Merge pull request #1323 from akohlmey/next-patch-release

Patch release 8 February 2019

.github/CODE_OF_CONDUCT.md

@@ -0,0 +1,67 @@
+# Code of Conduct for the LAMMPS Project on GitHub
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as LAMMPS
+developers, contributors, and maintainers pledge to making participation in
+our project a harassment-free experience for everyone.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of explicit language or imagery
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, issues, and other contributions that are not
+aligned to this Code of Conduct, or to ban temporarily or permanently any
+developer, maintainer, or contributor for this or other behaviors that they
+deem inappropriate, threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies to all public exchanges in the LAMMPS project
+on GitHub and in submitted code.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at developer@lammps.org. All
+complaints will be reviewed and investigated and will result in a response
+that is deemed necessary and appropriate to the circumstances. The project
+team is obligated to maintain confidentiality with regard to the reporter
+of an incident.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see
+https://www.contributor-covenant.org/faq
+

.github/CONTRIBUTING.md

@@ -2,10 +2,10 @@
 
 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.
+The following is a set of guidelines as well as explanations of policies and work flows 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 Section on submitting new features for inclusion in LAMMPS of the Manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
 * [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 ## Table of Contents
@@ -18,7 +18,7 @@ Thus please also have a look at:
 * [Suggesting Enhancements](#suggesting-enhancements)
 * [Contributing Code](#contributing-code)
 
-[GitHub Workflows](#github-workflows)
+[GitHub Work flows](#github-workflows)
 * [Issues](#issues)
 * [Pull Requests](#pull-requests)
 
@@ -26,17 +26,17 @@ __
 
 ## 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.
+> **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](https://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](https://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.
+to one of the [LAMMPS core developers](https://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.
+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](https://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.
 
@@ -44,7 +44,7 @@ If you post a message and you are a subscriber, your message will appear immedia
 
 ### 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.
+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](https://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).
@@ -62,13 +62,13 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 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/Howto_github.html)
+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](https://lammps.sandia.gov/doc/Howto_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 <stdio.h>, 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.
+* 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, style class header files should not import any system headers outside of <cstdio>, 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. There MUST NOT be any "using namespace XXX;" statements in headers. In the implementation file (<name>.cpp) system includes should be placed in angular brackets (<>) and for c-library functions the C++ style header files should be included (<cstdio> instead of <stdio.h>, or <cstring> instead of <string.h>). 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 `<name>.cpp` and `<name>.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.
@@ -102,10 +102,10 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 
 ### Pull Requests
 
-For submitting pull requests, there is a [detailed tutorial](http://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
+For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
 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.
+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. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
+You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also 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 receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request 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 nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.

.github/ISSUE_TEMPLATE.md

@@ -1,31 +0,0 @@
-## 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_

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,32 @@
+---
+name: Bug report
+about: Create a bug report to help us eliminate issues and improve LAMMPS
+title: "[BUG] _Replace With Suitable Title_"
+labels: bug
+assignees: ''
+
+---
+
+**Summary**
+
+_Please provide a clear and concise description of what the bug is._
+
+**LAMMPS Version and Platform**
+
+_Please specify precisely which LAMMPS version this issue was detected with (the first line of the output) and what platform (operating system and its version, hardware) you are running on. If possible, test with the most recent LAMMPS patch version_
+
+**Expected Behavior**
+
+_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**
+
+_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 area of research._
+
+**Steps to Reproduce**
+
+_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 an input set that is as minimal and small as possible and reproduces the bug as quickly as possible. **NOTE:** the less effort and time it takes to reproduce your reported bug, the more likely it becomes, that somebody will look into it and fix the problem._
+
+**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_

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,20 @@
+---
+name: Feature request
+about: Make a suggestion for a new feature or a change to LAMMPS
+title: "[Feature Request] _Replace with Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+_Please provide a brief and concise description of the suggested feature or change_
+
+**Detailed Description**
+
+_Please explain how you would like to see LAMMPS enhanced, what feature(s) you are looking for, what specific problems this will solve. If possible, provide references to relevant background information like publications or web pages, and whether you are planning to implement the enhancement yourself or would like to participate in the implementation. If applicable add a reference to an existing bug report or issue that this will address._
+
+**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_

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,28 +1,46 @@
-## Purpose
+**Summary**
 
-_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_
+_Briefly describe the new feature(s), enhancement(s), or bugfix(es) included in this pull request._
 
-## Author(s)
+**Related Issues**
 
-_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+__If this addresses an open GitHub Issue, mention the issue number here. Use the phrases `fixes #221` or `closes #135`, when you want those issues to be automatically closed when the pull request is merged_
 
-## Backward Compatibility
+**Author(s)**
+
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request. If this pull request adds new files to the distribution, please also provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+
+**Licensing**
+
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under the GNU General Public License version 2.
+
+_Please complete the following statement by adding "yes" or "no":_
+My contribution may be re-licensed as LGPL (for use of LAMMPS as a library linked to proprietary software):
+
+**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
+**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
+**Post Submission Checklist**
+
+_Please check the fields below as they are completed **after** the pull request has been submitted_
 
-_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
+- [ ] Licensing information is complete
+- [ ] Corresponding author information is complete
 - [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] Suitable new documentation files and/or updates to the existing docs are included
+- [ ] The added/updated documentation is integrated and tested with the documentation build system
+- [ ] The feature has been verified to work with the conventional build system
+- [ ] The feature has been verified to work with the CMake based build system
+- [ ] A package specific README file has been included or updated
+- [ ] One or more example input decks are included
 
-## Further Information, Files, and Links
+**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)_
 

.github/PULL_REQUEST_TEMPLATE/bug_fix.md

@@ -0,0 +1,42 @@
+---
+name: Bug fix
+about: Submit a pull request that fixes one or more bugs
+title: "[BUGFIX] _Replace With Suitable Title_"
+labels: bugfix
+assignees: ''
+
+---
+
+**Summary**
+
+_Briefly describe the bug or bugs, that are eliminated by this pull request._
+
+**Related Issue(s)**
+
+_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`._
+
+**Author(s)**
+
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+
+**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_
+
+**Detailed Description**
+
+_Provide any relevant details about how the fixed bug can be reproduced, 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 *after* the pull request is submitted_
+- [ ] The code in this pull request is complete
+- [ ] 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. to download input decks for testing)_

.github/PULL_REQUEST_TEMPLATE/maintenance_refactoring.md

@@ -0,0 +1,35 @@
+---
+name: Maintenance or Refactoring
+about: Submit a pull request that does code refactoring or other maintenance changes
+title: "[MAINTENANCE] _Replace With Suitable Title_"
+labels: maintenance
+assignees: ''
+
+---
+
+**Summary**
+
+_Briefly describe the included changes._
+
+**Related Issue(s)**
+
+_If this request addresses or is related to an existing (open) GitHub issue, e.g. a bug report, mention the issue number number here following a pound sign (aka hashmark), e.g.`#222`.
+
+**Author(s)**
+
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the files that are modified.
+
+**Detailed Description**
+
+_Provide any relevant details about the included changes._
+
+## Post Submission Checklist
+
+_Please check the fields below as they are completed *after* the pull request is submitted_
+- [ ] The pull request is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+

.github/PULL_REQUEST_TEMPLATE/new_feature.md

@@ -0,0 +1,56 @@
+---
+name: New Feature
+about: Submit a pull request that adds new Features (complete files) to LAMMPS
+title: "[New Feature] _Replace With Suitable Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+_Briefly describe the new feature(s) included in this pull request._
+
+**Related Issues**
+
+_If this addresses an existing (open) GitHub issue, e.g. a feature request, mention the issue number here following a pound sign (aka hashmark), e.g. `#331`._
+
+**Author(s)**
+
+_Please state name and affiliation of the author or authors that should be credited with the features added in this pull request. Please provide a suitable "long-lived" e-mail address (e.g. from gmail, yahoo, outlook, etc.) for the *corresponding* author, i.e. the person the LAMMPS developers can contact directly with questions and requests related to maintenance and support of this code. now and in the future_
+
+**Licensing**
+
+_Please add *yes* or *no* to the following two statements (please contact @lammps/core if you have questions about this)_
+
+My contribution may be licensed as GPL v2 (default LAMMPS license):
+My contribution may be licensed as LGPL (for use as a library with proprietary software):
+
+**Backward Compatibility**
+
+_Please state if any of the changes in this pull request will affect backward compatibility for inputs, and - if yes - explain what has been changed and why_
+
+**Implementation Notes**
+
+_Provide any relevant details about how the new features are implemented, how correctness was verified, what platforms (OS, compiler, MPI, hardware, number of processors, accelerator(s)) it was tested on_
+
+## Post Submission Checklist
+
+_Please check the fields below as they are completed *after* the pull request has been submitted_
+
+- [ ] The feature or features in this pull request is complete
+- [ ] Licensing information is complete
+- [ ] Corresponding author information is complete
+- [ ] The source code follows the LAMMPS formatting guidelines
+- [ ] Suitable new documentation files and/or updates to the existing docs are included
+- [ ] The added/updated documentation is integrated and tested with the documentation build system
+- [ ] The feature has been verified to work with the conventional build system
+- [ ] The feature has been verified to work with the CMake based build system
+- [ ] A package specific README file has been included or updated
+- [ ] One or more example input decks are included
+
+## 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)_
+
+

.github/PULL_REQUEST_TEMPLATE/update_enhancement.md

@@ -0,0 +1,42 @@
+---
+name: Update or Enhancement
+about: Submit a pull request that provides update or enhancements for a package or feature in LAMMPS
+title: "[UPDATE] _Replace With Suitable Title_"
+labels: enhancement
+assignees: ''
+
+---
+
+**Summary**
+
+_Briefly describe what kind of updates or enhancements for a package or feature are included. If you are not the original author of the package or feature, please mention, whether your contribution was created independently or in collaboration/cooperation with the original author._
+
+**Author(s)**
+
+_Please state name and affiliation of the author or authors that should be credited with the changes in this pull request_
+
+**Licensing**
+
+By submitting this pull request I implicitly accept, that my submission is subject to the same licensing terms as the original package or feature(s) that are updated or amended by 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 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)_
+
+

cmake/CMakeLists.txt

@@ -178,7 +178,7 @@ set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
   USER-MEAMC USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF
   USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-REAXC USER-SCAFACOS
   USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-VTK
-  USER-QUIP USER-QMMM)
+  USER-QUIP USER-QMMM USER-YAFF)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -559,10 +559,15 @@ if(PKG_USER-PLUMED)
     message(STATUS "PLUMED download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(plumed_build
-      URL https://github.com/plumed/plumed2/releases/download/v2.4.3/plumed-src-2.4.3.tgz
-      URL_MD5 b1be7c48971627febc11c61b70767fc5
+      URL https://github.com/plumed/plumed2/releases/download/v2.4.4/plumed-src-2.4.4.tgz
+      URL_MD5 71ed465bdc7c2059e282dbda8d564e71
       BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> ${CONFIGURE_REQUEST_PIC})
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                                --enable-modules=all
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+    )
     ExternalProject_get_property(plumed_build INSTALL_DIR)
     set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
     list(APPEND LAMMPS_DEPS plumed_build)
@@ -614,8 +619,8 @@ if(PKG_USER-SMD)
     message(STATUS "Eigen3 download requested - we will build our own")
     include(ExternalProject)
     ExternalProject_Add(Eigen3_build
-      URL http://bitbucket.org/eigen/eigen/get/3.3.4.tar.gz
-      URL_MD5 1a47e78efe365a97de0c022d127607c3
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
       CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     )
     ExternalProject_get_property(Eigen3_build SOURCE_DIR)
@@ -756,7 +761,7 @@ endif()
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
 include(CheckIncludeFileCXX)
-foreach(HEADER math.h)
+foreach(HEADER cmath)
   check_include_file_cxx(${HEADER} FOUND_${HEADER})
   if(NOT FOUND_${HEADER})
     message(FATAL_ERROR "Could not find needed header - ${HEADER}")

doc/.gitignore

@@ -1,4 +1,5 @@
 /html
+/latex
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi

doc/github-development-workflow.md

@@ -50,8 +50,8 @@ This is indicated by who the pull request is assigned to. LAMMPS core
 developers can self-assign or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine what this might be needed or not, and may either implement the
-required changes or ask the submitter of the pull request to implement
+determine whether this might be needed or not, and may either implement
+the required changes or ask the submitter of the pull request to implement
 them.  Even though, all LAMMPS developers may have write access to pull
 requests (if enabled by the submitter, which is the default), only the
 submitter or the assignee of a pull request may do so.  During this
@@ -76,12 +76,15 @@ People can be assigned to review a pull request in two ways:
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least one review from a LAMMPS developer with write access is required
-before merging in addition to the automated compilation tests.  The
-feature, that reviews from code owners are "hard" reviews (i.e. they
-must all be approved before merging is allowed), is currently disabled
-and it is in the discretion of the merge maintainer to assess when
-a sufficient degree of approval has been reached.  Reviews may be
+least two approvals from LAMMPS developers with write access are required
+before merging in addition to the automated compilation tests.
+Merging counts as implicit approval, so does submission of a pull request
+(by a LAMMPS developer). So the person doing the merge may not also submit
+an approving review. The feature, that reviews from code owners are "hard"
+reviews (i.e. they must all be approved before merging is allowed), is
+currently disabled and it is in the discretion of the merge maintainer to
+assess when a sufficient degree of approval, especially from external
+contributors, has been reached in these cases.  Reviews may be
 (automatically) dismissed, when the reviewed code has been changed,
 and then approval is required a second time.
 
@@ -120,7 +123,7 @@ Here are some items to check:
     * float.h -> cfloat
     * limits.h -> climits
     * math.h -> cmath
-    * omplex.h -> complex
+    * complex.h -> complex
     * setjmp.h -> csetjmp
     * signal.h -> csignal
     * stddef.h -> cstddef

doc/src/Build_extras.txt

@@ -95,6 +95,7 @@ which GPU hardware to build for.
 
 GPU_ARCH settings for different GPU hardware is as follows:
 
+sm_12 or sm_13 for GT200 (supported by CUDA 3.2 until CUDA 6.5)
 sm_20 or sm_21 for Fermi (supported by CUDA 3.2 until CUDA 7.5)
 sm_30 or sm_35 or sm_37 for Kepler (supported since CUDA 5)
 sm_50 or sm_52 for Maxwell (supported since CUDA 6)
@@ -135,7 +136,7 @@ specified by the "-m" switch.  For your convenience, machine makefiles
 for "mpi" and "serial" are provided, which have the same settings as
 the corresponding machine makefiles in the main LAMMPS source
 folder. In addition you can alter 4 important settings in the
-Makefile.machine you start from via the corresponding -h, -a, -p, -e
+Makefile.machine you start from via the corresponding -c, -a, -p, -e
 switches (as in the examples above), and also save a copy of the new
 Makefile if desired:
 

doc/src/Build_link.txt

@@ -78,7 +78,7 @@ description of the Python interface to LAMMPS, which wraps the C-style
 interface.
 
 See the sample codes in examples/COUPLE/simple for examples of C++ and
-C and Fortran codes that invoke LAMMPS thru its library interface.
+C and Fortran codes that invoke LAMMPS through its library interface.
 Other examples in the COUPLE directory use coupling ideas discussed on
 the "Howto couple"_Howto_couple.html doc page.
 

doc/src/Commands_bond.txt

@@ -37,6 +37,7 @@ OPT.
 "harmonic (iko)"_bond_harmonic.html,
 "harmonic/shift (o)"_bond_harmonic_shift.html,
 "harmonic/shift/cut (o)"_bond_harmonic_shift_cut.html,
+"mm3"_bond_mm3.html,
 "morse (o)"_bond_morse.html,
 "nonlinear (o)"_bond_nonlinear.html,
 "oxdna/fene"_bond_oxdna.html,
@@ -60,17 +61,19 @@ OPT.
 "charmm (iko)"_angle_charmm.html,
 "class2 (ko)"_angle_class2.html,
 "class2/p6"_angle_class2.html,
-"cosine (o)"_angle_cosine.html,
+"cosine (ko)"_angle_cosine.html,
 "cosine/buck6d"_angle_cosine_buck6d.html,
 "cosine/delta (o)"_angle_cosine_delta.html,
 "cosine/periodic (o)"_angle_cosine_periodic.html,
 "cosine/shift (o)"_angle_cosine_shift.html,
 "cosine/shift/exp (o)"_angle_cosine_shift_exp.html,
 "cosine/squared (o)"_angle_cosine_squared.html,
+"cross"_angle_cross.html,
 "dipole (o)"_angle_dipole.html,
 "fourier (o)"_angle_fourier.html,
 "fourier/simple (o)"_angle_fourier_simple.html,
 "harmonic (iko)"_angle_harmonic.html,
+"mm3"_angle_mm3.html,
 "quartic (o)"_angle_quartic.html,
 "sdk (o)"_angle_sdk.html,
 "table (o)"_angle_table.html :tb(c=4,ea=c)
@@ -120,8 +123,10 @@ OPT.
 "cossq (o)"_improper_cossq.html,
 "cvff (io)"_improper_cvff.html,
 "distance"_improper_distance.html,
+"distharm"_improper_distharm.html,
 "fourier (o)"_improper_fourier.html,
 "harmonic (iko)"_improper_harmonic.html,
 "inversion/harmonic"_improper_inversion_harmonic.html,
 "ring (o)"_improper_ring.html,
+"sqdistharm"_improper_sqdistharm.html,
 "umbrella (o)"_improper_umbrella.html :tb(c=4,ea=c)

doc/src/Commands_pair.txt

@@ -63,13 +63,13 @@ OPT.
 "comb (o)"_pair_comb.html,
 "comb3"_pair_comb.html,
 "coul/cut (gko)"_pair_coul.html,
-"coul/cut/soft (o)"_pair_lj_soft.html,
+"coul/cut/soft (o)"_pair_fep_soft.html,
 "coul/debye (gko)"_pair_coul.html,
 "coul/diel (o)"_pair_coul_diel.html,
 "coul/dsf (gko)"_pair_coul.html,
 "coul/long (gko)"_pair_coul.html,
 "coul/long/cs (g)"_pair_cs.html,
-"coul/long/soft (o)"_pair_lj_soft.html,
+"coul/long/soft (o)"_pair_fep_soft.html,
 "coul/msm (o)"_pair_coul.html,
 "coul/shield"_pair_coul_shield.html,
 "coul/streitz"_pair_coul.html,
@@ -114,32 +114,35 @@ OPT.
 "lj/charmm/coul/charmm (iko)"_pair_charmm.html,
 "lj/charmm/coul/charmm/implicit (ko)"_pair_charmm.html,
 "lj/charmm/coul/long (gikot)"_pair_charmm.html,
-"lj/charmm/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/charmm/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/charmm/coul/msm (o)"_pair_charmm.html,
 "lj/charmmfsw/coul/charmmfsh"_pair_charmm.html,
 "lj/charmmfsw/coul/long"_pair_charmm.html,
 "lj/class2 (gko)"_pair_class2.html,
 "lj/class2/coul/cut (ko)"_pair_class2.html,
+"lj/class2/coul/cut/soft"_pair_fep_soft.html,
 "lj/class2/coul/long (gko)"_pair_class2.html,
+"lj/class2/coul/long/soft"_pair_fep_soft.html,
+"lj/class2/soft"_pair_fep_soft.html,
 "lj/cubic (go)"_pair_lj_cubic.html,
 "lj/cut (gikot)"_pair_lj.html,
 "lj/cut/coul/cut (gko)"_pair_lj.html,
-"lj/cut/coul/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/debye (gko)"_pair_lj.html,
 "lj/cut/coul/dsf (gko)"_pair_lj.html,
 "lj/cut/coul/long (gikot)"_pair_lj.html,
 "lj/cut/coul/long/cs"_pair_cs.html,
-"lj/cut/coul/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/coul/long/soft (o)"_pair_fep_soft.html,
 "lj/cut/coul/msm (go)"_pair_lj.html,
 "lj/cut/coul/wolf (o)"_pair_lj.html,
 "lj/cut/dipole/cut (go)"_pair_dipole.html,
 "lj/cut/dipole/long (g)"_pair_dipole.html,
 "lj/cut/dipole/sf (go)"_pair_dipole.html,
-"lj/cut/soft (o)"_pair_lj_soft.html,
+"lj/cut/soft (o)"_pair_fep_soft.html,
 "lj/cut/thole/long (o)"_pair_thole.html,
 "lj/cut/tip4p/cut (o)"_pair_lj.html,
 "lj/cut/tip4p/long (ot)"_pair_lj.html,
-"lj/cut/tip4p/long/soft (o)"_pair_lj_soft.html,
+"lj/cut/tip4p/long/soft (o)"_pair_fep_soft.html,
 "lj/expand (gko)"_pair_lj_expand.html,
 "lj/expand/coul/long (g)"_pair_lj_expand.html,
 "lj/gromacs (gko)"_pair_gromacs.html,
@@ -154,6 +157,7 @@ OPT.
 "lj/sf/dipole/sf (go)"_pair_dipole.html,
 "lj/smooth (o)"_pair_lj_smooth.html,
 "lj/smooth/linear (o)"_pair_lj_smooth_linear.html,
+"lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html,
 "lj96/cut (go)"_pair_lj96.html,
 "lubricate (o)"_pair_lubricate.html,
 "lubricate/poly (o)"_pair_lubricate.html,
@@ -169,7 +173,7 @@ OPT.
 "momb"_pair_momb.html,
 "morse (gkot)"_pair_morse.html,
 "morse/smooth/linear (o)"_pair_morse.html,
-"morse/soft"_pair_morse.html,
+"morse/soft"_pair_fep_soft.html,
 "multi/lucy"_pair_multi_lucy.html,
 "multi/lucy/rx (k)"_pair_multi_lucy_rx.html,
 "nb3b/harmonic"_pair_nb3b_harmonic.html,
@@ -229,7 +233,7 @@ OPT.
 "thole"_pair_thole.html,
 "tip4p/cut (o)"_pair_coul.html,
 "tip4p/long (o)"_pair_coul.html,
-"tip4p/long/soft (o)"_pair_lj_soft.html,
+"tip4p/long/soft (o)"_pair_fep_soft.html,
 "tri/lj"_pair_tri_lj.html,
 "ufm (got)"_pair_ufm.html,
 "vashishta (gko)"_pair_vashishta.html,

doc/src/Eqs/angle_cross.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K_{SS} \left(r_{12}-r_{12,0}\right)\left(r_{32}-r_{32,0}\right) + K_{BS0}\left(r_{12}-r_{12,0}\right)\left(\theta-\theta_0\right) + K_{BS1}\left(r_{32}-r_{32,0}\right)\left(\theta-\theta_0\right)
+$$
+
+\end{document}

doc/src/Eqs/angle_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right]
+$$
+
+\end{document}

doc/src/Eqs/bond_mm3.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+$$
+
+\end{document}

doc/src/Eqs/improper_distharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d - d_0)^2
+$$
+
+\end{document}

doc/src/Eqs/improper_sqdistharm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+$$
+  E = K (d^2 - d_0^2)^2
+$$
+
+\end{document}

doc/src/Eqs/pair_coulgauss.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \frac{q_i q_j \mathrm{erf}\left( r/\sqrt{\gamma_1^2+\gamma_2^2} \right) }{\epsilon r_{ij}}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_lj_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+
+\begin{eqnarray*}
+  E = 4\epsilon \left[ \left(\frac{\sigma}{r}\right)^{12}-\left(\frac{\sigma}{r}\right)^{6} \right]
+% \qquad r < r_c \\
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_mm3_switch3.tex

@@ -0,0 +1,11 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+  \thispagestyle{empty}
+\begin{eqnarray*}
+  E &=& \epsilon_{ij} \left[ -2.25 \left(\frac{r_{v,ij}}{r_{ij}}\right)^6 + 1.84(10)^5 \exp\left[-12.0 r_{ij}/r_{v,ij}\right] \right] S_3(r_{ij}) \\
+  r_{v,ij} &=& r_{v,i} + r_{v,j} \\ 
+  \epsilon_{ij} &=& \sqrt{\epsilon_i \epsilon_j}
+\end{eqnarray*}
+
+\end{document}

doc/src/Eqs/pair_switch3.tex

@@ -0,0 +1,14 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+\thispagestyle{empty}
+
+\begin{eqnarray*}
+ S_3(r) = \left\lbrace \begin{array}{ll}
+                     1 & \quad\mathrm{if}\quad r < r_\mathrm{c} - w \\
+                     3x^2 - 2x^3 & \quad\mathrm{if}\quad r < r_\mathrm{c} \quad\mathrm{with\quad} x=\frac{r_\mathrm{c} - r}{w} \\
+                     0 & \quad\mathrm{if}\quad r >= r_\mathrm{c}
+                 \end{array} \right.
+\end{eqnarray*}
+
+\end{document}

doc/src/Errors_messages.txt

@@ -6917,7 +6917,7 @@ types. :dd
 
 {Invalid use of library file() function} :dt
 
-This function is called thru the library interface.  This
+This function is called through the library interface.  This
 error should not occur.  Contact the developers if it does. :dd
 
 {Invalid value in set command} :dt

doc/src/Howto_client_server.txt

@@ -82,7 +82,7 @@ Monte Carlo client code as the driver.
 
 The lammps_vasp dir shows how to couple LAMMPS as a client code
 running MD timestepping to VASP acting as a server providing quantum
-DFT forces, thru a Python wrapper script on VASP.
+DFT forces, through a Python wrapper script on VASP.
 
 Here is how to launch a client and server code together for any of the
 4 modes of message exchange that the "message"_message.html command

doc/src/Howto_couple.txt

@@ -50,7 +50,7 @@ In this scenario, the other code can be called as a library, as in
 (1), or it could be a stand-alone code, invoked by a system() call
 made by the command (assuming your parallel machine allows one or more
 processors to start up another program).  In the latter case the
-stand-alone code could communicate with LAMMPS thru files that the
+stand-alone code could communicate with LAMMPS through files that the
 command writes and reads.
 
 See the "Modify command"_Modify_command.html doc page for info on how

doc/src/Howto_library.txt

@@ -87,7 +87,7 @@ commands to LAMMPS to execute, the same as if they were coming from an
 input script.
 
 Via these functions, the calling code can read or generate a series of
-LAMMPS commands one or multiple at a time and pass it thru the library
+LAMMPS commands one or multiple at a time and pass it through the library
 interface to setup a problem and then run it in stages.  The caller
 can interleave the command function calls with operations it performs,
 calls to extract information from or set information within LAMMPS, or

doc/src/Install_git.txt

@@ -48,15 +48,8 @@ your machine and "unstable" is one of the 3 branches listed above.
 between them at any time using "git checkout <branch name>".)
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_svn.txt

@@ -36,15 +36,8 @@ where "mylammps" is the name of the directory you wish to create on
 your machine.
 
 Once the command completes, your directory will contain the same files
-as if you unpacked a current LAMMPS tarball, with two exceptions:
-
-1) No LAMMPS packages are initially installed in the src dir (a few
-packages are installed by default in the tarball src dir).  You can
-install whichever packages you wish before building LAMMPS; type "make
-package" from the src dir to see the options, and the
-"Packages"_Packages.html doc page for a discussion of packages.
-
-2) The HTML documentation files are not included.  They can be fetched
+as if you unpacked a current LAMMPS tarball, with the exception, that
+the HTML documentation files are not included.  They can be fetched
 from the LAMMPS website by typing "make fetch" in the doc directory.
 Or they can be generated from the content provided in doc/src by
 typing "make html" from the the doc directory.

doc/src/Install_windows.txt

@@ -12,7 +12,7 @@ Download an executable for Windows :h3
 Pre-compiled Windows installers which install LAMMPS executables on a
 Windows system can be downloaded from this site:
 
-"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html
+"http://packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for
@@ -42,7 +42,7 @@ environment manipulations.
 
 Note that to update to a newer version of LAMMPS, you should typically
 uninstall the version you currently have, download a new installer,
-and go thru the install procedure described above.  I.e. the same
+and go through the install procedure described above.  I.e. the same
 procedure for installing/updating most Windows programs.  You can
 install multiple versions of LAMMPS (in different directories), but
 only the executable for the last-installed package will be found

doc/src/Intro_features.txt

@@ -40,7 +40,7 @@ General features :h4,link(general)
   syntax for defining and using variables and formulas
   syntax for looping over runs and breaking out of loops
   run one or multiple simulations simultaneously (in parallel) from one script
-  build as library, invoke LAMMPS thru library interface or provided Python wrapper
+  build as library, invoke LAMMPS through library interface or provided Python wrapper
   couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both :ul
 
 Particle and model types :h4,link(particle)

doc/src/Intro_nonfeatures.txt

@@ -15,7 +15,7 @@ functionality for setting up simulations and analyzing their output.
 
 Specifically, LAMMPS was not conceived and designed for:
 
-being run thru a GUI
+being run through a GUI
 building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="4 Jan 2019 version">
+<META NAME="docnumber" CONTENT="8 Feb 2019 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@@ -21,7 +21,7 @@
 :line
 
 LAMMPS Documentation :c,h1
-4 Jan 2019 version :c,h2
+8 Feb 2019 version :c,h2
 
 "What is a LAMMPS version?"_Manual_version.html
 
@@ -37,27 +37,21 @@ LAMMPS is an open-source code, distributed freely under the terms of
 the GNU Public License (GPL).
 
 The "LAMMPS website"_lws has a variety of information about the code.
-It includes links to an on-line version of this manual, a "mail
+It includes links to an on-line version of this manual, a "mailing
 list"_http://lammps.sandia.gov/mail.html where users can post
-questions, and a "GitHub site"https://github.com/lammps/lammps where
+questions, and a "GitHub site"_https://github.com/lammps/lammps where
 all LAMMPS development is coordinated.
 
 :line
 
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
-
 The content for this manual is part of the LAMMPS distribution.  You
 can build a local copy of the Manual as HTML pages or a PDF file, by
 following the steps on the "Manual build"_Manual_build.html doc page.
-
 There is also a "Developer.pdf"_Developer.pdf document which gives
 a brief description of the basic code structure of LAMMPS.
 
 :line
 
-This manual is organized into the following sections.
-
 Once you are familiar with LAMMPS, you may want to bookmark "this
 page"_Commands.html since it gives quick access to a doc page for
 every LAMMPS command.

doc/src/Packages_details.txt

@@ -100,7 +100,8 @@ as contained in the file name.
 "USER-SPH"_#PKG-USER-SPH,
 "USER-TALLY"_#PKG-USER-TALLY,
 "USER-UEF"_#PKG-USER-UEF,
-"USER-VTK"_#PKG-USER-VTK :tb(c=6,ea=c)
+"USER-VTK"_#PKG-USER-VTK,
+"USER-YAFF"_#PKG-USER-YAFF, :tb(c=6,ea=c)
 
 :line
 
@@ -1305,7 +1306,7 @@ src/USER-FEP: filenames -> commands
 src/USER-FEP/README
 "fix adapt/fep"_fix_adapt_fep.html
 "compute fep"_compute_fep.html
-"pair_style */soft"_pair_lj_soft.html
+"pair_style */soft"_pair_fep_soft.html
 examples/USER/fep
 tools/fep/README
 tools/fep :ul
@@ -2067,3 +2068,39 @@ lib/vtk/README
 "dump vtk"_dump_vtk.html :ul
 
 
+:line
+
+USER-YAFF package :link(PKG-USER-YAFF),h4
+
+[Contents:]
+
+Some potentials that are also implemented in the Yet Another Force Field ("YAFF"_yaff) code.
+The expressions and their use are discussed in the following papers
+
+Vanduyfhuys et al., J. Comput. Chem., 36 (13), 1015-1027 (2015) "link"_vanduyfhuys2015
+Vanduyfhuys et al., J. Comput. Chem., 39 (16), 999-1011 (2018) "link"_vanduyfhuys2018 :ul
+
+which discuss the "QuickFF"_quickff methodology.
+
+
+:link(vanduyfhuys2015,http://dx.doi.org/10.1002/jcc.23877)
+:link(vanduyfhuys2018,http://dx.doi.org/10.1002/jcc.25173)
+:link(quickff,http://molmod.github.io/QuickFF)
+:link(yaff,https://github.com/molmod/yaff)
+
+
+[Author:] Steven Vandenbrande.
+
+[Supporting info:]
+
+src/USER-YAFF/README
+"angle_style cross"_angle_cross.html
+"angle_style mm3"_angle_mm3.html
+"bond_style mm3"_bond_mm3.html
+"improper_style distharm"_improper_distharm.html
+"improper_style sqdistharm"_improper_sqdistharm.html
+"pair_style mm3/switch3/coulgauss/long"_pair_mm3_switch3_coulgauss.html
+"pair_style lj/switch3/coulgauss/long"_pair_lj_switch3_coulgauss.html
+examples/USER/yaff :ul
+
+

doc/src/Packages_user.txt

@@ -75,7 +75,8 @@ Package, Description, Doc page, Example, Library
 "USER-SPH"_Packages_details.html#PKG-USER-SPH, smoothed particle hydrodynamics,"SPH User Guide"_PDF/SPH_LAMMPS_userguide.pdf, USER/sph, no
 "USER-TALLY"_Packages_details.html#PKG-USER-TALLY, pairwise tally computes,"compute XXX/tally"_compute_tally.html, USER/tally, no
 "USER-UEF"_Packages_details.html#PKG-USER-UEF, extensional flow,"fix nvt/uef"_fix_nh_uef.html, USER/uef, no
-"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext :tb(ea=c,ca1=l)
+"USER-VTK"_Packages_details.html#PKG-USER-VTK, dump output via VTK, "compute vtk"_dump_vtk.html, n/a, ext
+"USER-YAFF"_Packages_details.html#PKG-USER-YAFF, additional styles implemented in YAFF, "angle_style cross"_angle_cross.html, USER/yaff, no :tb(ea=c,ca1=l)
 
 :link(MOFplus,https://www.mofplus.org/content/show/MOF-FF)
 :link(PLUMED,http://www.plumed.org)

doc/src/Python_examples.txt

@@ -15,7 +15,7 @@ things that are possible when Python wraps LAMMPS.  If you create your
 own scripts, send them to us and we can include them in the LAMMPS
 distribution.
 
-trivial.py, read/run a LAMMPS input script thru Python,
+trivial.py, read/run a LAMMPS input script through Python,
 demo.py, invoke various LAMMPS library interface routines,
 simple.py, run in parallel, similar to examples/COUPLE/simple/simple.cpp,
 split.py, same as simple.py but running in parallel on a subset of procs,

doc/src/Python_run.txt

@@ -31,7 +31,7 @@ language is, and that it can be run interactively, enabling rapid
 development and debugging.  If you use it to mostly invoke costly
 operations within LAMMPS, such as running a simulation for a
 reasonable number of timesteps, then the overhead cost of invoking
-LAMMPS thru Python will be negligible.
+LAMMPS through Python will be negligible.
 
 The Python wrapper for LAMMPS uses the "ctypes" package in Python,
 which auto-generates the interface code needed between Python and a

doc/src/Python_test.txt

@@ -32,7 +32,7 @@ first importing from the lammps.py file:
 >>> from ctypes import CDLL
 >>> CDLL("liblammps.so") :pre
 
-If an error occurs, carefully go thru the steps on the
+If an error occurs, carefully go through the steps on the
 "Build_basics"_Build_basics.html doc page about building a shared
 library and the "Python_install"_Python_install.html doc page about
 insuring Python can find the necessary two files it needs.

doc/src/Tools.txt

@@ -391,15 +391,16 @@ definition file.  This tool was used to create the system for the
 
 moltemplate tool :h4,link(moltemplate)
 
-The moltemplate sub-directory contains a Python-based tool for
-building molecular systems based on a text-file description, and
-creating LAMMPS data files that encode their molecular topology as
-lists of bonds, angles, dihedrals, etc.  See the README.TXT file for
-more information.
+The moltemplate sub-directory contains instructions for installing
+moltemplate, a Python-based tool for building molecular systems based
+on a text-file description, and creating LAMMPS data files that encode
+their molecular topology as lists of bonds, angles, dihedrals, etc.
+See the README.txt file for more information.
 
 This tool was written by Andrew Jewett (jewett.aij at gmail.com), who
 supports it.  It has its own WWW page at
 "http://moltemplate.org"_http://moltemplate.org.
+The latest sources can be found "on its GitHub page"_https://github.com/jewettaij/moltemplate/releases
 
 :line
 

doc/src/angle_cosine.txt

@@ -8,6 +8,7 @@
 
 angle_style cosine command :h3
 angle_style cosine/omp command :h3
+angle_style cosine/kk command :h3
 
 [Syntax:]
 

doc/src/angle_cross.txt

@@ -0,0 +1,62 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+angle_style cross command :h3
+
+[Syntax:]
+
+angle_style cross :pre
+
+[Examples:]
+
+angle_style cross
+angle_coeff 1 200.0 100.0 100.0 1.25 1.25 107.0 :pre
+
+[Description:]
+
+The {cross} angle style uses a potential that couples the bond stretches of
+a bend with the angle stretch of that bend:
+
+:c,image(Eqs/angle_cross.jpg)
+
+where r12,0 is the rest value of the bond length between atom 1 and 2,
+r32,0 is the rest value of the bond length between atom 2 and 2,
+and theta0 is the rest value of the angle. KSS is the force constant of
+the bond stretch-bond stretch term and KBS0 and KBS1 are the force constants
+of the bond stretch-angle stretch terms.
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+KSS (energy/distance^2)
+KBS0 (energy/distance/rad)
+KBS1 (energy/distance/rad)
+r12,0 (distance)
+r32,0 (distance)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of KBS0 and KBS1 are in energy/distance/radian.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+
+

doc/src/angle_mm3.txt

@@ -0,0 +1,55 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+angle_style mm3 command :h3
+
+[Syntax:]
+
+angle_style mm3 :pre
+
+[Examples:]
+
+angle_style mm3
+angle_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} angle style uses the potential that is anharmonic in the angle
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/angle_mm3.jpg)
+
+where theta0 is the equilibrium value of the angle, and K is a
+prefactor. The anharmonic prefactors have units deg^(-n), for example
+-0.014 deg^(-1), 5.6(10)^(-5) deg^(-2), ...
+
+The following coefficients must be defined for each angle type via the
+"angle_coeff"_angle_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/radian^2)
+theta0 (degrees) :ul
+
+Theta0 is specified in degrees, but LAMMPS converts it to radians
+internally; hence the units of K are in energy/radian^2.
+
+[Restrictions:]
+
+This angle style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"angle_coeff"_angle_coeff.html
+
+[Default:] none
+
+:line
+

doc/src/angle_style.txt

@@ -81,10 +81,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 "cosine/shift"_angle_cosine_shift.html - angle cosine with a shift
 "cosine/shift/exp"_angle_cosine_shift_exp.html - cosine with shift and exponential term in spring constant
 "cosine/squared"_angle_cosine_squared.html - angle with cosine squared term
+"cross"_angle_cross.html - cross term coupling angle and bond lengths
 "dipole"_angle_dipole.html - angle that controls orientation of a point dipole
 "fourier"_angle_fourier.html - angle with multiple cosine terms
 "fourier/simple"_angle_fourier_simple.html - angle with a single cosine term
 "harmonic"_angle_harmonic.html - harmonic angle
+"mm3"_angle_mm3.html - anharmonic angle
 "quartic"_angle_quartic.html - angle with cubic and quartic terms
 "sdk"_angle_sdk.html - harmonic angle with repulsive SDK pair style between 1-3 atoms
 "table"_angle_table.html - tabulated by angle :ul

doc/src/angles.txt

@@ -14,11 +14,13 @@ Angle Styles :h1
    angle_cosine_shift
    angle_cosine_shift_exp
    angle_cosine_squared
+   angle_cross
    angle_dipole
    angle_fourier
    angle_fourier_simple
    angle_harmonic
    angle_hybrid
+   angle_mm3
    angle_none
    angle_quartic
    angle_sdk

doc/src/bond_mm3.txt

@@ -0,0 +1,58 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+bond_style mm3 command :h3
+
+[Syntax:]
+
+bond_style mm3 :pre
+
+[Examples:]
+
+bond_style mm3
+bond_coeff 1 100.0 107.0 :pre
+
+[Description:]
+
+The {mm3} bond style uses the potential that is anharmonic in the bond
+as defined in "(Allinger)"_#mm3-allinger1989
+
+:c,image(Eqs/bond_mm3.jpg)
+
+where r0 is the equilibrium value of the bond, and K is a
+prefactor. The anharmonic prefactors have units angstrom^(-n):
+-2.55 angstrom^(-1) and (7/12)2.55^2 angstrom^(-2). The code takes
+care of the necessary unit conversion for these factors internally.
+Note that the MM3 papers contains an error in Eq (1):
+(7/12)2.55 should be replaced with (7/12)2.55^2
+
+The following coefficients must be defined for each bond type via the
+"bond_coeff"_bond_coeff.html command as in the example above, or in
+the data file or restart files read by the "read_data"_read_data.html
+or "read_restart"_read_restart.html commands:
+
+K (energy/distance^2)
+r0 (distance) :ul
+
+[Restrictions:]
+
+This bond style can only be used if LAMMPS was built with the
+USER_YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"bond_coeff"_bond_coeff.html
+
+[Default:] none
+
+:line
+
+:link(mm3-allinger1989)
+[(Allinger)] Allinger, Yuh, Lii, JACS, 111(23), 8551-8566
+(1989),

doc/src/bond_style.txt

@@ -86,6 +86,7 @@ accelerated styles exist.
 "harmonic"_bond_harmonic.html - harmonic bond
 "harmonic/shift"_bond_harmonic_shift.html - shifted harmonic bond
 "harmonic/shift/cut"_bond_harmonic_shift_cut.html - shifted harmonic bond with a cutoff
+"mm3"_bond_mm3.html - MM3 anharmonic bond
 "morse"_bond_morse.html - Morse bond
 "nonlinear"_bond_nonlinear.html - nonlinear bond
 "oxdna/fene"_bond_oxdna.html - modified FENE bond suitable for DNA modeling

doc/src/bonds.txt

@@ -13,6 +13,7 @@ Bond Styles :h1
    bond_harmonic_shift
    bond_harmonic_shift_cut
    bond_hybrid
+   bond_mm3
    bond_morse
    bond_none
    bond_nonlinear

doc/src/compute_angmom_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the angular momentum
 vector for each chunk, due to the velocity/momentum of the individual
 atoms in the chunk around the center-of-mass of the chunk.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_com.txt

@@ -22,7 +22,7 @@ compute 1 all com :pre
 [Description:]
 
 Define a computation that calculates the center-of-mass of the group
-of atoms, including all effects due to atoms passing thru periodic
+of atoms, including all effects due to atoms passing through periodic
 boundaries.
 
 A vector of three quantities is calculated by this compute, which

doc/src/compute_com_chunk.txt

@@ -35,7 +35,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the center-of-mass
-for each chunk, which includes all effects due to atoms passing thru
+for each chunk, which includes all effects due to atoms passing through
 periodic boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_dipole_chunk.txt

@@ -38,7 +38,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the x,y,z coordinates of the dipole vector
 and the total dipole moment for each chunk, which includes all effects
-due to atoms passing thru periodic boundaries. For chunks with a net
+due to atoms passing through periodic boundaries. For chunks with a net
 charge the resulting dipole is made position independent by subtracting
 the position vector of the center of mass or geometric center times the
 net charge from the computed dipole vector.

doc/src/compute_displace_atom.txt

@@ -29,7 +29,7 @@ compute 1 all displace/atom refresh myVar :pre
 
 Define a computation that calculates the current displacement of each
 atom in the group from its original (reference) coordinates, including
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 A vector of four quantities per atom is calculated by this compute.
 The first 3 elements of the vector are the dx,dy,dz displacements.

doc/src/compute_fep.txt

@@ -128,24 +128,39 @@ commands to be changed, if the pair style supports it.
 
 The {pstyle} argument is the name of the pair style. For example,
 {pstyle} could be specified as "lj/cut".  The {pparam} argument is the
-name of the parameter to change.  This is a (non-exclusive) list of
+name of the parameter to change.  This is a list of
 pair styles and parameters that can be used with this compute.  See
 the doc pages for individual pair styles and their energy formulas for
 the meaning of these parameters:
 
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/coul/long"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"coul/cut/soft"_pair_lj_soft.html: lambda: type pairs:
-"coul/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/cut/coul/cut/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"lj/cut/tip4p/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
-"tip4p/long/soft"_pair_lj_soft.html: lambda: type pairs:
-"lj/charmm/coul/long/soft"_pair_lj_soft.html: epsilon,sigma,lambda: type pairs:
 "born"_pair_born.html: a,b,c: type pairs:
-"buck"_pair_buck.html: a,c : type pairs :tb(c=3,s=:)
+"buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
+"coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
+"soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 Note that it is easy to add new potentials and their parameters to
 this list.  All it typically takes is adding an extract() method to
@@ -236,7 +251,7 @@ package"_Build_package.html doc page for more info.
 [Related commands:]
 
 "fix adapt/fep"_fix_adapt_fep.html, "fix ave/time"_fix_ave_time.html,
-"pair_style lj/soft/coul/soft"_pair_lj_soft.html
+"pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/compute_gyration.txt

@@ -22,7 +22,7 @@ compute 1 molecule gyration :pre
 [Description:]
 
 Define a computation that calculates the radius of gyration Rg of the
-group of atoms, including all effects due to atoms passing thru
+group of atoms, including all effects due to atoms passing through
 periodic boundaries.
 
 Rg is a measure of the size of the group of atoms, and is computed as

doc/src/compute_gyration_chunk.txt

@@ -40,7 +40,7 @@ doc pages for details of how chunks can be defined and examples of how
 they can be used to measure properties of a system.
 
 This compute calculates the radius of gyration Rg for each chunk,
-which includes all effects due to atoms passing thru periodic
+which includes all effects due to atoms passing through periodic
 boundaries.
 
 Rg is a measure of the size of a chunk, and is computed by this

doc/src/compute_inertia_chunk.txt

@@ -36,7 +36,7 @@ they can be used to measure properties of a system.
 
 This compute calculates the 6 components of the symmetric inertia
 tensor for each chunk, ordered Ixx,Iyy,Izz,Ixy,Iyz,Ixz.  The
-calculation includes all effects due to atoms passing thru periodic
+calculation includes all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd.txt

@@ -29,7 +29,7 @@ compute 1 upper msd com yes average yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) of the group of atoms, including all effects due to atoms
-passing thru periodic boundaries.  For computation of the non-Gaussian
+passing through periodic boundaries.  For computation of the non-Gaussian
 parameter of mean-squared displacement, see the "compute
 msd/nongauss"_compute_msd_nongauss.html command.
 

doc/src/compute_msd_chunk.txt

@@ -38,7 +38,7 @@ Four quantities are calculated by this compute for each chunk.  The
 first 3 quantities are the squared dx,dy,dz displacements of the
 center-of-mass.  The 4th component is the total squared displacement,
 i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass.  These
-calculations include all effects due to atoms passing thru periodic
+calculations include all effects due to atoms passing through periodic
 boundaries.
 
 Note that only atoms in the specified group contribute to the

doc/src/compute_msd_nongauss.txt

@@ -28,7 +28,7 @@ compute 1 upper msd/nongauss com yes :pre
 
 Define a computation that calculates the mean-squared displacement
 (MSD) and non-Gaussian parameter (NGP) of the group of atoms,
-including all effects due to atoms passing thru periodic boundaries.
+including all effects due to atoms passing through periodic boundaries.
 
 A vector of three quantities is calculated by this compute.  The first
 element of the vector is the total squared dx,dy,dz displacements

doc/src/compute_omega_chunk.txt

@@ -38,7 +38,7 @@ This compute calculates the 3 components of the angular velocity
 vector for each chunk, via the formula L = Iw where L is the angular
 momentum vector of the chunk, I is its moment of inertia tensor, and w
 is omega = angular velocity of the chunk.  The calculation includes
-all effects due to atoms passing thru periodic boundaries.
+all effects due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/compute_rigid_local.txt

@@ -107,7 +107,7 @@ mass (COM) of the body.  The {x}, {y}, {z} attributes write the COM
 "unscaled", in the appropriate distance "units"_units.html (Angstroms,
 sigma, etc).  Use {xu}, {yu}, {zu} if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
-COM has passed thru a periodic boundary one or more times, the value
+COM has passed through a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been
 wrapped back into the periodic box.
 

doc/src/compute_sna_atom.txt

@@ -24,7 +24,7 @@ twojmax = band limit for bispectrum components (non-negative integer) :l
 R_1, R_2,... = list of cutoff radii, one for each type (distance units) :l
 w_1, w_2,... = list of neighbor weights, one for each type  :l
 zero or more keyword/value pairs may be appended :l
-keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag}:l
+keyword = {diagonal} or {rmin0} or {switchflag} or {bzeroflag} or {quadraticflag} :l
   {diagonal} value = {0} or {1} or {2} or {3}
      {0} = all j1, j2, j <= twojmax, j2 <= j1
      {1} = subset satisfying j1 == j2

doc/src/compute_torque_chunk.txt

@@ -37,7 +37,7 @@ they can be used to measure properties of a system.
 This compute calculates the 3 components of the torque vector for eqch
 chunk, due to the forces on the individual atoms in the chunk around
 the center-of-mass of the chunk.  The calculation includes all effects
-due to atoms passing thru periodic boundaries.
+due to atoms passing through periodic boundaries.
 
 Note that only atoms in the specified group contribute to the
 calculation.  The "compute chunk/atom"_compute_chunk_atom.html command

doc/src/displace_atoms.txt

@@ -83,7 +83,7 @@ used in such a way that the displacement of a particular atom is the
 same, regardless of how many processors are being used.
 
 The {rotate} style rotates each atom in the group by the angle {theta}
-around a rotation axis {R} = (Rx,Ry,Rz) that goes thru a point {P} =
+around a rotation axis {R} = (Rx,Ry,Rz) that goes through a point {P} =
 (Px,Py,Pz).  The direction of rotation for the atoms around the
 rotation axis is consistent with the right-hand rule: if your
 right-hand thumb points along {R}, then your fingers wrap around the

doc/src/dump.txt

@@ -312,7 +312,7 @@ so that any machine which supports XDR should be able to read them.
 The number of atoms per snapshot cannot change with the {xtc} style.
 The {unwrap} option of the "dump_modify"_dump_modify.html command allows
 XTC coordinates to be written "unwrapped" by the image flags for each
-atom.  Unwrapped means that if the atom has passed thru a periodic
+atom.  Unwrapped means that if the atom has passed through a periodic
 boundary one or more times, the value is printed for what the
 coordinate would be if it had not been wrapped back into the periodic
 box.  Note that these coordinates may thus be far outside the box size
@@ -534,7 +534,7 @@ on the "Howto triclinic"_Howto_triclinic.html doc page.
 
 Use {xu}, {yu}, {zu} if you want the coordinates "unwrapped" by the
 image flags for each atom.  Unwrapped means that if the atom has
-passed thru a periodic boundary one or more times, the value is
+passed through a periodic boundary one or more times, the value is
 printed for what the coordinate would be if it had not been wrapped
 back into the periodic box.  Note that using {xu}, {yu}, {zu} means
 that the coordinate values may be far outside the box bounds printed

doc/src/dump_modify.txt

@@ -344,7 +344,7 @@ The {image} keyword applies only to the dump {atom} style.  If the
 image value is {yes}, 3 flags are appended to each atom's coords which
 are the absolute box image of the atom in each dimension.  For
 example, an x image flag of -2 with a normalized coord of 0.5 means
-the atom is in the center of the box, but has passed thru the box
+the atom is in the center of the box, but has passed through the box
 boundary 2 times and is really 2 box lengths to the left of its
 current coordinate.  Note that for dump style {custom} these various
 values can be printed in the dump file by using the appropriate atom
@@ -622,7 +622,7 @@ threshold criterion is met.  Otherwise it is not met.
 
 The {unwrap} keyword only applies to the dump {dcd} and {xtc} styles.
 If set to {yes}, coordinates will be written "unwrapped" by the image
-flags for each atom.  Unwrapped means that if the atom has passed thru
+flags for each atom.  Unwrapped means that if the atom has passed through
 a periodic boundary one or more times, the value is printed for what
 the coordinate would be if it had not been wrapped back into the
 periodic box.  Note that these coordinates may thus be far outside the

doc/src/fix_adapt.txt

@@ -112,17 +112,43 @@ pages for individual pair styles and their energy formulas for the
 meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
+"born/coul/long, born/coul/msm"_pair_born.html: coulombic_cutoff: type global:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/coul/long, buck/coul/msm"_pair_buck.html: coulombic_cutoff: type global:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
 "coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
+"coul/dsf"_pair_coul.html: coulombic_cutoff: type global:
+"coul/long, coul/msm"_pair_coul.html: coulombic_cutoff, scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda, coulombic_cutoff: type pairs:
 "eam, eam/alloy, eam/fs"_pair_eam.html: scale: type pairs:
+"gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: A,B: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma,coulombic_cutoff: type pairs:
 "lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda,coulombic_cutoff: type pairs:
+"lj/cut/coul/dsf"_pair_lj.html: cutoff: type global:
+"lj/cut/tip4p/cut"_pair_lj.html: epsilon,sigma,coulombic_cutoff: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
 "lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
 "lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
 "lubricate"_pair_lubricate.html: mu: global:
-"gauss"_pair_gauss.html: a: type pairs:
-"morse"_pair_morse.html: d0,r0,alpha: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamma_repulsive,gamma_attractive: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: D0,R0,alpha: type pairs:
+"morse/soft"_pair_morse.html: D0,R0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: E0,R0,m,n: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: E0,R0,m,n,coulombic_cutoff: type pairs:
+"reax/c"_pair_reaxc.html: chi, eta, gamma: type global:
+"spin/dmi"_pair_spin_dmi.html: coulombic_cutoff: type global:
+"spin/exchange"_pair_spin_exchange.html: coulombic_cutoff: type global:
+"spin/magelec"_pair_spin_magelec.html: coulombic_cutoff: type global:
+"spin/neel"_pair_spin_neel.html: coulombic_cutoff: type global:
+"table"_pair_table.html: table_cutoff: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma: type pairs:
 "soft"_pair_soft.html: a: type pairs:
 "kim"_pair_kim.html: PARAM_FREE_*&#58i,j,...: global :tb(c=3,s=:)
 
@@ -217,6 +243,7 @@ Currently {bond} does not support bond_style hybrid nor bond_style
 hybrid/overlay as bond styles. The only bonds that currently are
 working with fix_adapt are
 
+"gromos"_bond_gromos.html: k, r0: type bonds:
 "harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
 
 :line

doc/src/fix_adapt_fep.txt

@@ -114,24 +114,37 @@ styles and their energy formulas for the meaning of these parameters:
 
 "born"_pair_born.html: a,b,c: type pairs:
 "buck"_pair_buck.html: a,c: type pairs:
+"buck/mdf"_pair_mdf.html: a,c: type pairs:
 "coul/cut"_pair_coul.html: scale: type pairs:
-"coul/debye"_pair_coul.html: scale: type pairs:
-"coul/long"_pair_coul.html: scale: type pairs:
-"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
-"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
-"lubricate"_pair_lubricate.html: mu: global:
+"coul/cut/soft"_pair_fep_soft.html: lambda: type pairs:
+"coul/long, coul/msm"_pair_coul.html: scale: type pairs:
+"coul/long/soft"_pair_fep_soft.html: scale, lambda: type pairs:
+"eam"_pair_eam.html: scale: type pairs:
 "gauss"_pair_gauss.html: a: type pairs:
+"lennard/mdf"_pair_mdf.html: a,b: type pairs:
+"lj/class2"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/class2/coul/cut, lj/class2/coul/long"_pair_class2.html: epsilon,sigma: type pairs:
+"lj/cut"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/coul/cut, lj/cut/coul/long, lj/cut/coul/msm"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/coul/cut/soft, lj/cut/coul/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/cut/tip4p/cut, lj/cut/tip4p/long"_pair_lj.html: epsilon,sigma: type pairs:
+"lj/cut/tip4p/long/soft"_pair_fep_soft.html: epsilon,sigma,lambda: type pairs:
+"lj/expand"_pair_lj_expand.html: epsilon,sigma,delta: type pairs:
+"lj/mdf"_pair_mdf.html: epsilon,sigma: type pairs:
+"lj/sf/dipole/sf"_pair_dipole.html: epsilon,sigma,scale: type pairs:
+"mie/cut"_pair_mie.html: epsilon,sigma,gamR,gamA: type pairs:
+"morse, morse/smooth/linear"_pair_morse.html: d0,r0,alpha: type pairs:
+"morse/soft"_pair_morse.html: d0,r0,alpha,lambda: type pairs:
+"nm/cut"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"nm/cut/coul/cut, nm/cut/coul/long"_pair_nm.html: e0,r0,nn,mm: type pairs:
+"ufm"_pair_ufm.html: epsilon,sigma,scale: type pairs:
 "soft"_pair_soft.html: a: type pairs :tb(c=3,s=:)
 
 NOTE: It is easy to add new potentials and their parameters to this
 list.  All it typically takes is adding an extract() method to the
 pair_*.cpp file associated with the potential.
 
-Some parameters are global settings for the pair style, e.g. the
-viscosity setting "mu" for "pair_style lubricate"_pair_lubricate.html.
-Other parameters apply to atom type pairs within the pair style,
-e.g. the prefactor "a" for "pair_style soft"_pair_soft.html.
-
 Note that for many of the potentials, the parameter that can be varied
 is effectively a prefactor on the entire energy expression for the
 potential, e.g. the lj/cut epsilon.  The parameters listed as "scale"
@@ -253,7 +266,7 @@ minimization"_minimize.html.
 [Related commands:]
 
 "compute fep"_compute_fep.html, "fix adapt"_fix_adapt.html, "compute
-ti"_compute_ti.html
+ti"_compute_ti.html, "pair_fep_soft"_pair_fep_soft.html
 
 [Default:]
 

doc/src/fix_ave_histo.txt

@@ -241,7 +241,7 @@ first bin and values > {hi} are counted in the last bin.  If {beyond}
 is set to {extend} then two extra bins are created, so that there are
 Nbins+2 total bins.  Values < {lo} are counted in the first bin and
 values > {hi} are counted in the last bin (Nbins+1).  Values between
-{lo} and {hi} (inclusive) are counted in bins 2 thru Nbins+1.  The
+{lo} and {hi} (inclusive) are counted in bins 2 through Nbins+1.  The
 "coordinate" stored and printed for these two extra bins is {lo} and
 {hi}.
 

doc/src/fix_bond_react.txt

@@ -36,10 +36,12 @@ react = mandatory argument indicating new reaction specification :l
   template-ID(post-reacted) = ID of a molecule template containing post-reaction topology :l
   map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates :l
   zero or more individual keyword/value pairs may be appended to each react argument :l
-  individual_keyword = {prob} or {stabilize_steps} or {update_edges} :l
+  individual_keyword = {prob} or {max_rxn} or {stabilize_steps} or {update_edges} :l
     {prob} values = fraction seed
       fraction = initiate reaction with this probability if otherwise eligible
       seed = random number seed (positive integer)
+    {max_rxn} value = N
+      N = maximum number of reactions allowed to occur
     {stabilize_steps} value = timesteps
       timesteps = number of timesteps to apply the internally-created "nve/limit"_fix_nve_limit.html fix to reacting atoms
     {update_edges} value = {none} or {charges} or {custom}
@@ -142,7 +144,7 @@ modified to match the post-reaction template.
 
 A bonding atom pair will be identified if several conditions are met.
 First, a pair of atoms I,J within the specified react-group-ID of type
-itype and jtype must separated by a distance between {Rmin} and
+itype and jtype must be separated by a distance between {Rmin} and
 {Rmax}. It is possible that multiple bonding atom pairs are
 identified: if the bonding atoms in the pre-reacted template are not
 1-2, 1-3, or 1-4 neighbors, the closest bonding atom partner is set as
@@ -211,9 +213,10 @@ mandatory keyword is 'equivalences' and the optional keywords are
 N {equivalences} = # of atoms N in the reaction molecule templates
 N {edgeIDs} = # of edge atoms N in the pre-reacted molecule template
 N {deleteIDs} = # of atoms N that are specified for deletion
-N {customIDs} = # of atoms N that are specified for a custom update :pre
+N {customIDs} = # of atoms N that are specified for a custom update
+N {constraints} = # of specified reaction constraints N :pre
 
-The body of the map file contains two mandatory sections and three
+The body of the map file contains two mandatory sections and four
 optional sections. The first mandatory section begins with the keyword
 'BondingIDs' and lists the atom IDs of the bonding atom pair in the
 pre-reacted molecule template. The second mandatory section begins
@@ -230,7 +233,10 @@ Edges' and allows for forcing the update of a specific atom's atomic
 charge. The first column is the ID of an atom near the edge of the
 pre-reacted molecule template, and the value of the second column is
 either 'none' or 'charges.' Further details are provided in the
-discussion of the 'update_edges' keyword.
+discussion of the 'update_edges' keyword. The fourth optional section
+begins with the keyword 'Constraints' and lists additional criteria
+that must be satisfied in order for the reaction to occur. Currently,
+there is one type of constraint available, as discussed below.
 
 A sample map file is given below:
 
@@ -263,6 +269,18 @@ Equivalences :pre
 
 :line
 
+Any number of additional constraints may be specified in the
+Constraints section of the map file. Currently there is one type of
+additional constraint, of type 'distance', whose syntax is as follows:
+
+distance {ID1} {ID2} {rmin} {rmax} :pre
+
+where 'distance' is the required keyword, {ID1} and {ID2} are
+pre-reaction atom IDs, and these two atoms must be separated by a
+distance between {rmin} and {rmax} for the reaction to occur. This
+constraint can be used to enforce a certain orientation between
+reacting molecules.
+
 Once a reaction site has been successfully identified, data structures
 within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
@@ -285,7 +303,8 @@ The {prob} keyword can affect whether an eligible reaction actually
 occurs. The fraction setting must be a value between 0.0 and 1.0. A
 uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
-fraction.
+fraction. Up to N reactions are permitted to occur, as optionally
+specified by the {max_rxn} keyword.
 
 The {stabilize_steps} keyword allows for the specification of how many
 timesteps a reaction site is stabilized before being returned to the

doc/src/fix_meso_move.txt

@@ -56,7 +56,7 @@ by other fixes (e.g. "fix meso"_fix_meso.html, "fix
 meso/stationary"_fix_meso_stationary.html), since that will change their
 positions and velocities twice.
 
-NOTE: As particles move due to this fix, they will pass thru periodic
+NOTE: As particles move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 meso"_fix_meso.html command).  It is up to you to decide whether periodic
@@ -126,7 +126,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates particles around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 particles around the rotation axis is consistent with the right-hand
 rule: if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_move.txt

@@ -51,7 +51,7 @@ integrated by other fixes (e.g. "fix nve"_fix_nve.html, "fix
 nvt"_fix_nh.html), since that will change their positions and
 velocities twice.
 
-NOTE: As atoms move due to this fix, they will pass thru periodic
+NOTE: As atoms move due to this fix, they will pass through periodic
 boundaries and be remapped to the other side of the simulation box,
 just as they would during normal time integration (e.g. via the "fix
 nve"_fix_nve.html command).  It is up to you to decide whether
@@ -121,7 +121,7 @@ variable v equal v_omega*($A-cwiggle(0.0,$A,$T))
 fix 1 boundary move variable v_x NULL NULL v_v NULL NULL :pre
 
 The {rotate} style rotates atoms around a rotation axis {R} =
-(Rx,Ry,Rz) that goes thru a point {P} = (Px,Py,Pz).  The {period} of
+(Rx,Ry,Rz) that goes through a point {P} = (Px,Py,Pz).  The {period} of
 the rotation is also specified.  The direction of rotation for the
 atoms around the rotation axis is consistent with the right-hand rule:
 if your right-hand thumb points along {R}, then your fingers wrap

doc/src/fix_qeq.txt

@@ -22,7 +22,7 @@ Nevery = perform charge equilibration every this many steps :l
 cutoff = global cutoff for charge-charge interactions (distance unit) :l
 tolerance = precision to which charges will be equilibrated :l
 maxiter = maximum iterations to perform charge equilibration :l
-qfile = a filename with QEq parameters :l
+qfile = a filename with QEq parameters or {coul/streitz} or {reax/c} :l
 
 zero or more keyword/value pairs may be appended :l
 keyword = {alpha} or {qdamp} or {qstep} :l
@@ -122,7 +122,9 @@ field"_#vanDuin paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
 as "fix qeq/reax"_fix_qeq_reax.html, and can be used with "pair_style
 reax/c"_pair_reaxc.html.  Only the {chi}, {eta}, and {gamma}
-parameters from the {qfile} file are used.  This style solves partial
+parameters from the {qfile} file are used. When using the string
+{reax/c} as filename, these parameters are extracted directly from
+an active {reax/c} pair style.  This style solves partial
 charges on atoms via the matrix inversion method.  A tolerance of
 1.0e-6 is usually a good number.
 
@@ -132,7 +134,9 @@ that the interaction between a pair of charged particles is the
 product of two Slater 1{s} orbitals.  The expression for the Slater
 1{s} orbital is given under equation (6) of the
 "Streitz-Mintmire"_#Streitz1 paper.  Only the {chi}, {eta}, {zeta}, and
-{qcore} parameters from the {qfile} file are used.  This style solves
+{qcore} parameters from the {qfile} file are used. When using the string
+{coul/streitz} as filename, these parameters are extracted directly from
+an active {coul/streitz} pair style.  This style solves
 partial charges on atoms via the matrix inversion method.  A tolerance
 of 1.0e-6 is usually a good number.  Keyword {alpha} can be used to
 change the Slater type orbital exponent.

doc/src/fix_srd.txt

@@ -117,7 +117,7 @@ Lamda cannot be smaller than 0.6 * hgrid, else an error is generated
 SRD particles are bounded by Vmax, which is set so that an SRD
 particle will not advect further than Dmax = 4*lamda in dt_SRD.  This
 means that roughly speaking, Dmax should not be larger than a big
-particle diameter, else SRDs may pass thru big particles without
+particle diameter, else SRDs may pass through big particles without
 colliding.  A warning is generated if this is the case.
 
 Collisions between SRD particles and big particles or walls are

doc/src/fix_wall_reflect.txt

@@ -41,7 +41,7 @@ fix top all wall/reflect zhi v_pressdown :pre
 [Description:]
 
 Bound the simulation with one or more walls which reflect particles
-in the specified group when they attempt to move thru them.
+in the specified group when they attempt to move through them.
 
 Reflection means that if an atom moves outside the wall on a timestep
 by a distance delta (e.g. due to "fix nve"_fix_nve.html), then it is

doc/src/if.txt

@@ -107,7 +107,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/improper_distharm.txt

@@ -0,0 +1,53 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+improper_style distharm command :h3
+
+[Syntax:]
+
+improper_style distharm
+
+[Examples:]
+
+improper_style distharm
+improper_coeff 1 25.0 0.5 :pre
+
+[Description:]
+
+The {distharm} improper style uses the potential
+
+:c,image(Eqs/improper_distharm.jpg)
+
+where d is the oriented distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance. The distance d is oriented and can take
+on negative values. This may lead to unwanted behavior if d0 is not equal to zero.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^2)
+d0 (distance) :ul
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-YAFF package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none

doc/src/improper_sqdistharm.txt

@@ -0,0 +1,54 @@
+"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+improper_style sqdistharm command :h3
+
+[Syntax:]
+
+improper_style sqdistharm
+
+[Examples:]
+
+improper_style sqdistharm
+improper_coeff 1 50.0 0.1 :pre
+
+[Description:]
+
+The {sqdistharm} improper style uses the potential
+
+:c,image(Eqs/improper_sqdistharm.jpg)
+
+where d is the distance between the central atom and the plane formed
+by the other three atoms.  If the 4 atoms in an improper quadruplet
+(listed in the data file read by the "read_data"_read_data.html
+command) are ordered I,J,K,L then the L-atom is assumed to be the
+central atom. Note that this is different from the convention used
+in the improper_style distance.
+
+The following coefficients must be defined for each improper type via
+the improper_coeff command as in the example above, or in the data
+file or restart files read by the read_data or read_restart commands:
+
+K (energy/distance^4)
+d0^2 (distance^2) :ul
+
+Note that d0^2 (in units distance^2) has be provided and not d0.
+
+:line
+
+[Restrictions:]
+
+This improper style can only be used if LAMMPS was built with the
+USER-MISC package.  See the "Build package"_Build_package.html doc
+page for more info.
+
+[Related commands:]
+
+"improper_coeff"_improper_coeff.html
+
+[Default:] none

doc/src/improper_style.txt

@@ -78,11 +78,13 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
 "cossq"_improper_cossq.html - improper with a cosine squared term
 "cvff"_improper_cvff.html - CVFF improper
 "distance"_improper_distance.html - improper based on distance between atom planes
+"distharm"_improper_distharm.html - improper that is harmonic in the out-of-plane distance
 "fourier"_improper_fourier.html - improper with multiple cosine terms
 "harmonic"_improper_harmonic.html - harmonic improper
 "inversion/harmonic"_improper_inversion_harmonic.html - harmonic improper with Wilson-Decius out-of-plane definition
 "ring"_improper_ring.html - improper which prevents planar conformations
 "umbrella"_improper_umbrella.html - DREIDING improper :ul
+"sqdistharm"_improper_sqdistharm.html - improper that is harmonic in the square of the out-of-plane distance
 
 :line
 

doc/src/impropers.txt

@@ -9,6 +9,7 @@ Improper Styles :h1
    improper_cossq
    improper_cvff
    improper_distance
+   improper_distharm
    improper_fourier
    improper_harmonic
    improper_hybrid
@@ -16,6 +17,7 @@ Improper Styles :h1
    improper_none
    improper_ring
    improper_umbrella
+   improper_sqdistharm
    improper_zero
 
 END_RST -->

doc/src/jump.txt

@@ -100,7 +100,7 @@ print "ALL DONE" :pre
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
-condition is met, then continues iterating thru the outer loop.
+condition is met, then continues iterating through the outer loop.
 
 label       loopa
 variable    a loop 5

doc/src/kspace_style.txt

@@ -370,8 +370,7 @@ of these styles.
 
 All of the kspace styles are part of the KSPACE package.  They are
 only enabled if LAMMPS was built with that package.  See the "Build
-package"_Build_package.html doc page for more info.  Note that the
-KSPACE package is installed by default.
+package"_Build_package.html doc page for more info.
 
 For MSM, a simulation must be 3d and one can use any combination of
 periodic, non-periodic, or shrink-wrapped boundaries (specified using

doc/src/lammps.book

@@ -595,7 +595,8 @@ pair_lj_expand.html
 pair_lj_long.html
 pair_lj_smooth.html
 pair_lj_smooth_linear.html
-pair_lj_soft.html
+pair_fep_soft.html
+pair_lj_switch3_coulgauss.html
 pair_lubricate.html
 pair_lubricateU.html
 pair_mdf.html
@@ -605,6 +606,7 @@ pair_meam_sw_spline.html
 pair_meso.html
 pair_mgpt.html
 pair_mie.html
+pair_mm3_switch3_coulgauss.html
 pair_momb.html
 pair_morse.html
 pair_multi_lucy.html
@@ -668,6 +670,7 @@ bond_harmonic_shift.html
 bond_harmonic_shift_cut.html
 bond_hybrid.html
 bond_morse.html
+bond_mm3.html
 bond_none.html
 bond_nonlinear.html
 bond_oxdna.html
@@ -687,11 +690,13 @@ angle_cosine_periodic.html
 angle_cosine_shift.html
 angle_cosine_shift_exp.html
 angle_cosine_squared.html
+angle_cross.html
 angle_dipole.html
 angle_fourier.html
 angle_fourier_simple.html
 angle_harmonic.html
 angle_hybrid.html
+angle_mm3.html
 angle_none.html
 angle_quartic.html
 angle_sdk.html
@@ -725,6 +730,7 @@ improper_class2.html
 improper_cossq.html
 improper_cvff.html
 improper_distance.html
+improper_distharm.html
 improper_fourier.html
 improper_harmonic.html
 improper_hybrid.html
@@ -732,6 +738,7 @@ improper_inversion_harmonic.html
 improper_none.html
 improper_ring.html
 improper_umbrella.html
+improper_sqdistharm.html
 improper_zero.html
 
 lammps_commands_kspace.html

doc/src/minimize.txt

@@ -82,12 +82,12 @@ coordinates:
 
 where the first term is the sum of all non-bonded "pairwise
 interactions"_pair_style.html including "long-range Coulombic
-interactions"_kspace_style.html, the 2nd thru 5th terms are
+interactions"_kspace_style.html, the 2nd through 5th terms are
 "bond"_bond_style.html, "angle"_angle_style.html,
 "dihedral"_dihedral_style.html, and "improper"_improper_style.html
 interactions respectively, and the last term is energy due to
 "fixes"_fix.html which can act as constraints or apply force to atoms,
-such as thru interaction with a wall.  See the discussion below about
+such as through interaction with a wall.  See the discussion below about
 how fix commands affect minimization.
 
 The starting point for the minimization is the current configuration