS_UPDATE_BRANCH=develop +fi + +if [ -z $TRILINOS_PRISTINE_BRANCH ] +then + TRILINOS_PRISTINE_BRANCH=develop +fi + +module load devpack/openmpi/1.10.4/gcc/5.4.0/cuda/8.0.44 +export OMP_NUM_THREADS=8 +export JENKINS_DO_CUDA=OFF +export JENKINS_DO_OPENMP=ON +export JENKINS_DO_PTHREAD=OFF +export JENKINS_DO_SERIAL=OFF +export JENKINS_DO_COMPLEX=OFF + +export JENKINS_ARCH_CXX_FLAG="-mcpu=power8" +export JENKINS_ARCH_C_FLAG="-mcpu=power8" +export BLAS_LIBRARIES="${BLAS_ROOT}/lib/libblas.a;gfortran;gomp" +export LAPACK_LIBRARIES="${LAPACK_ROOT}/lib/liblapack.a;gfortran;gomp" + +export JENKINS_DO_TESTS=ON +export JENKINS_DO_EXAMPLES=ON + +export QUEUE=rhel7F + +module load python + +export KOKKOS_PATH=${PWD}/kokkos + +#Already done: +if [ ! -d "${KOKKOS_PATH}" ]; then + git clone https://github.com/kokkos/kokkos ${KOKKOS_PATH} +fi + +cd ${KOKKOS_PATH} +git checkout $KOKKOS_BRANCH +git pull +cd .. + +source ${KOKKOS_PATH}/config/trilinos-integration/prepare_trilinos_repos.sh $TRILINOS_UPDATE_BRANCH $TRILINOS_PRISTINE_BRANCH + +${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/run_repo_comparison_lsf ${TRILINOS_UPDATED_PATH} ${TRILINOS_PRISTINE_PATH} ${TRILINOS_UPDATED_PATH}/sampleScripts/Sandia-SEMS/configure-testbeds-jenkins-all TestCompare ${QUEUE} + diff --git a/lib/kokkos/containers/performance_tests/Makefile b/lib/kokkos/containers/performance_tests/Makefile index fa3bc77701..edaaf1ee51 100644 --- a/lib/kokkos/containers/performance_tests/Makefile +++ b/lib/kokkos/containers/performance_tests/Makefile @@ -8,7 +8,7 @@ default: build_all echo "End Build" ifneq (,$(findstring Cuda,$(KOKKOS_DEVICES))) - CXX = $(KOKKOS_PATH)/config/nvcc_wrapper + CXX = $(KOKKOS_PATH)/bin/nvcc_wrapper else CXX = g++ endif @@ -21,8 +21,8 @@ include $(KOKKOS_PATH)/Makefile.kokkos KOKKOS_CXXFLAGS += -I$(GTEST_PATH) -I${KOKKOS_PATH}/containers/performance_tests -TEST_TARGETS = -TARGETS = +TEST_TARGETS = +TARGETS = ifeq ($(KOKKOS_INTERNAL_USE_CUDA), 1) OBJ_CUDA = TestCuda.o TestMain.o gtest-all.o @@ -65,7 +65,7 @@ build_all: $(TARGETS) test: $(TEST_TARGETS) -clean: kokkos-clean +clean: kokkos-clean rm -f *.o $(TARGETS) # Compilation rules @@ -73,6 +73,5 @@ clean: kokkos-clean %.o:%.cpp $(KOKKOS_CPP_DEPENDS) $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $< -gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc +gtest-all.o:$(GTEST_PATH)/gtest/gtest-all.cc $(CXX) $(KOKKOS_CPPFLAGS) $(KOKKOS_CXXFLAGS) $(CXXFLAGS) $(EXTRA_INC) -c $(GTEST_PATH)/gtest/gtest-all.cc - diff --git a/lib/kokkos/containers/performance_tests/TestCuda.cpp b/lib/kokkos/containers/performance_tests/TestCuda.cpp index d5cad06a47..208387425f 100644 --- a/lib/kokkos/containers/performance_tests/TestCuda.cpp +++ b/lib/kokkos/containers/performance_tests/TestCuda.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,12 +36,15 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ -#include +#include +#if defined( KOKKOS_ENABLE_CUDA ) + +#include #include #include #include @@ -52,8 +55,6 @@ #include -#if defined( KOKKOS_ENABLE_CUDA ) - #include #include @@ -79,7 +80,7 @@ protected: } }; -TEST_F( cuda, dynrankview_perf ) +TEST_F( cuda, dynrankview_perf ) { std::cout << "Cuda" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -105,5 +106,6 @@ TEST_F( cuda, unordered_map_performance_far) } } - +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTCUDA_PREVENT_EMPTY_LINK_ERROR() {} #endif /* #if defined( KOKKOS_ENABLE_CUDA ) */ diff --git a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp index d96a3f7432..4c0ccb6b88 100644 --- a/lib/kokkos/containers/performance_tests/TestDynRankView.hpp +++ b/lib/kokkos/containers/performance_tests/TestDynRankView.hpp @@ -1,13 +1,13 @@ //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER @@ -263,3 +263,4 @@ void test_dynrankview_op_perf( const int par_size ) } //end Performance #endif + diff --git a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp index da74d32ac1..b674ec4a74 100644 --- a/lib/kokkos/containers/performance_tests/TestOpenMP.cpp +++ b/lib/kokkos/containers/performance_tests/TestOpenMP.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#if defined( KOKKOS_ENABLE_OPENMP ) + #include #include @@ -93,7 +96,7 @@ protected: } }; -TEST_F( openmp, dynrankview_perf ) +TEST_F( openmp, dynrankview_perf ) { std::cout << "OpenMP" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -137,4 +140,7 @@ TEST_F( openmp, unordered_map_performance_far) } } // namespace test +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTOPENMP_PREVENT_EMPTY_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/containers/performance_tests/TestThreads.cpp b/lib/kokkos/containers/performance_tests/TestThreads.cpp index 4179b7de4c..a8910a3c72 100644 --- a/lib/kokkos/containers/performance_tests/TestThreads.cpp +++ b/lib/kokkos/containers/performance_tests/TestThreads.cpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,11 +36,14 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ +#include +#if defined( KOKKOS_ENABLE_THREADS ) + #include #include @@ -87,7 +90,7 @@ protected: } }; -TEST_F( threads, dynrankview_perf ) +TEST_F( threads, dynrankview_perf ) { std::cout << "Threads" << std::endl; std::cout << " DynRankView vs View: Initialization Only " << std::endl; @@ -132,4 +135,7 @@ TEST_F( threads, unordered_map_performance_far) } // namespace Performance +#else +void KOKKOS_CONTAINERS_PERFORMANCE_TESTS_TESTTHREADS_PREVENT_EMPTY_LINK_ERROR() {} +#endif diff --git a/lib/kokkos/containers/src/Kokkos_Bitset.hpp b/lib/kokkos/containers/src/Kokkos_Bitset.hpp index 74da5f61b5..7714506e92 100644 --- a/lib/kokkos/containers/src/Kokkos_Bitset.hpp +++ b/lib/kokkos/containers/src/Kokkos_Bitset.hpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ @@ -435,3 +435,4 @@ void deep_copy( ConstBitset & dst, ConstBitset const& src) } // namespace Kokkos #endif //KOKKOS_BITSET_HPP + diff --git a/lib/kokkos/containers/src/Kokkos_DualView.hpp b/lib/kokkos/containers/src/Kokkos_DualView.hpp index 3a0196ee4c..937eab0d88 100644 --- a/lib/kokkos/containers/src/Kokkos_DualView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DualView.hpp @@ -442,6 +442,17 @@ public: modified_host () = (modified_device () > modified_host () ? modified_device () : modified_host ()) + 1; } + +#ifdef KOKKOS_ENABLE_DEBUG_DUALVIEW_MODIFY_CHECK + if (modified_host() && modified_device()) { + std::string msg = "Kokkos::DualView::modify ERROR: "; + msg += "Concurrent modification of host and device views "; + msg += "in DualView \""; + msg += d_view.label(); + msg += "\"\n"; + Kokkos::abort(msg.c_str()); + } +#endif } //@} @@ -624,3 +635,4 @@ deep_copy (const ExecutionSpace& exec , } // namespace Kokkos #endif + diff --git a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp index acb37f7f75..8e464506f9 100644 --- a/lib/kokkos/containers/src/Kokkos_DynRankView.hpp +++ b/lib/kokkos/containers/src/Kokkos_DynRankView.hpp @@ -1,13 +1,13 @@ /* //@HEADER // ************************************************************************ -// +// // Kokkos v. 2.0 // Copyright (2014) Sandia Corporation -// +// // Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, // the U.S. Government retains certain rights in this software. -// +// // Redistribution and use in source and binary forms, with or without // modification, are permitted provided that the following conditions are // met: @@ -36,7 +36,7 @@ // SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. // // Questions? Contact H. Carter Edwards (hcedwar@sandia.gov) -// +// // ************************************************************************ //@HEADER */ @@ -140,21 +140,21 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value) , Layout>::type createLayout( const Layout& layout ) { return Layout( layout.dimension[0] != unspecified ? layout.dimension[0] : 1 - , layout.stride[0] + , layout.stride[0] , layout.dimension[1] != unspecified ? layout.dimension[1] : 1 - , layout.stride[1] + , layout.stride[1] , layout.dimension[2] != unspecified ? layout.dimension[2] : 1 - , layout.stride[2] + , layout.stride[2] , layout.dimension[3] != unspecified ? layout.dimension[3] : 1 - , layout.stride[3] + , layout.stride[3] , layout.dimension[4] != unspecified ? layout.dimension[4] : 1 - , layout.stride[4] + , layout.stride[4] , layout.dimension[5] != unspecified ? layout.dimension[5] : 1 - , layout.stride[5] + , layout.stride[5] , layout.dimension[6] != unspecified ? layout.dimension[6] : 1 - , layout.stride[6] + , layout.stride[6] , layout.dimension[7] != unspecified ? layout.dimension[7] : 1 - , layout.stride[7] + , layout.stride[7] ); } @@ -188,7 +188,7 @@ struct DynRankDimTraits { KOKKOS_INLINE_FUNCTION static typename std::enable_if< (std::is_same::value || std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { - return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) + return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) , dynrank > 1 ? layout.dimension[1] : ~size_t(0) , dynrank > 2 ? layout.dimension[2] : ~size_t(0) , dynrank > 3 ? layout.dimension[3] : ~size_t(0) @@ -205,27 +205,27 @@ struct DynRankDimTraits { static typename std::enable_if< (std::is_same::value) && std::is_integral::value , Layout >::type reconstructLayout( const Layout& layout , iType dynrank ) { return Layout( dynrank > 0 ? layout.dimension[0] : ~size_t(0) - , dynrank > 0 ? layout.stride[0] : (0) + , dynrank > 0 ? layout.stride[0] : (0) , dynrank > 1 ? layout.dimension[1] : ~size_t(0) - , dynrank > 1 ? layout.stride[1] : (0) + , dynrank > 1 ? layout.stride[1] : (0) , dynrank > 2 ? layout.dimension[2] : ~size_t(0) - , dynrank > 2 ? layout.stride[2] : (0) + , dynrank > 2 ? layout.stride[2] : (0) , dynrank > 3 ? layout.dimension[3] : ~size_t(0) - , dynrank > 3 ? layout.stride[3] : (0) + , dynrank > 3 ? layout.stride[3] : (0) , dynrank > 4 ? layout.dimension[4] : ~size_t(0) - , dynrank > 4 ? layout.stride[4] : (0) + , dynrank > 4 ? layout.stride[4] : (0) , dynrank > 5 ? layout.dimension[5] : ~size_t(0) - , dynrank > 5 ? layout.stride[5] : (0) + , dynrank > 5 ? layout.stride[5] : (0) , dynrank > 6 ? layout.dimension[6] : ~size_t(0) - , dynrank > 6 ? layout.stride[6] : (0) + , dynrank > 6 ? layout.stride[6] : (0) , dynrank > 7 ? layout.dimension[7] : ~size_t(0) - , dynrank > 7 ? layout.stride[7] : (0) + , dynrank > 7 ? layout.stride[7] : (0) ); } /** \brief Debug bounds-checking routines */ -// Enhanced debug checking - most infrastructure matches that of functions in +// Enhanced debug checking - most infrastructure matches that of functions in // Kokkos_ViewMapping; additional checks for extra arguments beyond rank are 0 template< unsigned , typename iType0 , class MapType > KOKKOS_INLINE_FUNCTION @@ -235,20 +235,20 @@ bool dyn_rank_view_verify_operator_bounds( const iType0 & , const MapType & ) template< unsigned R , typename iType0 , class MapType , typename iType1 , class ... Args > KOKKOS_INLINE_FUNCTION bool dyn_rank_view_verify_operator_bounds - ( const iType0 & rank + ( const iType0 & rank , const MapType & map , const iType1 & i , Args ... args ) { - if ( static_cast(R) < rank ) { + if ( static_cast(R) < rank ) { return ( size_t(i) < map.extent(R) ) && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); } else if ( i != 0 ) { printf("DynRankView Debug Bounds Checking Error: at rank %u\n Extra arguments beyond the rank must be zero \n",R); return ( false ) - && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); + && dyn_rank_view_verify_operator_bounds( rank , map , args ... ); } else { return ( true ) @@ -281,20 +281,24 @@ void dyn_rank_view_error_operator_bounds } // op_rank = rank of the operator version that was called -template< typename iType0 , typename iType1 , class MapType , class ... Args > +template< typename MemorySpace + , typename iType0 , typename iType1 , class MapType , class ... Args > KOKKOS_INLINE_FUNCTION void dyn_rank_view_verify_operator_bounds - ( const iType0 & op_rank , const iType1 & rank , const char* label , const MapType & map , Args ... args ) + ( const iType0 & op_rank , const iType1 & rank + , const Kokkos::Impl::SharedAllocationTracker & tracker + , const MapType & map , Args ... args ) { if ( static_cast(rank) > op_rank ) { - Kokkos::abort( "DynRankView Bounds Checking Error: Need at least rank arguments to the operator()" ); + Kokkos::abort( "DynRankView Bounds Checking Error: Need at least rank arguments to the operator()" ); } if ( ! dyn_rank_view_verify_operator_bounds<0>( rank , map , args ... ) ) { #if defined( KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST ) enum { LEN = 1024 }; char buffer[ LEN ]; - int n = snprintf(buffer,LEN,"DynRankView bounds error of view %s (", label); + const std::string label = tracker.template get_label(); + int n = snprintf(buffer,LEN,"DynRankView bounds error of view %s (", label.c_str()); dyn_rank_view_error_operator_bounds<0>( buffer + n , LEN - n , map , args ... ); Kokkos::Impl::throw_runtime_exception(std::string(buffer)); #else @@ -347,7 +351,7 @@ private: std::is_same< typename DstTraits::array_layout , typename SrcTraits::array_layout >::value || std::is_same< typename DstTraits::array_layout - , Kokkos::LayoutStride >::value + , Kokkos::LayoutStride >::value }; public: @@ -381,9 +385,9 @@ public: } //end Impl /* \class DynRankView - * \brief Container that creates a Kokkos view with rank determined at runtime. + * \brief Container that creates a Kokkos view with rank determined at runtime. * Essentially this is a rank 7 view that wraps the access operators - * to yield the functionality of a view + * to yield the functionality of a view * * Changes from View * 1. The rank of the DynRankView is returned by the method rank() @@ -410,14 +414,14 @@ class DynRankView : public ViewTraits< DataType , Properties ... > { static_assert( !std::is_array::value && !std::is_pointer::value , "Cannot template DynRankView with array or pointer datatype - must be pod" ); -private: +private: template < class , class ... > friend class DynRankView ; template < class , class ... > friend class Impl::ViewMapping ; -public: +public: typedef ViewTraits< DataType , Properties ... > drvtraits ; - typedef View< DataType******* , Properties...> view_type ; + typedef View< DataType******* , Properties...> view_type ; typedef ViewTraits< DataType******* , Properties ... > traits ; @@ -430,7 +434,7 @@ private: map_type m_map ; unsigned m_rank; -public: +public: KOKKOS_INLINE_FUNCTION view_type & DownCast() const { return ( view_type & ) (*this); } KOKKOS_INLINE_FUNCTION @@ -588,7 +592,7 @@ private: // rank of the calling operator - included as first argument in ARG #define KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( ARG ) \ DynRankView::template verify_space< Kokkos::Impl::ActiveExecutionMemorySpace >::check(); \ - Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds ARG ; + Kokkos::Experimental::Impl::dyn_rank_view_verify_operator_bounds< typename traits::memory_space > ARG ; #else @@ -607,14 +611,10 @@ public: // Rank 0 KOKKOS_INLINE_FUNCTION reference_type operator()() const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() , NULL , m_map) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank() , m_track.template get_label().c_str(),m_map) ) - #endif + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (0 , this->rank(), m_track, m_map) ) return implementation_map().reference(); - //return m_map.reference(0,0,0,0,0,0,0); + //return m_map.reference(0,0,0,0,0,0,0); } // Rank 1 @@ -624,6 +624,8 @@ public: typename std::enable_if< std::is_same::value && std::is_integral::value, reference_type>::type operator[](const iType & i0) const { + //Phalanx is violating this, since they use the operator to access ALL elements in the allocation + //KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map) ) return data()[i0]; } @@ -647,14 +649,10 @@ public: template< typename iType > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType & i0 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label().c_str(),m_map,i0) ) - #endif - return m_map.reference(i0); + operator()(const iType & i0 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) + return m_map.reference(i0); } template< typename iType > @@ -662,11 +660,7 @@ public: typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type operator()(const iType & i0 ) const { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , NULL , m_map , i0) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank() , m_track.template get_label().c_str(),m_map,i0) ) - #endif + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (1 , this->rank(), m_track, m_map, i0) ) return m_map.reference(i0,0,0,0,0,0,0); } @@ -674,155 +668,111 @@ public: template< typename iType0 , typename iType1 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1) ) - #endif - return m_map.reference(i0,i1); + operator()(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1); } template< typename iType0 , typename iType1 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , NULL , m_map , i0 , i1) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1) ) - #endif - return m_map.reference(i0,i1,0,0,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (2 , this->rank(), m_track, m_map, i0, i1) ) + return m_map.reference(i0,i1,0,0,0,0,0); } // Rank 3 template< typename iType0 , typename iType1 , typename iType2 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2) ) - #endif - return m_map.reference(i0,i1,i2); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2); } template< typename iType0 , typename iType1 , typename iType2 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , NULL , m_map , i0 , i1 , i2) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2) ) - #endif - return m_map.reference(i0,i1,i2,0,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (3 , this->rank(), m_track, m_map, i0, i1, i2) ) + return m_map.reference(i0,i1,i2,0,0,0,0); } // Rank 4 template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3) ) - #endif - return m_map.reference(i0,i1,i2,i3); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3) ) - #endif - return m_map.reference(i0,i1,i2,i3,0,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (4 , this->rank(), m_track, m_map, i0, i1, i2, i3) ) + return m_map.reference(i0,i1,i2,i3,0,0,0); } // Rank 5 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,0,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (5 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4) ) + return m_map.reference(i0,i1,i2,i3,i4,0,0); } // Rank 6 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_same::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5); } template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 > KOKKOS_INLINE_FUNCTION typename std::enable_if< !(std::is_same::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5,0); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (6 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,0); } // Rank 7 template< typename iType0 , typename iType1 , typename iType2 , typename iType3, typename iType4 , typename iType5 , typename iType6 > KOKKOS_INLINE_FUNCTION typename std::enable_if< (std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value && std::is_integral::value), reference_type>::type - operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const - { - #ifndef KOKKOS_ACTIVE_EXECUTION_MEMORY_SPACE_HOST - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , NULL , m_map , i0 , i1 , i2 , i3, i4 , i5 , i6) ) - #else - KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank() , m_track.template get_label().c_str(),m_map,i0,i1,i2,i3,i4,i5,i6) ) - #endif - return m_map.reference(i0,i1,i2,i3,i4,i5,i6); + operator()(const iType0 & i0 , const iType1 & i1 , const iType2 & i2 , const iType3 & i3 , const iType4 & i4 , const iType5 & i5 , const iType6 & i6 ) const + { + KOKKOS_IMPL_VIEW_OPERATOR_VERIFY( (7 , this->rank(), m_track, m_map, i0, i1, i2, i3, i4, i5, i6) ) + return m_map.reference(i0,i1,i2,i3,i4,i5,i6); } #undef KOKKOS_IMPL_VIEW_OPERATOR_VERIFY //---------------------------------------- - // Standard constructor, destructor, and assignment operators... + // Standard constructor, destructor, and assignment operators... KOKKOS_INLINE_FUNCTION ~DynRankView() {} @@ -840,7 +790,7 @@ public: DynRankView & operator = ( const DynRankView & rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } KOKKOS_INLINE_FUNCTION - DynRankView & operator = ( DynRankView && rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } + DynRankView & operator = ( DynRankView && rhs ) { m_track = rhs.m_track; m_map = rhs.m_map; m_rank = rhs.m_rank; return *this; } //---------------------------------------- // Compatible view copy constructor and assignment @@ -1068,7 +1018,7 @@ public: DynRankView( const Label & arg_label , typename std::enable_if< Kokkos::Experimental::Impl::is_view_label