Merge pull request #1350 from akohlmey/next-patch-release

Step version string for next patch release

.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/ISSUE_TEMPLATE/generic.md

@@ -0,0 +1,21 @@
+---
+name: Generic Issue
+about: For issues that do not fit any of the other categories
+title: "_Replace With a Descriptive Title_"
+labels: 
+assignees: ''
+
+---
+
+**Summary**
+
+_Please provide a clear and concise description of what this issue report is about._
+
+**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_
+
+**Details**
+
+_Please explain the issue in detail here_
+

.github/ISSUE_TEMPLATE/help_request.md

@@ -0,0 +1,15 @@
+---
+name: Request for Help
+about: "Don't post help requests here, email the lammps-users mailing list"
+title: ""
+labels: invalid
+assignees: ''
+
+---
+
+Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
+Instead send an e-mail to the lammps-users mailing list.
+
+This issue tracker is for tracking LAMMPS development related issues only.
+
+Thanks for your cooperation.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,28 +1,43 @@
-## 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 (ideally something that can outlive your institution's e-mail, in case you change jobs) 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 contributed code._
+
+**Licensing**
+
+By submitting this pull request, I agree, that my contribution will be included in LAMMPS and redistributed under either the GNU General Public License version 2 (GPL v2) or the GNU Lesser General Public License version 2.1 (LGPL v2.1).
+
+**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

@@ -171,14 +171,14 @@ set(LAMMPS_DEPS)
 set(LAMMPS_API_DEFINES)
 
 set(DEFAULT_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE GRANULAR
-  KSPACE MANYBODY MC MEAM MESSAGE MISC MOLECULE PERI REAX REPLICA RIGID SHOCK
+  KSPACE MANYBODY MC MESSAGE MISC MOLECULE PERI REPLICA RIGID SHOCK
   SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI POEMS LATTE USER-ATC USER-AWPMD
   USER-BOCS USER-CGDNA USER-MESO USER-CGSDK USER-COLVARS USER-DIFFRACTION
   USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB USER-MANIFOLD
   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 USER-ADIOS)
 set(ACCEL_PACKAGES USER-OMP KOKKOS OPT USER-INTEL GPU)
 set(OTHER_PACKAGES CORESHELL QEQ)
 foreach(PKG ${DEFAULT_PACKAGES})
@@ -191,16 +191,27 @@ endforeach()
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
-if(PKG_REAX OR PKG_MEAM OR PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
+if(PKG_USER-QUIP OR PKG_USER-QMMM OR PKG_LATTE OR PKG_USER-SCAFACOS)
   enable_language(Fortran)
 endif()
 
-if(PKG_MEAM OR PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
+if(PKG_USER-H5MD OR PKG_USER-QMMM OR PKG_USER-SCAFACOS)
   enable_language(C)
 endif()
 
 include_directories(${LAMMPS_SOURCE_DIR})
 
+
+if(PKG_USER-ADIOS)
+  # The search for ADIOS2 must come before MPI because
+  # it includes its own MPI search with the latest FindMPI.cmake
+  # script that defines the MPI::MPI_C target 
+  enable_language(C)
+  find_package(ADIOS2 REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS adios2::adios2)
+endif()
+
+
 # do MPI detection after language activation, if MPI for these language is required
 find_package(MPI QUIET)
 option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
@@ -221,7 +232,7 @@ else()
 endif()
 
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS size limit")
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
 set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
@@ -453,7 +464,7 @@ if(PKG_VORONOI)
     set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
 
     ExternalProject_Add(voro_build
-      URL http://math.lbl.gov/voro++/download/dir/voro++-0.4.6.tar.gz
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
       URL_MD5 2338b824c3b7b25590e18e8df5d68af9
       CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
       )
@@ -559,10 +570,15 @@ 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)
@@ -608,14 +624,15 @@ if(PKG_USER-NETCDF)
   add_definitions(-DLMP_HAS_NETCDF -DNC_64BIT_DATA=0x0020)
 endif()
 
+
 if(PKG_USER-SMD)
   option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" OFF)
   if(DOWNLOAD_EIGEN3)
     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)
@@ -651,28 +668,34 @@ if(PKG_USER-VTK)
 endif()
 
 if(PKG_KIM)
-  option(DOWNLOAD_KIM "Download KIM-API v1 from OpenKIM instead of using an already installed one)" OFF)
+  option(DOWNLOAD_KIM "Download KIM-API v2 from OpenKIM instead of using an already installed one" OFF)
   if(DOWNLOAD_KIM)
-    message(STATUS "KIM-API v1 download requested - we will build our own")
+    message(STATUS "KIM-API v2 download requested - we will build our own")
+    enable_language(C)
+    enable_language(Fortran)
     include(ExternalProject)
     ExternalProject_Add(kim_build
-      URL https://github.com/openkim/kim-api/archive/v1.9.5.tar.gz
-      URL_MD5 9f66efc128da33039e30659f36fc6d00
-      BUILD_IN_SOURCE 1
-      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+      URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.1.txz
+      URL_MD5 289c57f0c3bc2a549662283cac1c4ef1
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
       )
     ExternalProject_get_property(kim_build INSTALL_DIR)
-    set(KIM_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v1)
-    set(KIM_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v1.so)
+    set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
+    set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api-v2${CMAKE_SHARED_LIBRARY_SUFFIX})
     list(APPEND LAMMPS_DEPS kim_build)
   else()
-    find_package(KIM)
-    if(NOT KIM_FOUND)
-      message(FATAL_ERROR "KIM-API v1 not found, help CMake to find it by setting KIM_LIBRARY and KIM_INCLUDE_DIR, or set DOWNLOAD_KIM=ON to download it")
+    find_package(KIM-API-V2)
+    if(NOT KIM-API-V2_FOUND)
+      message(FATAL_ERROR "KIM-API v2 not found, help CMake to find it by setting PKG_CONFIG_PATH, or set DOWNLOAD_KIM=ON to download it")
     endif()
   endif()
-  list(APPEND LAMMPS_LINK_LIBS ${KIM_LIBRARIES})
-  include_directories(${KIM_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API-V2_LDFLAGS}")
+  include_directories(${KIM-API-V2_INCLUDE_DIRS})
 endif()
 
 if(PKG_MESSAGE)
@@ -756,7 +779,7 @@ 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 - ${HEADER}")
@@ -826,7 +849,7 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB REAX MEAM POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
+foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-COLVARS USER-H5MD
   USER-QMMM)
   if(PKG_${SIMPLE_LIB})
     string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
@@ -856,6 +879,9 @@ if(PKG_USER-AWPMD)
 endif()
 
 if(PKG_USER-ATC)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
   target_link_libraries(atc ${LAPACK_LIBRARIES})
 endif()
 
@@ -1322,7 +1348,7 @@ if(BUILD_LIB)
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_LIB_SUFFIX}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
   configure_file(FindLAMMPS.cmake.in ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake @ONLY)
-  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Module)
+  install(FILES ${CMAKE_CURRENT_BINARY_DIR}/FindLAMMPS${LAMMPS_LIB_SUFFIX}.cmake DESTINATION ${CMAKE_INSTALL_DATADIR}/cmake/Modules)
 else()
   list(APPEND LMP_SOURCES ${LIB_SOURCES})
 endif()
@@ -1346,6 +1372,7 @@ if(BUILD_EXE)
   endif()
 endif()
 
+
 ###############################################################################
 # Build documentation
 ###############################################################################

cmake/Modules/FindKIM-API-V2.cmake

@@ -0,0 +1,50 @@
+#
+# CDDL HEADER START
+#
+# The contents of this file are subject to the terms of the Common Development
+# and Distribution License Version 1.0 (the "License").
+#
+# You can obtain a copy of the license at
+# http://www.opensource.org/licenses/CDDL-1.0.  See the License for the
+# specific language governing permissions and limitations under the License.
+#
+# When distributing Covered Code, include this CDDL HEADER in each file and
+# include the License file in a prominent location with the name LICENSE.CDDL.
+# If applicable, add the following below this CDDL HEADER, with the fields
+# enclosed by brackets "[]" replaced with your own identifying information:
+#
+# Portions Copyright (c) [yyyy] [name of copyright owner]. All rights reserved.
+#
+# CDDL HEADER END
+#
+
+#
+# Copyright (c) 2013--2018, Regents of the University of Minnesota.
+# All rights reserved.
+#
+# Contributors:
+#    Richard Berger
+#    Christoph Junghans
+#    Ryan S. Elliott
+#
+
+# - Find KIM-API-V2
+#
+# sets standard pkg_check_modules variables plus:
+#
+# KIM-API-V2-CMAKE_C_COMPILER
+# KIM-API-V2-CMAKE_CXX_COMPILER
+# KIM-API-V2-CMAKE_Fortran_COMPILER
+#
+find_package(PkgConfig REQUIRED)
+include(FindPackageHandleStandardArgs)
+
+pkg_check_modules(KIM-API-V2 REQUIRED libkim-api-v2>=2.0)
+
+pkg_get_variable(KIM-API-V2-CMAKE_C_COMPILER libkim-api-v2 CMAKE_C_COMPILER)
+pkg_get_variable(KIM-API-V2-CMAKE_CXX_COMPILER libkim-api-v2 CMAKE_CXX_COMPILER)
+pkg_get_variable(KIM-API-V2_CMAKE_Fortran_COMPILER libkim-api-v2 CMAKE_Fortran_COMPILER)
+
+# handle the QUIETLY and REQUIRED arguments and set KIM-API-V2_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(KIM-API-V2 REQUIRED_VARS KIM-API-V2_LIBRARIES)

cmake/Modules/FindKIM.cmake

@@ -1,22 +0,0 @@
-# - Find kim
-# Find the native KIM headers and libraries.
-#
-#  KIM_INCLUDE_DIRS - where to find kim.h, etc.
-#  KIM_LIBRARIES    - List of libraries when using kim.
-#  KIM_FOUND        - True if kim found.
-#
-
-find_path(KIM_INCLUDE_DIR KIM_API.h PATH_SUFFIXES kim-api-v1)
-
-find_library(KIM_LIBRARY NAMES kim-api-v1)
-
-set(KIM_LIBRARIES ${KIM_LIBRARY})
-set(KIM_INCLUDE_DIRS ${KIM_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set KIM_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(KIM DEFAULT_MSG KIM_LIBRARY KIM_INCLUDE_DIR)
-
-mark_as_advanced(KIM_INCLUDE_DIR KIM_LIBRARY )

cmake/Modules/StyleHeaderUtils.cmake

@@ -50,6 +50,7 @@ function(CreateStyleHeader path filename)
         list(REMOVE_AT ARGV 0 1)
         set(header_list)
         foreach(FNAME ${ARGV})
+            set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
             get_filename_component(FNAME ${FNAME} NAME)
             list(APPEND header_list ${FNAME})
         endforeach()
@@ -61,6 +62,7 @@ function(CreateStyleHeader path filename)
     message(STATUS "Generating ${filename}...")
     file(WRITE "${path}/${filename}.tmp" "${temp}" )
     execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${path}/${filename}.tmp" "${path}/${filename}")
+    set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${path}/${filename}")
 endfunction(CreateStyleHeader)
 
 function(GenerateStyleHeader path property style)

cmake/README.md

@@ -24,7 +24,7 @@ tasks, act as a reference and provide examples of typical use cases.
       * [Build directory vs. Source Directory](#build-directory-vs-source-directory)
    * [Defining and using presets](#defining-and-using-presets)
    * [Reference](#reference)
-      * [Common CMAKE Configuration Options](#common-cmake-configuration-options)
+      * [Common CMake Configuration Options](#common-cmake-configuration-options)
       * [LAMMPS Configuration Options](#lammps-configuration-options)
       * [Parallelization and Accelerator Packages](#parallelization-and-accelerator-packages)
       * [Default Packages](#default-packages)
@@ -179,7 +179,7 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
 
 # Reference
 
-## Common CMAKE Configuration Options
+## Common CMake Configuration Options
 
 
 <table>
@@ -208,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code><CMAKE_VERBOSE_MAKEFILE/code></td>
+  <td>Enable verbose output from Makefile builds (useful for debugging), the same can be achived by adding `VERBOSE=1` to the `make` call.</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 </tbody>
 </table>
 
@@ -1729,6 +1739,13 @@ cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
   value of `FC` environment variable at first `cmake` run
   </td>
 </tr>
+<tr>
+  <td><code>CXX_COMPILER_LAUNCHER</code></td>
+  <td>CMake will run this tool and pass the compiler and its arguments to the tool. Some example tools are distcc and ccache.</td>
+  <td>
+  (empty)
+  </td>
+</tr>
 </tbody>
 </table>
 

doc/.gitignore

@@ -1,4 +1,6 @@
+/old
 /html
+/latex
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi

doc/Makefile

@@ -39,7 +39,7 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
 	@echo "  pdf        create Developer.pdf and Manual.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  old        create old-style HTML doc pages and Manual.pdf in old dir"
 	@echo "  fetch      fetch HTML and PDF files from LAMMPS web site"
 	@echo "  epub       create ePUB format manual for e-book readers"
 	@echo "  mobi       convert ePUB to MOBI format manual for e-book readers (e.g. Kindle)"
@@ -48,6 +48,7 @@ help:
 	@echo "  clean-all  reset the entire build environment"
 	@echo "  txt2html   build txt2html tool"
 	@echo "  anchor_check  scan for duplicate anchor labels"
+	@echo "  spelling   spell-check the manual"
 
 # ------------------------------------------
 
@@ -55,7 +56,7 @@ clean-all: clean
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html old epub
+	rm -rf $(RSTDIR) html old epub latex
 	rm -rf spelling
 
 clean-spelling:
@@ -114,21 +115,44 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: utils/txt2html/txt2html.exe
+pdf: $(OBJECTS) $(ANCHORCHECK)
+	@(\
+                . $(VENV)/bin/activate ;\
+                cp -r src/* $(RSTDIR)/ ;\
+                sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+                echo "############################################" ;\
+                doc_anchor_check src/*.txt ;\
+                echo "############################################" ;\
+                deactivate ;\
+	)
+	@cd latex && \
+          sed 's/latexmk -pdf -dvi- -ps-/pdflatex/g' Makefile > temp && \
+	  mv temp Makefile && \
+	  sed 's/\\begin{equation}//g' LAMMPS.tex > tmp.tex && \
+	  mv tmp.tex LAMMPS.tex && \
+	  sed 's/\\end{equation}//g' LAMMPS.tex > tmp.tex && \
+	  mv tmp.tex LAMMPS.tex && \
+	  make && \
+	  make && \
+	  mv LAMMPS.pdf ../Manual.pdf && \
+	  cd ../; 
 	@(\
-		set -e; \
 		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
-		cd ..; \
-		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q ^$$s lammps.book || \
-			echo WARNING: doc file $$s missing in src/lammps.book; done; \
-		rm *.html; \
+		cd ../../; \
 	)
+	@rm -rf latex/_sources
+	@rm -rf latex/PDF
+	@rm -rf latex/USER
+	@cp -r src/PDF latex/PDF
+	@cp -r src/USER latex/USER
+	@rm -rf latex/PDF/.[sg]*
+	@rm -rf latex/USER/.[sg]*
+	@rm -rf latex/USER/*/.[sg]*
+	@rm -rf latex/USER/*/*.[sg]*
+	@echo "Build finished. Manual.pdf and Developer.pdf are in this directory."
 
 old: utils/txt2html/txt2html.exe
 	@rm -rf old
@@ -138,6 +162,18 @@ old: utils/txt2html/txt2html.exe
 	  cp Eqs/*.jpg ../old/Eqs; \
 	  cp JPG/* ../old/JPG; \
 	  cp PDF/* ../old/PDF;
+	@(      set -e;\
+		cd src/Developer; \
+		pdflatex developer; \
+		pdflatex developer; \
+		mv developer.pdf ../../old/Developer.pdf; \
+		cd ../../old; \
+	        for s in `echo ../src/*.txt | sed -e 's,\.\./src/,,g' -e 's/ \(pairs\|bonds\|angles\|dihedrals\|impropers\|commands_list\|fixes\|computes\).txt/ /g' | sed -e 's,\.txt,\.html,g'` ; \
+			do grep -q ^$$s ../src/lammps.book || \
+			echo WARNING: doc file $$s missing in src/lammps.book; done; \
+		htmldoc --batch ../src/lammps.book;          \
+	)
+
 
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf

doc/github-development-workflow.md

@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2018-11-15.
+adapt accordingly. Last change 2018-12-19.
 
 ## Table of Contents
 
@@ -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
@@ -129,16 +132,17 @@ Here are some items to check:
     * stdlib.h -> cstdlib
     * string.h -> cstring
     * time.h -> ctime
-  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
+    * Do NOT replace (as they are C++-11): `inttypes.h` and `stdint.h`.
   * Code should follow the C++-98 standard. C++-11 is only accepted
   in individual special purpose packages
-  * indentation is two spaces per level
-  * there should be no tabs and no trailing whitespace
+  * indentation is 2 spaces per level
+  * there should be NO tabs and no trailing whitespace
   * header files, especially of new styles, should not include any
   other headers, except the header with the base class or cstdio.
   Forward declarations should be used instead when possible.
   * iostreams should be avoided. LAMMPS uses stdio from the C-library.
   * use of STL in headers and class definitions should be avoided.
+  * there MUST NOT be any "using namespace XXX;" statements in headers.
   * static class members should be avoided at all cost.
   * anything storing atom IDs should be using `tagint` and not `int`.
   This can be flagged by the compiler only for pointers and only when

doc/src/Build_basics.txt

@@ -116,6 +116,18 @@ enables OpenMP. For GNU compilers it is -fopenmp.  For (recent) Intel
 compilers it is -qopenmp.  If you are using a different compiler,
 please refer to its documentation.
 
+[OpenMP Compiler compatibility info]: :link(default-none-issues)
+
+Some compilers do not fully support the 'default(none)' directive
+and others (e.g. GCC version 9 and beyond) may implement OpenMP 4.0
+semantics, which are incompatible with the OpenMP 3.1 directives used
+in LAMMPS (for maximal compatibility with compiler versions in use).
+In those case, all 'default(none)' directives (which aid in detecting
+incorrect and unwanted sharing) can be replaced with 'default(shared)'
+while dropping all 'shared()' directives. The script
+'src/USER-OMP/hack_openmp_for_pgi_gcc9.sh' can be used to automate
+this conversion.
+
 :line
 
 Choice of compiler and compile/link options :h4,link(compile)

doc/src/Build_extras.txt

@@ -36,8 +36,8 @@ This is the list of packages that may require additional steps.
 "OPT"_#opt,
 "POEMS"_#poems,
 "PYTHON"_#python,
-"REAX"_#reax,
 "VORONOI"_#voronoi,
+"USER-ADIOS"_#user-adios,
 "USER-ATC"_#user-atc,
 "USER-AWPMD"_#user-awpmd,
 "USER-COLVARS"_#user-colvars,
@@ -96,6 +96,7 @@ 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)
@@ -136,7 +137,7 @@ 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:
 
@@ -191,16 +192,12 @@ package?" page.
 
 [CMake build]:
 
--D DOWNLOAD_KIM=value    # download OpenKIM API v1 for build, value = no (default) or yes
--D KIM_LIBRARY=path      # KIM library file (only needed if a custom location)
--D KIM_INCLUDE_DIR=path  # KIM include directory (only needed if a custom location) :pre
+-D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes :pre
 
 If DOWNLOAD_KIM is set, the KIM library will be downloaded and built
 inside the CMake build directory.  If the KIM library is already on
-your system (in a location CMake cannot find it), KIM_LIBRARY is the
-filename (plus path) of the KIM library file, not the directory the
-library file is in.  KIM_INCLUDE_DIR is the directory the KIM include
-file is in.
+your system (in a location CMake cannot find it), set the PKG_CONFIG_PATH
+environment variable so that libkim-api-v2 can be found.
 
 [Traditional make]:
 
@@ -214,8 +211,8 @@ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
 make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
 make lib-kim args="-b -a everything"     # install KIM API lib with all models
 make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-make lib-kim args="-p /usr/local/kim-api" # use an existing KIM API installation at the provided location
-make lib-kim args="-p /usr/local/kim-api -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
+make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver :pre
 
 :line
 
@@ -536,45 +533,6 @@ build fails.
 
 :line
 
-REAX package :h4,link(reax)
-
-NOTE: the use of the REAX package and its "pair_style
-reax"_pair_reax.html command is discouraged, as it is no longer
-maintained.  Please use the USER-REAXC package and its "pair_style
-reax/c"_pair_reaxc.html command instead, and possibly its KOKKOS
-enabled variant (pair_style reax/c/kk), which has a more robust memory
-management.  See the "pair_style reax/c"_pair_reaxc.html doc page for
-details.
-
-[CMake build]:
-
-No additional settings are needed besides "-D PKG_REAX=yes".
-
-[Traditional make]:
-
-Before building LAMMPS, you must build the REAX library in lib/reax.
-You can do this manually if you prefer; follow the instructions in
-lib/reax/README.  You can also do it in one step from the lammps/src
-dir, using a command like these, which simply invoke the
-lib/reax/Install.py script with the specified args:
-
-make lib-reax                    # print help message
-make lib-reax args="-m serial"   # build with GNU Fortran compiler (settings as with "make serial")
-make lib-reax args="-m mpi"      # build with default MPI Fortran compiler (settings as with "make mpi")
-make lib-reax args="-m ifort"    # build with Intel ifort compiler :pre
-
-The build should produce two files: lib/reax/libreax.a and
-lib/reax/Makefile.lammps.  The latter is copied from an existing
-Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with
-Fortran (REAX library).  Typically the two compilers used for LAMMPS
-and the REAX library need to be consistent (e.g. both Intel or both
-GNU compilers).  If necessary, you can edit/create a new
-lib/reax/Makefile.machine file for your system, which should define an
-EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine
-file.
-
-:line
-
 VORONOI package :h4,link(voronoi)
 
 To build with this package, you must download and build the "Voro++
@@ -615,14 +573,40 @@ the lib/voronoi/Makefile.lammps file.
 
 :line
 
+USER-ADIOS package :h4,link(user-adios)
+
+The USER-ADIOS package requires the "ADIOS I/O library"_https://github.com/ornladios/ADIOS2,
+version 2.3.1 or newer. Make sure that you have ADIOS built either with or
+without MPI to match if you build LAMMPS with or without MPI.
+ADIOS compilation settings for LAMMPS are automatically detected, if the PATH
+and LD_LIBRARY_PATH environment variables have been updated for the local ADIOS
+installation and the instructions below are followed for the respective build systems.
+
+[CMake build]:
+
+-D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
+-D PKG_USER-ADIOS=yes     :pre
+
+[Traditional make]:
+
+Turn on the USER-ADIOS package before building LAMMPS. If the ADIOS 2.x software is installed in PATH, there is nothing else to do:
+
+make yes-user-adios                       :pre
+
+otherwise, set ADIOS2_DIR environment variable when turning on the package:
+
+ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed :pre
+
+:line
+
 USER-ATC package :h4,link(user-atc)
 
 The USER-ATC package requires the MANYBODY package also be installed.
 
 [CMake build]:
 
-No additional settings are needed besides "-D PKG_REAX=yes" and "-D
-PKG_MANYBODY=yes".
+No additional settings are needed besides "-D PKG_USER-ATC=yes"
+and "-D PKG_MANYBODY=yes".
 
 [Traditional make]:
 
@@ -971,7 +955,9 @@ LINKFLAGS: -fopenmp             # for GNU Compilers
 LINKFLAGS: -qopenmp             # for Intel compilers on Linux :pre
 
 For other platforms and compilers, please consult the documentation
-about OpenMP support for your compiler.
+about OpenMP support for your compiler. Please see the note about
+how to address compatibility "issues with the 'default(none)'
+directive"_Build_basics.html#default-none-issues of some compilers.
 
 :line
 

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/Build_package.txt

@@ -47,8 +47,8 @@ packages:
 "OPT"_Build_extras.html#opt,
 "POEMS"_Build_extras.html#poems,
 "PYTHON"_Build_extras.html#python,
-"REAX"_Build_extras.html#reax,
 "VORONOI"_Build_extras.html#voronoi,
+"USER-ADIOS"_Build_extras.html#user-adios,
 "USER-ATC"_Build_extras.html#user-atc,
 "USER-AWPMD"_Build_extras.html#user-awpmd,
 "USER-COLVARS"_Build_extras.html#user-colvars,

doc/src/Commands_all.txt

@@ -48,12 +48,14 @@ An alphabetic list of all general LAMMPS commands.
 "dimension"_dimension.html,
 "displace_atoms"_displace_atoms.html,
 "dump"_dump.html,
+"dump adios"_dump_adios.html,
 "dump image"_dump_image.html,
 "dump_modify"_dump_modify.html,
 "dump movie"_dump_image.html,
 "dump netcdf"_dump_netcdf.html,
 "dump netcdf/mpiio"_dump_netcdf.html,
 "dump vtk"_dump_vtk.html,
+"dynamical_matrix"_dynamical_matrix.html,
 "echo"_echo.html,
 "fix"_fix.html,
 "fix_modify"_fix_modify.html,

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_fix.txt

@@ -169,8 +169,7 @@ OPT.
 "qmmm"_fix_qmmm.html,
 "qtb"_fix_qtb.html,
 "rattle"_fix_shake.html,
-"reax/bonds"_fix_reax_bonds.html,
-"reax/c/bonds (k)"_fix_reax_bonds.html,
+"reax/c/bonds (k)"_fix_reaxc_bonds.html,
 "reax/c/species (k)"_fix_reaxc_species.html,
 "recenter"_fix_recenter.html,
 "restrain"_fix_restrain.html,

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,
@@ -107,38 +107,42 @@ OPT.
 "kolmogorov/crespi/full"_pair_kolmogorov_crespi_full.html,
 "kolmogorov/crespi/z"_pair_kolmogorov_crespi_z.html,
 "lcbop"_pair_lcbop.html,
+"lebedeva/z"_pair_lebedeva_z.html,
 "lennard/mdf"_pair_mdf.html,
 "line/lj"_pair_line_lj.html,
 "list"_pair_list.html,
 "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,
@@ -153,6 +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,
@@ -160,8 +165,7 @@ OPT.
 "lubricateU/poly"_pair_lubricateU.html,
 "mdpd"_pair_meso.html,
 "mdpd/rhosum"_pair_meso.html,
-"meam"_pair_meam.html,
-"meam/c"_pair_meam.html,
+"meam/c"_pair_meamc.html,
 "meam/spline (o)"_pair_meam_spline.html,
 "meam/sw/spline"_pair_meam_sw_spline.html,
 "mgpt"_pair_mgpt.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,
@@ -194,7 +198,6 @@ OPT.
 "polymorphic"_pair_polymorphic.html,
 "python"_pair_python.html,
 "quip"_pair_quip.html,
-"reax"_pair_reax.html,
 "reax/c (ko)"_pair_reaxc.html,
 "rebo (io)"_pair_airebo.html,
 "resquared (go)"_pair_resquared.html,
@@ -230,7 +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_common.txt

@@ -74,7 +74,7 @@ is an integer or floating-point number, respectively, and reject the
 input with an error message (for instance, when an integer is required,
 but a floating-point number 1.0 is provided):
 
-ERROR: Expected integer parameter in input script or data file :pre
+ERROR: Expected integer parameter instead of '1.0' in input script or data file :pre
 
 Some commands allow for using variable references in place of numeric
 constants so that the value can be evaluated and may change over the
@@ -85,6 +85,9 @@ reading the input and before parsing commands,
 
 NOTE: Using a variable reference (i.e. {v_name}) is only allowed if
 the documentation of the corresponding command explicitly says it is.
+Otherwise, you will receive an error message of this kind:
+
+ERROR: Expected floating point parameter instead of 'v_name' in input script or data file :pre
 
 Generally, LAMMPS will print a message to the screen and logfile and
 exit gracefully when it encounters a fatal error.  Sometimes it will

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
@@ -6988,12 +6988,6 @@ The atom style defined does not have this attribute. :dd
 
 The atom style defined does not have these attributes. :dd
 
-{KIM neighbor iterator exceeded range} :dt
-
-This should not happen.  It likely indicates a bug
-in the KIM implementation of the interatomic potential
-where it is requesting neighbors incorrectly. :dd
-
 {KOKKOS package does not yet support comm_style tiled} :dt
 
 Self-explanatory. :dd
@@ -10185,10 +10179,6 @@ valid. :dd
 
 Self-explanatory. :dd
 
-{Unrecognized virial argument in pair_style command} :dt
-
-Only two options are supported: LAMMPSvirial and KIMvirial :dd
-
 {Unsupported mixing rule in kspace_style ewald/disp} :dt
 
 Only geometric mixing is supported. :dd

doc/src/Errors_warnings.txt

@@ -178,12 +178,6 @@ When using fixes like box/relax, the potential energy used by the minimizer
 is augmented by an additional energy provided by the fix. Thus the printed
 converged energy may be different from the total potential energy. :dd
 
-{Energy tally does not account for 'zero yes'} :dt
-
-The energy removed by using the 'zero yes' flag is not accounted
-for in the energy tally and thus energy conservation cannot be
-monitored in this case. :dd
-
 {Estimated error in splitting of dispersion coeffs is %g} :dt
 
 Error is greater than 0.0001 percent. :dd

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_linux.txt

@@ -15,7 +15,7 @@ Binaries are available for different versions of Linux:
 "Pre-built Fedora Linux executables"_#fedora
 "Pre-built EPEL Linux executables (RHEL, CentOS)"_#epel
 "Pre-built OpenSuse Linux executables"_#opensuse
-"Pre-built Gentoo Linux executable"_#gentoo :all(b)
+"Gentoo Linux executable"_#gentoo :all(b)
 
 :line
 
@@ -87,11 +87,11 @@ linking to the C library interface (lammps-devel, lammps-mpich-devel,
 lammps-openmpi-devel), the header for compiling programs using
 the C library interface (lammps-headers), and the LAMMPS python
 module for Python 3. All packages can be installed at the same
-time and the name of the LAMMPS executable is {lmp} in all 3 cases.
-By default, {lmp} will refer to the serial executable, unless
-one of the MPI environment modules is loaded
+time and the name of the LAMMPS executable is {lmp} and {lmp_openmpi}
+or {lmp_mpich} respectively.  By default, {lmp} will refer to the
+serial executable, unless one of the MPI environment modules is loaded
 ("module load mpi/mpich-x86_64" or "module load mpi/openmpi-x86_64").
-Then the corresponding parallel LAMMPS executable is used.
+Then the corresponding parallel LAMMPS executable can be used.
 The same mechanism applies when loading the LAMMPS python module.
 
 To install LAMMPS with OpenMPI and run an input in.lj with 2 CPUs do:
@@ -150,7 +150,7 @@ Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
 
 :line
 
-Pre-built Gentoo Linux executable :h4,link(gentoo)
+Gentoo Linux executable :h4,link(gentoo)
 
 LAMMPS is part of Gentoo's main package tree and can be installed by
 typing:

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
@@ -23,8 +23,8 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
 needed to run in parallel.
 
 The LAMMPS binaries contain all optional packages included in the
-source distribution except: KIM, REAX, KOKKOS, USER-INTEL,
-and USER-QMMM.  The serial version also does not include the MPIIO and
+source distribution except: KIM, KOKKOS, USER-INTEL, and USER-QMMM.
+The serial version also does not include the MPIIO and
 USER-LB packages.  GPU support is provided for OpenCL.
 
 The installer site also has instructions on how to run LAMMPS under
@@ -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

@@ -15,8 +15,8 @@ functionality for setting up simulations and analyzing their output.
 
 Specifically, LAMMPS was not conceived and designed for:
 
-being run thru a GUI
-build molecular systems, or building molecular topologies
+being run through a GUI
+building molecular systems, or building molecular topologies
 assign force-field coefficients automagically
 perform sophisticated analysis of your MD simulation
 visualize your MD simulation interactively
@@ -24,18 +24,18 @@ plot your output data :ul
 
 Although over the years these limitations have been somewhat
 reduced through features added to LAMMPS or external tools
-that either interface with LAMMPS or extend LAMMPS.
+that either closely interface with LAMMPS or extend LAMMPS.
 
 Here are suggestions on how to perform these tasks:
 
-GUI: LAMMPS can be built as a library and a Python wrapper that wraps
+[GUI:] LAMMPS can be built as a library and a Python wrapper that wraps
 the library interface is provided.  Thus, GUI interfaces can be
 written in Python (or C or C++ if desired) that run LAMMPS and
 visualize or plot its output.  Examples of this are provided in the
 python directory and described on the "Python"_Python_head.html doc
-page.  Also, there are several external wrappers or GUI front ends.:ulb,l
+page.  Also, there are several external wrappers or GUI front ends. :ulb,l
 
-Builder: Several pre-processing tools are packaged with LAMMPS.  Some
+[Builder:] Several pre-processing tools are packaged with LAMMPS.  Some
 of them convert input files in formats produced by other MD codes such
 as CHARMM, AMBER, or Insight into LAMMPS input formats.  Some of them
 are simple programs that will build simple molecular systems, such as
@@ -45,15 +45,20 @@ the "Tools"_Tools.html doc page for details on tools packaged with
 LAMMPS.  The "Pre/post processing
 page"_http:/lammps.sandia.gov/prepost.html of the LAMMPS website
 describes a variety of 3rd party tools for this task.  Furthermore,
-some LAMMPS internal commands to reconstruct topology, as well as
-the option to insert molecule templates instead of atoms.:l
+some LAMMPS internal commands allow to reconstruct, or selectively add
+topology information, as well as provide the option to insert molecule
+templates instead of atoms for building bulk molecular systems. :l
 
-Force-field assignment: The conversion tools described in the previous
+[Force-field assignment:] The conversion tools described in the previous
 bullet for CHARMM, AMBER, and Insight will also assign force field
 coefficients in the LAMMPS format, assuming you provide CHARMM, AMBER,
-or BIOVIA (formerly Accelrys) force field files. :l
+or BIOVIA (formerly Accelrys) force field files. The tools
+"ParmEd"_https://parmed.github.io/ParmEd/html/index.html and
+"InterMol"_https://github.com/shirtsgroup/InterMol are particularly
+powerful and flexible in converting force field and topology data
+between various MD simulation programs.  :l
 
-Simulation analysis: If you want to perform analysis on-the-fly as
+[Simulation analysis:] If you want to perform analysis on-the-fly as
 your simulation runs, see the "compute"_compute.html and
 "fix"_fix.html doc pages, which list commands that can be used in a
 LAMMPS input script.  Also see the "Modify"_Modify.html doc page for
@@ -71,22 +76,22 @@ tools/python directory can extract and massage data in dump files to
 make it easier to import into other programs.  See the
 "Tools"_Tools.html doc page for details on these various options. :l
 
-Visualization: LAMMPS can produce JPG or PNG snapshot images
+[Visualization:] LAMMPS can produce NETPBM, JPG or PNG snapshot images
 on-the-fly via its "dump image"_dump_image.html command and pass
-them to an external program FFmpeg to generate movies from them.  For
-high-quality, interactive visualization there are many excellent and
-free tools available.  See the "Other Codes
+them to an external program, "FFmpeg"_https://www.ffmpeg.org to generate
+movies from them.  For high-quality, interactive visualization there are
+many excellent and free tools available.  See the "Other Codes
 page"_http://lammps.sandia.gov/viz.html page of the LAMMPS website for
 visualization packages that can use LAMMPS output data. :l
 
-Plotting: See the next bullet about Pizza.py as well as the
+[Plotting:] See the next bullet about Pizza.py as well as the
 "Python"_Python_head.html doc page for examples of plotting LAMMPS
 output.  Scripts provided with the {python} tool in the tools
 directory will extract and massage data in log and dump files to make
 it easier to analyze and plot.  See the "Tools"_Tools.html doc page
 for more discussion of the various tools. :l
 
-Pizza.py: Our group has also written a separate toolkit called
+[Pizza.py:] Our group has also written a separate toolkit called
 "Pizza.py"_http://pizza.sandia.gov which can do certain kinds of
 setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
 simulations.  It thus provides some functionality for several of the

doc/src/Manual.txt

@@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="7 Dec 2018 version">
+<META NAME="docnumber" CONTENT="28 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
-7 Dec 2018 version :c,h2
+28 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/Manual_build.txt

@@ -65,6 +65,8 @@ make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make mobi         # generate LAMMPS.mobi in MOBI format using ebook-convert
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data :pre
+make anchor_check # check for duplicate anchor labels
+make spelling     # spell-check the manual
 
 :line
 
@@ -106,7 +108,14 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
+Building the PDF manual requires a working C++ compiler (to
+compile the txt2html tool and a working installation of
+"HTMLDOC"_https://www.msweet.org/htmldoc/
+HTMLDOC has its own list of prerequisites, but in most cases
+you can install a binary package of it either through your
+Linux package manager or MacOS (dmg) and Windows installer
+(msi) packages from its
+"GitHub releases page at"_https://github.com/michaelrsweet/htmldoc/releases
 
 :line
 

doc/src/Modify_contribute.txt

@@ -108,9 +108,13 @@ 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.
+the C-style stdio library (mixing of stdio and iostreams is generally
+discouraged), class header files should not import any system headers
+outside of <cstdio>, STL containers should be avoided in headers,
+system header from the C library should use the C++-style names
+(<cstdlib>, <cstdio>, or <cstring>) instead of the C-style names
+<stdlib.h>, <stdio.h>, or <string.h>), and forward declarations
+used where possible or needed to avoid including headers.
 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.

doc/src/Packages_details.txt

@@ -45,7 +45,6 @@ as contained in the file name.
 "LATTE"_#PKG-LATTE,
 "MANYBODY"_#PKG-MANYBODY,
 "MC"_#PKG-MC,
-"MEAM"_#PKG-MEAM,
 "MESSAGE"_#PKG-MESSAGE,
 "MISC"_#PKG-MISC,
 "MOLECULE"_#PKG-MOLECULE,
@@ -56,7 +55,6 @@ as contained in the file name.
 "POEMS"_#PKG-POEMS,
 "PYTHON"_#PKG-PYTHON,
 "QEQ"_#PKG-QEQ,
-"REAX"_#PKG-REAX,
 "REPLICA"_#PKG-REPLICA2,
 "RIGID"_#PKG-RIGID,
 "SHOCK"_#PKG-SHOCK,
@@ -65,6 +63,7 @@ as contained in the file name.
 "SRD"_#PKG-SRD,
 "VORONOI"_#PKG-VORONOI :tb(c=6,ea=c)
 
+"USER-ADIOS"_#PKG-USER-ADIOS,
 "USER-ATC"_#PKG-USER-ATC,
 "USER-AWPMD"_#PKG-USER-AWPMD,
 "USER-BOCS"_#PKG-USER-BOCS,
@@ -102,7 +101,8 @@ 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
 
@@ -347,12 +347,11 @@ system.
 
 Information about the KIM project can be found at its website:
 https://openkim.org.  The KIM project is led by Ellad Tadmor and Ryan
-Elliott (U Minnesota) and James Sethna (Cornell U).
+Elliott (U Minnesota).
 
 [Authors:] Ryan Elliott (U Minnesota) is the main developer for the KIM
 API which the "pair_style kim"_pair_kim.html command uses.  He
-developed the pair style in collaboration with Valeriu Smirichinski (U
-Minnesota).
+developed the pair style.
 
 [Install:]
 
@@ -533,37 +532,6 @@ http://lammps.sandia.gov/movies.html#gcmc :ul
 
 :line
 
-MEAM package :link(PKG-MEAM),h4
-
-[Contents:]
-
-A pair style for the modified embedded atom (MEAM) potential.
-
-Please note that the use of the MEAM package is discouraged as
-it has been superseded by the "USER-MEAMC"_#PKG-USER-MEAMC package,
-which is a direct translation of the MEAM package to C++.
-USER-MEAMC contains additional optimizations making it run faster
-than MEAM on most machines, while providing the identical features
-and user interface.
-
-[Author:] Greg Wagner (Northwestern U) while at Sandia.
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/MEAM: filenames -> commands
-src/meam/README
-lib/meam/README
-"pair_style meam"_pair_meam.html
-examples/meam :ul
-
-:line
-
 MESSAGE package :link(PKG-MESSAGE),h4
 
 [Contents:]
@@ -834,38 +802,6 @@ examples/streitz :ul
 
 :line
 
-REAX package :link(PKG-REAX),h4
-
-[Contents:]
-
-NOTE: the use of the REAX package is discouraged, as it is no longer
-maintained. Please use the "USER-REAXC"_#PKG-USER-REAXC package instead,
-and possibly the KOKKOS enabled variant of that, which has a more robust
-memory management.
-
-A pair style which wraps a Fortran library which implements the ReaxFF
-potential, which is a universal reactive force field.  Also included is
-a "fix reax/bonds"_fix_reax_bonds.html command for monitoring molecules
-as bonds are created and destroyed.
-
-[Author:] Aidan Thompson (Sandia).
-
-[Install:]
-
-This package has "specific installation
-instructions"_Build_extras.html#gpu on the "Build
-extras"_Build_extras.html doc page.
-
-[Supporting info:]
-
-src/REAX: filenames -> commands
-lib/reax/README
-"pair_style reax"_pair_reax.html
-"fix reax/bonds"_fix_reax_bonds.html
-examples/reax :ul
-
-:line
-
 REPLICA package :link(PKG-REPLICA2),h4
 
 [Contents:]
@@ -1039,6 +975,31 @@ examples/voronoi :ul
 
 :line
 
+USER-ADIOS package :link(PKG-USER-ADIOS),h4
+
+[Contents:]
+
+ADIOS is a high-performance I/O library. This package implements the 
+dump "atom/adios" and dump "custom/adios" commands to write data using
+the ADIOS library. 
+
+[Authors:] Norbert Podhorszki (ORNL) from the ADIOS developer team.
+
+[Install:]
+
+This package has "specific installation
+instructions"_Build_extras.html#user-adios on the "Build
+extras"_Build_extras.html doc page.
+
+[Supporting info:]
+
+src/USER-ADIOS: filenames -> commands
+src/USER-ADIOS/README
+examples/USER/adios
+https://github.com/ornladios/ADIOS2 :ul
+
+:line
+
 USER-ATC package :link(PKG-USER-ATC),h4
 
 [Contents:]
@@ -1370,7 +1331,7 @@ 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
@@ -1552,10 +1513,9 @@ USER-MEAMC package :link(PKG-USER-MEAMC),h4
 [Contents:]
 
 A pair style for the modified embedded atom (MEAM) potential
-translated from the Fortran version in the "MEAM"_#PKG-MEAM package
-to plain C++. In contrast to the MEAM package, no library
-needs to be compiled and the pair style can be instantiated
-multiple times.
+translated from the Fortran version in the (obsolete) "MEAM" package
+to plain C++. The USER-MEAMC fully replaces the MEAM package, which
+has been removed from LAMMPS after the 12 December 2018 version.
 
 [Author:] Sebastian Huetter, (Otto-von-Guericke University Magdeburg)
 based on the Fortran version of Greg Wagner (Northwestern U) while at
@@ -1565,8 +1525,8 @@ Sandia.
 
 src/USER-MEAMC: filenames -> commands
 src/USER-MEAMC/README
-"pair_style meam/c"_pair_meam.html
-examples/meam :ul
+"pair_style meam/c"_pair_meamc.html
+examples/meamc :ul
 
 :line
 
@@ -1765,14 +1725,19 @@ USER-PHONON package :link(PKG-USER-PHONON),h4
 A "fix phonon"_fix_phonon.html command that calculates dynamical
 matrices, which can then be used to compute phonon dispersion
 relations, directly from molecular dynamics simulations.
+And a "dynamical_matrix" command to compute the dynamical matrix
+from finite differences.
+
+[Authors:] Ling-Ti Kong (Shanghai Jiao Tong University) for "fix phonon"
+and Charlie Sievers (UC Davis) for "dynamical_matrix"
 
-[Author:] Ling-Ti Kong (Shanghai Jiao Tong University).
 
 [Supporting info:]
 
 src/USER-PHONON: filenames -> commands
 src/USER-PHONON/README
 "fix phonon"_fix_phonon.html
+"dynamical_matrix"_dynamical_matrix.html
 examples/USER/phonon :ul
 
 :line
@@ -1894,9 +1859,8 @@ USER-REAXC package :link(PKG-USER-REAXC),h4
 
 [Contents:]
 
-A pair style which implements the ReaxFF potential in C/C++ (in
-contrast to the "REAX package"_#PKG-REAX and its Fortran library).  ReaxFF
-is universal reactive force field.  See the src/USER-REAXC/README file
+A pair style which implements the ReaxFF potential in C/C++.  ReaxFF
+is a universal reactive force field.  See the src/USER-REAXC/README file
 for more info on differences between the two packages.  Also two fixes
 for monitoring molecules as bonds are created and destroyed.
 
@@ -1907,7 +1871,7 @@ for monitoring molecules as bonds are created and destroyed.
 src/USER-REAXC: filenames -> commands
 src/USER-REAXC/README
 "pair_style reax/c"_pair_reaxc.html
-"fix reax/c/bonds"_fix_reax_bonds.html
+"fix reax/c/bonds"_fix_reaxc_bonds.html
 "fix reax/c/species"_fix_reaxc_species.html
 examples/reax :ul
 
@@ -2134,3 +2098,37 @@ 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_standard.txt

@@ -46,7 +46,6 @@ Package, Description, Doc page, Example, Library
 "LATTE"_Packages_details.html#PKG-LATTE, quantum DFTB forces via LATTE, "fix latte"_fix_latte.html, latte, ext
 "MANYBODY"_Packages_details.html#PKG-MANYBODY, many-body potentials, "pair_style tersoff"_pair_tersoff.html, shear, no
 "MC"_Packages_details.html#PKG-MC, Monte Carlo options, "fix gcmc"_fix_gcmc.html, n/a, no
-"MEAM"_Packages_details.html#PKG-MEAM, modified EAM potential, "pair_style meam"_pair_meam.html, meam, int
 "MESSAGE"_Packages_details.html#PKG-MESSAGE, client/server messaging, "message"_message.html, message, int
 "MISC"_Packages_details.html#PKG-MISC, miscellaneous single-file commands, n/a, no, no
 "MOLECULE"_Packages_details.html#PKG-MOLECULE, molecular system force fields, "Howto bioFF"_Howto_bioFF.html, peptide, no
@@ -57,7 +56,6 @@ Package, Description, Doc page, Example, Library
 "POEMS"_Packages_details.html#PKG-POEMS, coupled rigid body motion, "fix poems"_fix_poems.html, rigid, int
 "PYTHON"_Packages_details.html#PKG-PYTHON, embed Python code in an input script, "python"_python.html, python, sys
 "QEQ"_Packages_details.html#PKG-QEQ, QEq charge equilibration, "fix qeq"_fix_qeq.html, qeq, no
-"REAX"_Packages_details.html#PKG-REAX, ReaxFF potential (Fortran), "pair_style reax"_pair_reax.html, reax, int
 "REPLICA"_Packages_details.html#PKG-REPLICA2, multi-replica methods, "Howto replica"_Howto_replica.html, tad, no
 "RIGID"_Packages_details.html#PKG-RIGID, rigid bodies and constraints, "fix rigid"_fix_rigid.html, rigid, no
 "SHOCK"_Packages_details.html#PKG-SHOCK, shock loading methods, "fix msst"_fix_msst.html, n/a, no

doc/src/Packages_user.txt

@@ -38,6 +38,7 @@ int = internal library: provided with LAMMPS, but you may need to build it
 ext = external library: you will need to download and install it on your machine :ul
 
 Package, Description, Doc page, Example, Library
+"USER-ADIOS"_Packages_details.html#PKG-USER-ADIOS, dump output via ADIOS, "dump adios"_dump_adios.html, USER/adios, ext
 "USER-ATC"_Packages_details.html#PKG-USER-ATC, Atom-to-Continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
 "USER-AWPMD"_Packages_details.html#PKG-USER-AWPMD, wave packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
 "USER-BOCS"_Packages_details.html#PKG-USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, no
@@ -53,7 +54,7 @@ Package, Description, Doc page, Example, Library
 "USER-INTEL"_Packages_details.html#PKG-USER-INTEL, optimized Intel CPU and KNL styles,"Speed intel"_Speed_intel.html, "Benchmarks"_http://lammps.sandia.gov/bench.html, no
 "USER-LB"_Packages_details.html#PKG-USER-LB, Lattice Boltzmann fluid,"fix lb/fluid"_fix_lb_fluid.html, USER/lb, no
 "USER-MANIFOLD"_Packages_details.html#PKG-USER-MANIFOLD, motion on 2d surfaces,"fix manifoldforce"_fix_manifoldforce.html, USER/manifold, no
-"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meam.html, meam, no
+"USER-MEAMC"_Packages_details.html#PKG-USER-MEAMC, modified EAM potential (C++), "pair_style meam/c"_pair_meamc.html, meamc, no
 "USER-MESO"_Packages_details.html#PKG-USER-MESO, mesoscale DPD models, "pair_style edpd"_pair_meso.html, USER/meso, no
 "USER-MGPT"_Packages_details.html#PKG-USER-MGPT, fast MGPT multi-ion potentials, "pair_style mgpt"_pair_mgpt.html, USER/mgpt, no
 "USER-MISC"_Packages_details.html#PKG-USER-MISC, single-file contributions, USER-MISC/README, USER/misc, no
@@ -75,7 +76,8 @@ 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
 
@@ -485,9 +486,9 @@ README for more info on Pizza.py and how to use these scripts.
 
 reax tool :h4,link(reax_tool)
 
-The reax sub-directory contains stand-alond codes that can
-post-process the output of the "fix reax/bonds"_fix_reax_bonds.html
-command from a LAMMPS simulation using "ReaxFF"_pair_reax.html.  See
+The reax sub-directory contains stand-alone codes that can
+post-process the output of the "fix reax/c/bonds"_fix_reaxc_bonds.html
+command from a LAMMPS simulation using "ReaxFF"_pair_reaxc.html.  See
 the README.txt file for more info.
 
 These tools were written by Aidan Thompson at Sandia.

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/commands_list.txt

@@ -32,6 +32,7 @@ Commands :h1
    dimension
    displace_atoms
    dump
+   dump_adios
    dump_cfg_uef
    dump_h5md
    dump_image
@@ -39,6 +40,7 @@ Commands :h1
    dump_molfile
    dump_netcdf
    dump_vtk
+   dynamical_matrix
    echo
    fix
    fix_modify

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_group_group.txt

@@ -137,11 +137,12 @@ Not all pair styles can be evaluated in a pairwise mode as required by
 this compute.  For example, 3-body and other many-body potentials,
 such as "Tersoff"_pair_tersoff.html and
 "Stillinger-Weber"_pair_sw.html cannot be used.  "EAM"_pair_eam.html
-potentials only include the pair potential portion of the EAM
-interaction when used by this compute, not the embedding term.
+potentials will re-use previously computed embedding term contributions,
+so the computed pairwise forces and energies are based on the whole
+system and not valid if particles have been moved since.
 
-Not all Kspace styles support calculation of group/group interactions.
-The {ewald} and {pppm} styles do.
+Not all "Kspace styles"_kspace_style.html support the calculation of
+group/group interactions. The regular {ewald} and {pppm} styles do.
 
 [Related commands:] none
 

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_pair.txt

@@ -24,7 +24,7 @@ nsub = {n}-instance of a sub-style, if a pair style is used multiple times in a
 compute 1 all pair gauss
 compute 1 all pair lj/cut/coul/cut ecoul
 compute 1 all pair tersoff 2 epair
-compute 1 all pair reax :pre
+compute 1 all pair reax/c :pre
 
 [Description:]
 
@@ -60,8 +60,8 @@ corrections, even if they are enabled via the
 "pair_modify"_pair_modify.html command.
 
 Some pair styles tally additional quantities, e.g. a breakdown of
-potential energy into a dozen or so components is tallied by the
-"pair_style reax"_pair_reax.html command.  These values (1 or more)
+potential energy into 14 components is tallied by the "pair_style
+reax/c"_pair_reaxc.html command.  These values (1 or more)
 are stored as a global vector by this compute.  See the doc page for
 "individual pair styles"_pair_style.html for info on these values.