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

Step version string for next patch release

.github/CODEOWNERS

@@ -17,6 +17,8 @@ src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
+src/MESSAGE/*         @sjplimp
+src/SPIN/*            @julient31
 src/USER-CGDNA/*      @ohenrich
 src/USER-CGSDK/*      @akohlmey
 src/USER-COLVARS/*    @giacomofiorin
@@ -27,23 +29,92 @@ src/USER-MEAMC/*      @martok
 src/USER-MOFFF/*      @hheenen
 src/USER-MOLFILE/*    @akohlmey
 src/USER-NETCDF/*     @pastewka
+src/USER-PLUMED/*     @gtribello
 src/USER-PHONON/*     @lingtikong
+src/USER-PTM/*        @pmla
 src/USER-OMP/*        @akohlmey
 src/USER-QMMM/*       @akohlmey
 src/USER-REAXC/*      @hasanmetin
+src/USER-SCAFACOS/*   @rhalver
 src/USER-TALLY/*      @akohlmey
 src/USER-UEF/*        @danicholson
 src/USER-VTK/*        @rbberger
 
+
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
+src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/USER-MISC/fix_bond_react.*      @jrgissing
 src/USER-MISC/*_grem.*              @dstelter92
+src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+
+# core LAMMPS classes
+src/lammps.*              @sjplimp
+src/pointers.h            @sjplimp
+src/atom.*                @sjplimp
+src/atom_vec.*            @sjplimp
+src/angle.*               @sjplimp
+src/bond.*                @sjplimp
+src/comm*.*               @sjplimp
+src/compute.*             @sjplimp
+src/dihedral.*            @sjplimp
+src/domain.*              @sjplimp
+src/dump*.*               @sjplimp
+src/error.*               @sjplimp
+src/finish.*              @sjplimp
+src/fix.*                 @sjplimp
+src/force.*               @sjplimp
+src/group.*               @sjplimp
+src/improper.*            @sjplimp
+src/kspace.*              @sjplimp
+src/lmptyp.h              @sjplimp
+src/library.*             @sjplimp
+src/main.cpp              @sjplimp
+src/memory.*              @sjplimp
+src/modify.*              @sjplimp
+src/molecule.*            @sjplimp
+src/my_page.h             @sjplimp
+src/my_pool_chunk.h       @sjplimp
+src/npair*.*              @sjplimp
+src/ntopo*.*              @sjplimp
+src/nstencil*.*           @sjplimp
+src/neighbor.*            @sjplimp
+src/nbin*.*               @sjplimp
+src/neigh_*.*             @sjplimp
+src/output.*              @sjplimp
+src/pair.*                @sjplimp
+src/rcb.*                 @sjplimp
+src/random_*.*            @sjplimp
+src/region*.*             @sjplimp
+src/rcb.*                 @sjplimp
+src/read*.*               @sjplimp
+src/rerun.*               @sjplimp
+src/run.*                 @sjplimp
+src/respa.*               @sjplimp
+src/set.*                 @sjplimp
+src/special.*             @sjplimp
+src/suffix.h              @sjplimp
+src/thermo.*              @sjplimp
+src/universe.*            @sjplimp
+src/update.*              @sjplimp
+src/variable.*            @sjplimp
+src/verlet.*              @sjplimp
+src/velocity.*            @sjplimp
+src/write_data.*          @sjplimp
+src/write_restart.*       @sjplimp
+
+# overrides for specific files
+src/dump_movie.*          @akohlmey
+src/exceptions.h          @rbberger
+src/fix_nh.*              @athomps
+src/info.*                @akohlmey @rbberger
+src/timer.*               @akohlmey
 
 # tools
 tools/msi2lmp/*       @akohlmey
+tools/emacs/*         @HaoZeke
 
 # cmake
 cmake/*               @junghans @rbberger
@@ -55,3 +126,6 @@ python/*              @rbberger
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+
+# for releases
+src/version.h         @sjplimp

.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

@@ -2,11 +2,11 @@
 
 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 LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/tutorial_github.html)
+* [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/tutorial_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.
@@ -102,11 +102,11 @@ 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/tutorial_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here.
+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 be assigned to the LAMMPS lead developer, Steve Plimpton (@sjplimp), who will then have the final decision on whether the submission will be included, additional changes are required or it will be ultimately rejected. After the pull request is merged, you may delete the pull request branch in your personal LAMMPS fork.
-Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and not set in stone.
+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)_
+
+

.gitignore

@@ -1,6 +1,7 @@
 *~
 *.o
 *.so
+*.lo
 *.cu_o
 *.ptx
 *_ptx.h
@@ -21,6 +22,7 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*
@@ -32,6 +34,7 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 
 #cmake
 /build*

README

@@ -36,7 +36,14 @@ tools			   pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-doc/Manual.html	           the LAMMPS manual
-doc/Section_intro.html	   hi-level introduction to LAMMPS
-doc/Section_start.html	   how to build and use LAMMPS
-doc/Developer.pdf          LAMMPS developer guide
+http://lammps.sandia.gov/doc/Manual.html         the LAMMPS manual
+http://lammps.sandia.gov/doc/Intro.html          hi-level introduction
+http://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
+http://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
+http://lammps.sandia.gov/doc/Developer.pdf       LAMMPS developer guide
+
+You can also create these doc pages locally:
+
+% cd doc
+% make html                # creates HTML pages in doc/html
+% make pdf                 # creates Manual.pdf and Developer.pdf

cmake/FindLAMMPS.cmake.in

@@ -0,0 +1,48 @@
+# - Find liblammps
+# Find the native liblammps headers and libraries.
+#
+# The following variables will set:
+#  LAMMPS_INCLUDE_DIRS - where to find lammps/library.h, etc.
+#  LAMMPS_LIBRARIES    - List of libraries when using lammps.
+#  LAMMPS_API_DEFINES  - lammps library api defines
+#  LAMMPS_VERSION      - lammps library version 
+#  LAMMPS_FOUND        - True if liblammps found.
+#
+# In addition a LAMMPS::LAMMPS imported target is getting created.
+#
+#  LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+#  http://lammps.sandia.gov, Sandia National Laboratories
+#  Steve Plimpton, sjplimp@sandia.gov
+#
+#  Copyright (2003) Sandia Corporation.  Under the terms of Contract
+#  DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+#  certain rights in this software.  This software is distributed under
+#  the GNU General Public License.
+#
+#  See the README file in the top-level LAMMPS directory.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_LAMMPS liblammps@LAMMPS_LIB_SUFFIX@)
+find_path(LAMMPS_INCLUDE_DIR lammps/library.h HINTS ${PC_LAMMPS_INCLUDE_DIRS} @CMAKE_INSTALL_FULL_INCLUDEDIR@)
+
+set(LAMMPS_VERSION @LAMMPS_VERSION@)
+set(LAMMPS_API_DEFINES @LAMMPS_API_DEFINES@)
+
+find_library(LAMMPS_LIBRARY NAMES lammps@LAMMPS_LIB_SUFFIX@ HINTS ${PC_LAMMPS_LIBRARY_DIRS} @CMAKE_INSTALL_FULL_LIBDIR@)
+
+set(LAMMPS_INCLUDE_DIRS "${LAMMPS_INCLUDE_DIR}")
+set(LAMMPS_LIBRARIES "${LAMMPS_LIBRARY}")
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set LAMMPS_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(LAMMPS REQUIRED_VARS LAMMPS_LIBRARY LAMMPS_INCLUDE_DIR VERSION_VAR LAMMPS_VERSION)
+
+mark_as_advanced(LAMMPS_INCLUDE_DIR LAMMPS_LIBRARY)
+
+if(LAMMPS_FOUND AND NOT TARGET LAMMPS::LAMMPS)
+  add_library(LAMMPS::LAMMPS UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::LAMMPS PROPERTIES IMPORTED_LOCATION "${LAMMPS_LIBRARY}" INTERFACE_INCLUDE_DIRECTORIES "${LAMMPS_INCLUDE_DIR}" INTERFACE_COMPILE_DEFINITIONS "${LAMMPS_API_DEFINES}")
+endif()

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/FindQUIP.cmake

@@ -1,8 +1,8 @@
 # - Find quip
 # Find the native QUIP libraries.
 #
-#  QUIP_LIBRARIES    - List of libraries when using fftw3.
-#  QUIP_FOUND        - True if fftw3 found.
+#  QUIP_LIBRARIES    - List of libraries of the QUIP package
+#  QUIP_FOUND        - True if QUIP library was found.
 #
 
 find_library(QUIP_LIBRARY NAMES quip)

cmake/Modules/FindTBB.cmake

@@ -0,0 +1,46 @@
+# - Find parts of TBB
+# Find the native TBB headers and libraries.
+#
+#  TBB_INCLUDE_DIRS - where to find tbb.h, etc.
+#  TBB_LIBRARIES    - List of libraries when using tbb.
+#  TBB_FOUND        - True if tbb found.
+#
+
+########################################################
+# TBB
+
+# TODO use more generic FindTBB
+
+find_path(TBB_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_LIBRARY NAMES tbb PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+                                         $ENV{TBBROOT}/lib/intel64/gcc4.4
+                                         $ENV{TBBROOT}/lib/intel64/gcc4.1)
+set(TBB_LIBRARIES ${TBB_LIBRARY})
+set(TBB_INCLUDE_DIRS ${TBB_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB DEFAULT_MSG TBB_LIBRARY TBB_INCLUDE_DIR)
+
+mark_as_advanced(TBB_INCLUDE_DIR TBB_LIBRARY )
+
+########################################################
+# TBB Malloc
+
+find_path(TBB_MALLOC_INCLUDE_DIR NAMES tbb/tbb.h PATHS $ENV{TBBROOT}/include)
+find_library(TBB_MALLOC_LIBRARY NAMES tbbmalloc PATHS $ENV{TBBROOT}/lib/intel64/gcc4.7
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.4
+                                                      $ENV{TBBROOT}/lib/intel64/gcc4.1)
+
+set(TBB_MALLOC_LIBRARIES ${TBB_MALLOC_LIBRARY})
+set(TBB_MALLOC_INCLUDE_DIRS ${TBB_MALLOC_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set TBB_MALLOC_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(TBB_MALLOC DEFAULT_MSG TBB_MALLOC_LIBRARY TBB_MALLOC_INCLUDE_DIR)
+
+mark_as_advanced(TBB_MALLOC_INCLUDE_DIR TBB_MALLOC_LIBRARY )

cmake/Modules/FindZMQ.cmake

@@ -0,0 +1,8 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)

cmake/Modules/PreventInSourceBuilds.cmake

@@ -0,0 +1,23 @@
+# - Prevent in-source builds.
+# https://stackoverflow.com/questions/1208681/with-cmake-how-would-you-disable-in-source-builds/
+
+function(prevent_in_source_builds)
+  # make sure the user doesn't play dirty with symlinks
+  get_filename_component(srcdir "${CMAKE_SOURCE_DIR}" REALPATH)
+  get_filename_component(srcdir2 "${CMAKE_SOURCE_DIR}/.." REALPATH)
+  get_filename_component(srcdir3 "${CMAKE_SOURCE_DIR}/../src" REALPATH)
+  get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
+
+  # disallow in-source builds
+  if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
+    message(FATAL_ERROR "\
+
+CMake must not to be run in the source directory. \
+Rather create a dedicated build directory and run CMake there. \
+To clean up after this aborted in-place compilation:
+  rm -r CMakeCache.txt CMakeFiles
+")
+  endif()
+endfunction()
+
+prevent_in_source_builds()

cmake/Modules/StyleHeaderUtils.cmake

@@ -48,14 +48,21 @@ function(CreateStyleHeader path filename)
     set(temp "")
     if(ARGC GREATER 2)
         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()
+        list(SORT header_list)
+        foreach(FNAME ${header_list})
             set(temp "${temp}#include \"${FNAME}\"\n")
         endforeach()
     endif()
     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)
@@ -80,19 +87,23 @@ function(RegisterNPairStyle path)
     AddStyleHeader(${path} NPAIR)
 endfunction(RegisterNPairStyle)
 
+function(RegisterFixStyle path)
+    AddStyleHeader(${path} FIX)
+endfunction(RegisterFixStyle)
+
 function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
     FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
     FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
     FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   ""         COMMAND   ) # command   ) # input
+    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
     FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
     FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
     FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
     FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
     FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS ""         INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    ""         KSPACE    ) # kspace    ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
     FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
     FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
     FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor

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)
@@ -62,7 +62,7 @@ should get you started.
 git clone https://github.com/lammps/lammps.git
 mkdir lammps/build
 cd lammps/build
-cmake ../cmake [-DOPTION_A=VALUE_A -DOPTION_B=VALUE_B ...]
+cmake [-D OPTION_A=VALUE_A -D OPTION_B=VALUE_B ...] ../cmake
 make
 ```
 
@@ -174,12 +174,12 @@ presets can be found in the `cmake/presets` folder.
 # build LAMMPS with all "standard" packages which don't use libraries and enable GPU package
 mkdir build
 cd build
-cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
+cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake
 ```
 
 # Reference
 
-## Common CMAKE Configuration Options
+## Common CMake Configuration Options
 
 
 <table>
@@ -195,6 +195,7 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   <td><code>CMAKE_INSTALL_PREFIX</code></td>
   <td>Install location where LAMMPS files will be copied to. In the Unix/Linux case with Makefiles this controls what `make install` will do.</td>
   <td>
+   Default setting is <code>$HOME/.local</code>.
   </td>
 </tr>
 <tr>
@@ -207,6 +208,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   </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>
 
@@ -265,6 +276,26 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BUILD_LIB</code></td>
+  <td>control whether to build LAMMPS as a library</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
+<tr>
+  <td><code>BUILD_EXE</code></td>
+  <td>control whether to build LAMMPS executable</td>
+  <td>
+  <dl>
+    <dt><code>on</code> (default)</dt>
+    <dt><code>off</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>BUILD_SHARED_LIBS</code></td>
   <td>control whether to build LAMMPS as a shared-library</td>
@@ -275,6 +306,16 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BUILD_DOC</code></td>
+  <td>control whether to build LAMMPS documentation</td>
+  <td>
+  <dl>
+    <dt><code>off</code> (default)</dt>
+    <dt><code>on</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>LAMMPS_LONGLONG_TO_LONG</code></td>
   <td>Workaround if your system or MPI version does not recognize <code>long long</code> data types</td>
@@ -305,8 +346,8 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   `mpicxx` in your path and use this MPI implementation.</td>
   <td>
   <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
+    <dt><code>on</code> (default, if found)</dt>
+    <dt><code>off</code></dt>
   </dl>
   </td>
 </tr>
@@ -315,8 +356,8 @@ cmake -C ../cmake/presets/std_nolib.cmake ../cmake -DPKG_GPU=on
   <td>control whether to build LAMMPS with OpenMP support.</td>
   <td>
   <dl>
-    <dt><code>off</code> (default)</dt>
-    <dt><code>on</code></dt>
+    <dt><code>on</code> (default, if found)</dt>
+    <dt><code>off</code></dt>
   </dl>
   </td>
 </tr>
@@ -1261,7 +1302,7 @@ providing the identical features and USER interface.</strong></p>
   </td>
   <td>
   <dl>
-    <dt><code>KISSFFT</code></dt>
+    <dt><code>KISS</code></dt>
     <dt><code>FFTW3</code></dt>
     <dt><code>FFTW2</code></dt>
     <dt><code>MKL</code></dt>
@@ -1269,13 +1310,13 @@ providing the identical features and USER interface.</strong></p>
   </td>
 </tr>
 <tr>
-  <td><code>PACK_ARRAY</code></td>
+  <td><code>FFT_PACK</code></td>
   <td>Optimization for FFT</td>
   <td>
   <dl>
-    <dt><code>PACK_ARRAY</code></dt>
-    <dt><code>PACK_POINTER</code></dt>
-    <dt><code>PACK_MEMCPY</code></dt>
+    <dt><code>array (default)</code></dt>
+    <dt><code>pointer</code></dt>
+    <dt><code>memcpy</code></dt>
   </dl>
   </td>
 </tr>
@@ -1367,6 +1408,29 @@ TODO
 
 ### PYTHON Package
 
+### USER-INTEL Package
+
+<table>
+<thead>
+<tr>
+  <th>Option</th>
+  <th>Description</th>
+  <th>Values</th>
+</tr>
+</thead>
+<tbody>
+<tr>
+  <td><code>INTEL_ARCH</code></td>
+  <td>Target architecture for USER-INTEL package</td>
+  <td>
+  <dl>
+    <dt><code>cpu</code> (default)</dt>
+    <dt><code>knl</code></dt>
+  </dl>
+  </td>
+</tr>
+</tbody>
+</table>
 
 ### GPU Package
 The GPU package builds a support library which can either use OpenCL or CUDA as
@@ -1386,8 +1450,8 @@ target API.
   <td>API used by GPU package</td>
   <td>
   <dl>
-    <dt><code>OpenCL</code> (default)</dt>
-    <dt><code>CUDA</code></dt>
+    <dt><code>opencl</code> (default)</dt>
+    <dt><code>cuda</code></dt>
   </dl>
   </td>
 </tr>
@@ -1396,9 +1460,9 @@ target API.
   <td>Precision size used by GPU package kernels</td>
   <td>
   <dl>
-    <dt><code>SINGLE_DOUBLE</code></dt>
-    <dt><code>SINGLE_SINGLE</code></dt>
-    <dt><code>DOUBLE_DOUBLE</code></dt>
+    <dt><code>mixed</code> (default)</dt>
+    <dt><code>single</code></dt>
+    <dt><code>double</code></dt>
   </dl>
   </td>
 </tr>
@@ -1407,12 +1471,12 @@ target API.
   <td>Tuning target for OpenCL driver code</td>
   <td>
   <dl>
-    <dt><code>GENERIC</code> (default)</dt>
-    <dt><code>INTEL</code> (Intel CPU)</dt>
-    <dt><code>PHI</code> (Intel Xeon Phi)</dt>
-    <dt><code>FERMI</code> (NVIDIA)</dt>
-    <dt><code>KEPLER</code> (NVIDIA)</dt>
-    <dt><code>CYPRESS</code> (AMD)</dt>
+    <dt><code>generic</code> (default)</dt>
+    <dt><code>intel</code> (Intel CPU)</dt>
+    <dt><code>phi</code> (Intel Xeon Phi)</dt>
+    <dt><code>fermi</code> (NVIDIA)</dt>
+    <dt><code>kepler</code> (NVIDIA)</dt>
+    <dt><code>cypress</code> (AMD)</dt>
   </dl>
   </td>
 </tr>
@@ -1421,11 +1485,11 @@ target API.
   <td>CUDA SM architecture targeted by GPU package</td>
   <td>
   <dl>
-    <dt><code>sm20</code> (Fermi)</dt>
-    <dt><code>sm30</code> (Kepler)</dt>
-    <dt><code>sm50</code> (Maxwell)</dt>
-    <dt><code>sm60</code> (Pascal)</dt>
-    <dt><code>sm70</code> (Volta)</dt>
+    <dt><code>sm_20</code> (Fermi)</dt>
+    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_50</code> (Maxwell)</dt>
+    <dt><code>sm_60</code> (Pascal)</dt>
+    <dt><code>sm_70</code> (Volta)</dt>
   </dl>
   </td>
 </tr>
@@ -1439,6 +1503,11 @@ target API.
   </dl>
   </td>
 </tr>
+<tr>
+  <td><code>BIN2C</code> (CUDA only)</td>
+  <td>Path to bin2c executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
+</tr>
 </tbody>
 </table>
 
@@ -1507,6 +1576,16 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>WITH_JPEG</code></td>
+  <td>Enables/Disable JPEG support in LAMMPS</td>
+  <td>
+  <dl>
+    <dt><code>yes</code> (default, if found)</dt>
+    <dt><code>no</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>JPEG_INCLUDE_DIR</code></td>
   <td></td>
@@ -1534,6 +1613,16 @@ Requires a Eigen3 installation
 </tr>
 </thead>
 <tbody>
+<tr>
+  <td><code>WITH_PNG</code></td>
+  <td>Enables/Disable PNG support in LAMMPS</td>
+  <td>
+  <dl>
+    <dt><code>yes</code> (default, if found)</dt>
+    <dt><code>no</code></dt>
+  </dl>
+  </td>
+</tr>
 <tr>
   <td><code>PNG_INCLUDE_DIR</code></td>
   <td></td>
@@ -1563,11 +1652,20 @@ requires `gzip` to be in your `PATH`
 </thead>
 <tbody>
 <tr>
-  <td><code>GZIP_EXECUTABLE</code></td>
-  <td></td>
+  <td><code>WITH_GZIP</code></td>
+  <td>Enables/Disable GZIP support in LAMMPS</td>
   <td>
+  <dl>
+    <dt><code>yes</code> (default, if found)</dt>
+    <dt><code>no</code></dt>
+  </dl>
   </td>
 </tr>
+<tr>
+  <td><code>GZIP_EXECUTABLE</code></td>
+  <td>Path to gzip executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
+</tr>
 </tbody>
 </table>
 
@@ -1585,19 +1683,33 @@ requires `ffmpeg` to be in your `PATH`
 </thead>
 <tbody>
 <tr>
-  <td><code>FFMPEG_EXECUTABLE</code></td>
-  <td></td>
+  <td><code>WITH_FFMPEG</code></td>
+  <td>Enables/Disable FFMPEG support in LAMMPS</td>
   <td>
+  <dl>
+    <dt><code>yes</code> (default, if found)</dt>
+    <dt><code>no</code></dt>
+  </dl>
   </td>
 </tr>
+<tr>
+  <td><code>FFMPEG_EXECUTABLE</code></td>
+  <td>Path to ffmpeg executable, will automatically pick up the first one in your $PATH.</td>
+  <td>(automatic)</td>
+</tr>
 </tbody>
 </table>
 
 
 ## Compilers
 
-By default, `cmake` will use your environment C/C++/Fortran compilers for a build. It uses the `CC`, `CXX` and `FC` environment variables to detect which compilers should be used. However, these values
-will be cached after the first run of `cmake`. Subsequent runs of `cmake` will ignore changes in these environment variables. To ensure the correct values are used you avoid the cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`, `CMAKE_Fortran_COMPILER` options directly.
+By default, `cmake` will use your environment C/C++/Fortran compilers for a
+build. It uses the `CC`, `CXX` and `FC` environment variables to detect which
+compilers should be used. However, these values will be cached after the first
+run of `cmake`. Subsequent runs of `cmake` will ignore changes in these
+environment variables. To ensure the correct values are used you avoid the
+cache by setting the `CMAKE_C_COMPILER`, `CMAKE_CXX_COMPILER`,
+`CMAKE_Fortran_COMPILER` options directly.
 
 <table>
 <thead>
@@ -1627,26 +1739,33 @@ will be cached after the first run of `cmake`. Subsequent runs of `cmake` will i
   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>
 
 ### Building with GNU Compilers
 
 ```bash
-cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+cmake -D CMAKE_C_COMPILER=gcc -D CMAKE_CXX_COMPILER=g++ -D CMAKE_Fortran_COMPILER=gfortran ../cmake
 ```
 
 ### Building with Intel Compilers
 
 ```bash
-cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+cmake -D CMAKE_C_COMPILER=icc -D CMAKE_CXX_COMPILER=icpc -D CMAKE_Fortran_COMPILER=ifort ../cmake
 ```
 
 
 ### Building with LLVM/Clang Compilers
 
 ```bash
-cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+cmake -D CMAKE_C_COMPILER=clang -D CMAKE_CXX_COMPILER=clang++ -D CMAKE_Fortran_COMPILER=flang ../cmake
 ```
 
 

cmake/etc/profile.d/lammps.csh.in

@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_POTENTIALS_DIR@

cmake/etc/profile.d/lammps.sh.in

@@ -0,0 +1,2 @@
+# set environment for LAMMPS executables to find potential files
+export LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_POTENTIALS_DIR@}

cmake/pkgconfig/liblammps.pc.in

@@ -1,18 +1,38 @@
 # pkg-config file for lammps
 # https://people.freedesktop.org/~dbn/pkg-config-guide.html
-# Usage: cc `pkg-config --cflags --libs liblammps` -o myapp myapp.c
-# after you added @CMAKE_INSTALL_FULL_LIBDIR@/pkg-config to PKG_CONFIG_PATH,
+
+# Add the directory where lammps.pc got installed to your PKG_CONFIG_PATH
 # e.g. export PKG_CONFIG_PATH=@CMAKE_INSTALL_FULL_LIBDIR@/pkgconfig
 
-prefix=@CMAKE_INSTALL_FULL_PREFIX@
+# Use this on commandline with:
+# c++ `pkg-config --cflags --libs lammps` -o myapp myapp.cpp
+
+# Use this in a Makefile:
+# myapp: myapp.cpp
+# 	$(CC) `pkg-config --cflags --libs lammps` -o $@ $<
+
+# Use this in autotools:
+# configure.ac:
+# PKG_CHECK_MODULES([LAMMPS], [lammps])
+# Makefile.am:
+# myapp_CFLAGS = $(LAMMPS_CFLAGS)
+# myapp_LDADD = $(LAMMPS_LIBS)
+
+# Use this in CMake:
+# CMakeLists.txt:
+# find_package(PkgConfig)
+# pkg_check_modules(LAMMPS IMPORTED_TARGET lammps)
+# target_link_libraries(<lib> PkgConfig::LAMMPS)
+
+prefix=@CMAKE_INSTALL_PREFIX@
 libdir=@CMAKE_INSTALL_FULL_LIBDIR@
 includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
 URL: http://lammps.sandia.gov
-Version:
+Version: @LAMMPS_VERSION@
 Requires:
-Libs: -L${libdir} -llammps@LIB_SUFFIX@@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/all_on.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/manual_selection.cmake

@@ -56,11 +56,13 @@ set(PKG_USER-MOFFF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-MOLFILE OFF CACHE BOOL "" FORCE)
 set(PKG_USER-NETCDF OFF CACHE BOOL "" FORCE)
 set(PKG_USER-OMP OFF CACHE BOOL "" FORCE)
-set(PKG_USER-PHOFFOFF OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PHONON OFF CACHE BOOL "" FORCE)
+set(PKG_USER-PLUMED OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QMMM OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QTB OFF CACHE BOOL "" FORCE)
 set(PKG_USER-QUIP OFF CACHE BOOL "" FORCE)
 set(PKG_USER-REAXC OFF CACHE BOOL "" FORCE)
+set(PKG_USER-SDPD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMD OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SMTBQ OFF CACHE BOOL "" FORCE)
 set(PKG_USER-SPH OFF CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

cmake/presets/std.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/std_nolib.cmake

@@ -8,7 +8,7 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI

cmake/presets/user.cmake

@@ -8,12 +8,12 @@ set(USER_PACKAGES USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVA
                   USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESO
                   USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
                   USER-NETCDF USER-OMP USER-PHONON USER-QMMM USER-QTB
-                  USER-QUIP USER-REAXC USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+                  USER-QUIP USER-REAXC USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
                   USER-UEF USER-VTK)
 
 set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MEAM MPIIO MSCG POEMS PYTHON REAX VORONOI
                       USER-ATC USER-AWPMD USER-COLVARS USER-H5MD USER-LB USER-MOLFILE
-                      USER-NETCDF USER-QMMM USER-QUIP USER-SMD USER-VTK)
+                      USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP USER-SMD USER-VTK)
 
 set(ALL_PACKAGES ${STANDARD_PACKAGES} ${USER_PACKAGES})
 

doc/.gitignore

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

doc/Makefile

@@ -1,7 +1,7 @@
 # Makefile for LAMMPS documentation
 
-SHELL 	      = /bin/bash
-SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
+SHELL         = /bin/bash
+SHA1          = $(shell echo ${USER}-${PWD} | python utils/sha1sum.py)
 BUILDDIR      = /tmp/lammps-docs-$(SHA1)
 RSTDIR        = $(BUILDDIR)/rst
 VENV          = $(BUILDDIR)/docenv
@@ -31,29 +31,32 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 SOURCES=$(filter-out $(wildcard src/lammps_commands*.txt) src/lammps_support.txt src/lammps_tutorials.txt,$(wildcard src/*.txt))
 OBJECTS=$(SOURCES:src/%.txt=$(RSTDIR)/%.rst)
 
-.PHONY: help clean-all clean epub html pdf old venv spelling anchor_check
+.PHONY: help clean-all clean epub mobi html pdf old venv spelling anchor_check
 
 # ------------------------------------------
 
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       create HTML doc pages in html dir"
-	@echo "  pdf        create Manual.pdf and Developer.pdf in this dir"
-	@echo "  old        create old-style HTML doc pages in old dir"
+	@echo "  pdf        create Developer.pdf and Manual.pdf in this 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)"
+	@echo "                      (requires ebook-convert tool from calibre)"
 	@echo "  clean      remove all intermediate RST files"
 	@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"
 
 # ------------------------------------------
 
-clean-all:
+clean-all: clean
 	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
 
 clean:
-	rm -rf $(RSTDIR) html
+	rm -rf $(RSTDIR) html old epub latex
 	rm -rf spelling
 
 clean-spelling:
@@ -93,9 +96,10 @@ spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
 	@echo "Spell check finished."
 
 epub: $(OBJECTS)
-	@mkdir -p epub
+	@mkdir -p epub/JPG
 	@rm -f LAMMPS.epub
 	@cp src/JPG/lammps-logo.png epub/
+	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
 		cp -r src/* $(RSTDIR)/ ;\
@@ -106,21 +110,49 @@ epub: $(OBJECTS)
 	@rm -rf epub
 	@echo "Build finished. The ePUB manual file is created."
 
-pdf: utils/txt2html/txt2html.exe
+mobi: epub
+	@rm -f LAMMPS.mobi
+	@ebook-convert LAMMPS.epub LAMMPS.mobi
+	@echo "Conversion finished. The MOBI manual file is created."
+
+pdf: $(OBJECTS) $(ANCHORCHECK)
 	@(\
-		set -e; \
-		cd src; \
-		../utils/txt2html/txt2html.exe -b *.txt; \
-		htmldoc --batch lammps.book;          \
-		for s in `echo *.txt | sed -e 's,\.txt,\.html,g'` ; \
-			do grep -q $$s lammps.book || \
-			echo doc file $$s missing in src/lammps.book; done; \
-		rm *.html; \
-		cd Developer; \
+                . $(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 ../; 
+	@(\
+		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
+		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
@@ -130,6 +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
@@ -157,7 +201,7 @@ $(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
 	@(\
 		mkdir -p $(RSTDIR) ; \
 		. $(VENV)/bin/activate ;\
-		txt2rst $< > $@ ;\
+		txt2rst -v $< > $@ ;\
 		deactivate ;\
 	)
 
@@ -168,7 +212,6 @@ $(VENV):
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
-		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 

doc/github-development-workflow.md

@@ -0,0 +1,196 @@
+# Outline of the GitHub Development Workflow
+
+This purpose of this document is to provide a point of reference for the
+core LAMMPS developers and other LAMMPS contributors to understand the
+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 2018-12-19.
+
+## Table of Contents
+
+  * [GitHub Merge Management](#github-merge-management)
+  * [Pull Requests](#pull-requests)
+    * [Pull Request Assignments](#pull-request-assignments)
+    * [Pull Request Reviews](#pull-request-reviews)
+    * [Pull Request Discussions](#pull-request-discussions)
+    * [Checklist for Pull Requests](#checklist-for-pull-requests)
+  * [GitHub Issues](#github-issues)
+  * [Milestones and Release Planning](#milestones-and-release-planning)
+
+## GitHub Merge Management
+
+In the interest of consistency, ONLY ONE of the core LAMMPS developers
+should doing the merging itself.  This is currently
+[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
+If this assignment needs to be changed, it shall be done right after a
+stable release.  If the currently assigned developer cannot merge outstanding pull 
+requests in a timely manner, or in other extenuating circumstances, 
+other core LAMMPS developers with merge rights can merge pull requests,
+when necessary. 
+
+## Pull Requests
+
+ALL changes to the LAMMPS code and documentation, however trivial, MUST
+be submitted as a pull request to GitHub. All changes to the "master"
+branch must be made exclusively through merging pull requests. The
+"unstable" and "stable" branches, respectively are only to be updated
+upon patch or stable releases with fast-forward merges based on the
+associated tags. Pull requests may also be submitted to (long-running)
+feature branches created by LAMMPS developers inside the LAMMPS project,
+if needed. Those are not subject to the merge and review restrictions
+discussed in this document, though, but get managed as needed on a
+case-by-case basis.
+
+### Pull Request Assignments
+
+Pull requests can be "chaperoned" by one of the LAMMPS core developers.
+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 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
+period the `work_in_progress` label shall be applied to the pull
+request.  The assignee gets to decide what happens to the pull request
+next, e.g. whether it should be assigned to a different developer for
+additional checks and changes, or is recommended to be merged.  Removing
+the `work_in_progress` label and assigning the pull request to the
+developer tasked with merging signals that a pull request is ready to be
+merged.
+
+### Pull Request Reviews
+
+People can be assigned to review a pull request in two ways:
+
+  * They can be assigned manually to review a pull request
+    by the submitter or a LAMMPS developer
+  * They can be automatically assigned, because a developers matches
+    a file pattern in the `.github/CODEOWNERS` file, which associates
+    developers with the code they contributed and maintain.
+
+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 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.
+
+### Pull Request Discussions
+
+All discussions about a pull request should be kept as much as possible
+on the pull request discussion page on GitHub, so that other developers
+can later review the entire discussion after the fact and understand the
+rationale behind choices made.  Exceptions to this policy are technical
+discussions, that are centered on tools or policies themselves
+(git, github, c++) rather than on the content of the pull request.
+
+### Checklist for Pull Requests
+
+Here are some items to check:
+  * source and text files should not have CR/LF line endings (use dos2unix to remove)
+  * every new command or style should have documentation. The names of
+  source files (c++ and manual) should follow the name of the style.
+  (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  * all new style names should be lower case, the must be no dashes,
+  blanks, or underscores separating words, only forward slashes.
+  * new style docs should be added to the "overview" files in
+  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
+  and `doc/src/lammps.book`
+  * check whether manual cleanly translates with `make html` and `make pdf`
+  * check spelling of manual with `make spelling` in doc folder
+  * new source files in packages should be added to `src/.gitignore`
+  * removed or renamed files in packages should be added to `src/Purge.list`
+  * C++ source files should use C++ style include files for accessing
+  C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
+  And they should use angular brackets instead of double quotes. Full list:
+    * assert.h -> cassert
+    * ctype.h -> cctype
+    * errno.h -> cerrno
+    * float.h -> cfloat
+    * limits.h -> climits
+    * math.h -> cmath
+    * complex.h -> complex
+    * setjmp.h -> csetjmp
+    * signal.h -> csignal
+    * stddef.h -> cstddef
+    * stdint.h -> cstdint
+    * stdio.h -> cstdio
+    * stdlib.h -> cstdlib
+    * string.h -> cstring
+    * time.h -> ctime
+    * 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 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
+  compiling LAMMPS with `-DLAMMPS_BIGBIG`.
+  * when including both `lmptype.h` (and using defines or macros from it)
+  and `mpi.h`, `lmptype.h` must be included first.
+  * when pair styles are added, check if settings for flags like
+  `single_enable`, `writedata`, `reinitflag`, `manybody_flag`
+  and others are correctly set and supported.
+
+## GitHub Issues
+
+The GitHub issue tracker is the location where the LAMMPS developers
+and other contributors or LAMMPS users can report issues or bugs with
+the LAMMPS code or request new features to be added. Feature requests
+are usually indicated by a `[Feature Request]` marker in the subject.
+Issues are assigned to a person, if this person is working on this
+feature or working to resolve an issue. Issues that have nobody working
+on them at the moment, have the label `volunteer needed` attached.
+
+When an issue, say `#125` is resolved by a specific pull request,
+the comment for the pull request shall contain the text `closes #125`
+or `fixes #125`, so that the issue is automatically deleted when
+the pull request is merged.
+
+## Milestones and Release Planning
+
+LAMMPS uses a continuous release development model with incremental
+changes, i.e. significant effort is made - including automated pre-merge
+testing - that the code in the branch "master" does not get broken.
+More extensive testing (including regression testing) is performed after
+code is merged to the "master" branch. There are patch releases of
+LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
+a sufficient amount of changes have happened, and the post-merge testing
+has been successful. These patch releases are marked with a
+`patch_<version date>` tag and the "unstable" branch follows only these
+versions (and thus is always supposed to be of production quality,
+unlike "master", which may be temporary broken, in the case of larger
+change sets or unexpected incompatibilities or side effects.
+
+About 3-4 times each year, there are going to be "stable" releases
+of LAMMPS.  These have seen additional, manual testing and review of
+results from testing with instrumented code and static code analysis.
+Also, in the last 2-3 patch releases before a stable release are
+"release candidate" versions which only contain bugfixes and
+documentation updates.  For release planning and the information of
+code contributors, issues and pull requests being actively worked on
+are assigned a "milestone", which corresponds to the next stable
+release or the stable release after that, with a tentative release
+date.
+

doc/lammps.1

@@ -0,0 +1,45 @@
+.TH LAMMPS "2018-08-22"
+.SH NAME
+.B LAMMPS
+\- Molecular Dynamics Simulator.
+
+.SH SYNOPSIS
+.B lmp 
+-in in.file
+
+or
+
+mpirun \-np 2 
+.B lmp 
+-in in.file
+
+.SH DESCRIPTION
+.B LAMMPS 
+LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale 
+Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for soft 
+materials (biomolecules, polymers) and solid-state materials (metals, 
+semiconductors) and coarse-grained or mesoscopic systems. It can be used to 
+model atoms or, more generically, as a parallel particle simulator at the 
+atomic, meso, or continuum scale.
+
+See http://lammps.sandia.gov/ for documentation.
+
+.SH OPTIONS
+See https://lammps.sandia.gov/doc/Run_options.html for details on
+command-line options.
+
+.SH COPYRIGHT 
+© 2003--2018 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License as published by
+the Free Software Foundation; either version 2 of the License, or
+(at your option) any later version.
+
+This package is distributed in the hope that it will be useful,
+but WITHOUT ANY WARRANTY; without even the implied warranty of
+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+GNU General Public License for more details.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL-2'.

doc/src/Build.txt

@@ -0,0 +1,49 @@
+"Previous Section"_Install.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next Section"_Run_head.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Build LAMMPS :h2
+
+LAMMPS can be built as an executable or library from source code via
+either traditional makefiles (which may require manual editing)
+for use with GNU make or gmake, or a build environment generated by CMake
+(Unix Makefiles, Xcode, Visual Studio, KDevelop or more).  As an
+alternative you can download a package with pre-built executables
+as described on the "Install"_Install.html doc page.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Build LAMMPS with CMake"_Build_cmake.html
+"Build LAMMPS with make"_Build_make.html
+"Link LAMMPS as a library to another code"_Build_link.html
+"Basic build options"_Build_basics.html
+"Optional build settings"_Build_settings.html
+"Include packages in build"_Build_package.html
+"Packages with extra build options"_Build_extras.html
+"Notes for building LAMMPS on Windows"_Build_windows.html  :all(b)
+
+If you have problems building LAMMPS, it is often due to software
+issues on your local machine.  If you can, find a local expert to
+help.  If you're still stuck, send an email to the "LAMMPS mail
+list"_http://lammps.sandia.gov/mail.html.

doc/src/Build_basics.txt

@@ -0,0 +1,331 @@
+"Higher level section"_Build.html - "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
+
+Basic build options :h3
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+"Serial vs parallel build"_#serial
+"Choice of compiler and compile/link options"_#compile
+"Build LAMMPS as an executable or a library"_#exe
+"Build the LAMMPS documentation"_#doc
+"Install LAMMPS after a build"_#install :ul
+
+:line
+
+Serial vs parallel build :h4,link(serial)
+
+LAMMPS can be built to run in parallel using the ubiquitous "MPI
+(message-passing
+interface)"_https://en.wikipedia.org/wiki/Message_Passing_Interface
+library.  Or it can built to run on a single processor (serial)
+without MPI.  It can also be built with support for OpenMP threading
+(see more discussion below).
+
+[CMake variables]:
+
+-D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+-D BUILD_OMP=value        # yes or no (default)
+-D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                          # no default value :pre
+
+The executable created by CMake (after running make) is lmp_name.  If
+the LAMMPS_MACHINE variable is not specified, the executable is just
+lmp.  Using BUILD_MPI=no will produce a serial executable.
+
+[Traditional make]:
+
+cd lammps/src
+make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+make serial             # serial build, produces lmp_serial using Makefile/serial
+make mybox :pre         # uses Makefile.mybox to produce lmp_mybox :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+MPI_INC =       -I../STUBS
+MPI_PATH =      -L../STUBS
+MPI_LIB =	-lmpi_stubs :pre
+
+For a parallel build, if MPI is installed on your system in the usual
+place (e.g. under /usr/local), you do not need to specify the 3
+variables MPI_INC, MPI_PATH, MPI_LIB.  The MPI wrapper on the compiler
+(e.g. mpicxx, mpiCC) knows where to find the needed include and
+library files.  Failing this, these 3 variables can be used to specify
+where the mpi.h file (MPI_INC), and the MPI library files (MPI_PATH)
+are found, and the name of the library files (MPI_LIB).
+
+For a serial build, you need to specify the 3 variables, as shown
+above.
+
+For a serial LAMMPS build, use the dummy MPI library provided in
+src/STUBS.  You also need to build the STUBS library for your platform
+before making LAMMPS itself.  A "make serial" build does this for.
+Otherwise, type "make mpi-stubs" from the src directory, or "make"
+from the src/STUBS dir.  If the build fails, you will need to edit the
+STUBS/Makefile for your platform.
+
+The file STUBS/mpi.c provides a CPU timer function called MPI_Wtime()
+that calls gettimeofday() .  If your system doesn't support
+gettimeofday() , you'll need to insert code to call another timer.
+Note that the ANSI-standard function clock() rolls over after an hour
+or so, and is therefore insufficient for timing long LAMMPS
+simulations.
+
+[CMake and make info]:
+
+If you are installing MPI yourself, we recommend MPICH2 from Argonne
+National Laboratory or OpenMPI.  MPICH can be downloaded from the
+"Argonne MPI site"_http://www.mcs.anl.gov/research/projects/mpich2/.
+OpenMPI can be downloaded from the "OpenMPI
+site"_http://www.open-mpi.org.  Other MPI packages should also work.
+If you are running on a large parallel machine, your system admins or
+the vendor should have already installed a version of MPI, which is
+likely to be faster than a self-installed MPICH or OpenMPI, so find
+out how to build and link with it.
+
+The majority of OpenMP (threading) support in LAMMPS is provided by
+the USER-OMP package; see the "Speed omp"_Speed_omp.html doc page for
+details. The USER-INTEL package also provides OpenMP support (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with the Intel compilers on top of that. Also, the KOKKOS package can
+be compiled for using OpenMP threading.
+
+However, there are a few commands in LAMMPS that have native OpenMP
+support.  These are commands in the MPIIO, SNAP, USER-DIFFRACTION, and
+USER-DPD packages.  In addition some packages support OpenMP threading
+indirectly through the libraries they interface to: e.g. LATTE and
+USER-COLVARS.  See the "Packages details"_Packages_details.html doc
+page for more info on these packages and the doc pages for their
+respective commands for OpenMP threading info.
+
+For CMake, if you use BUILD_OMP=yes, you can use these packages and
+turn on their native OpenMP support and turn on their native OpenMP
+support at run time, by setting the OMP_NUM_THREADS environment
+variable before you launch LAMMPS.
+
+For building via conventional make, the CCFLAGS and LINKFLAGS
+variables in Makefile.machine need to include the compiler flag that
+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)
+
+The choice of compiler and compiler flags can be important for
+performance.  Vendor compilers can produce faster code than
+open-source compilers like GNU.  On boxes with Intel CPUs, we suggest
+trying the "Intel C++ compiler"_intel.
+
+:link(intel,https://software.intel.com/en-us/intel-compilers)
+
+On parallel clusters or supercomputers which use "modules" for their
+compile/link environments, you can often access different compilers by
+simply loading the appropriate module before building LAMMPS.
+
+[CMake variables]:
+
+-D CMAKE_CXX_COMPILER=name            # name of C++ compiler
+-D CMAKE_C_COMPILER=name              # name of C compiler
+-D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler :pre
+
+-D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
+-D CMAKE_C_FLAGS=string               # flags to use with C compiler
+-D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler :pre
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any "accelerator
+packages"_Speed_packages.html you have included in the build.
+
+You can tell CMake to look for a specific compiler with these variable
+settings.  Likewise you can specify the FLAGS variables if you want to
+experiment with alternate optimization flags.  You should specify all
+3 compilers, so that the small number of LAMMPS source files written
+in C or Fortran are built with a compiler consistent with the one used
+for all the C++ files:
+
+Building with GNU Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+Building with Intel Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+Building with LLVM/Clang Compilers:
+cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang :pre
+
+NOTE: When the cmake command completes, it prints info to the screen
+as to which compilers it is using, and what flags will be used in the
+compilation.  Note that if the top-level compiler is mpicxx, it is
+simply a wrapper on a real compiler.  The underlying compiler info is
+what will be listed in the CMake output.  You should check to insure
+you are using the compiler and optimization flags are the ones you
+want.
+
+[Makefile.machine settings]:
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+CC =		mpicxx
+CCFLAGS =	-g -O3
+LINK =		mpicxx
+LINKFLAGS =	-g -O :pre
+
+Serial build (see src/MAKE/Makefile.serial):
+
+CC =		g++
+CCFLAGS =	-g -O3
+LINK =		g++
+LINKFLAGS =	-g -O :pre
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  You should always use mpicxx or mpiCC for
+a parallel build, since these compiler wrappers will include
+a variety of settings appropriate for your MPI installation.
+
+NOTE: If you build LAMMPS with any "accelerator
+packages"_Speed_packages.html included, they have specific
+optimization flags that are either required or recommended for optimal
+performance.  You need to include these in the CCFLAGS and LINKFLAGS
+settings above.  For details, see the individual package doc pages
+listed on the "Speed packages"_Speed_packages.html doc page.  Or
+examine these files in the src/MAKE/OPTIONS directory.  They
+correspond to each of the 5 accelerator packages and their hardware
+variants:
+
+Makefile.opt                   # OPT package
+Makefile.omp                   # USER-OMP package
+Makefile.intel_cpu             # USER-INTEL package for CPUs
+Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+Makefile.gpu                   # GPU package
+Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
+Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)
+Makefile.kokkos_phi            # KOKKOS package for KNLs (OpenMP) :pre
+
+:line
+
+Build LAMMPS as an executable or a library :h4,link(exe)
+
+LAMMPS can be built as either an executable or as a static or shared
+library.  The LAMMPS library can be called from another application or
+a scripting language.  See the "Howto couple"_Howto_couple.html doc
+page for more info on coupling LAMMPS to other codes.  See the
+"Python"_Python_head.html doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
+
+[CMake variables]:
+
+-D BUILD_EXE=value           # yes (default) or no
+-D BUILD_LIB=value           # yes or no (default)
+-D BUILD_SHARED_LIBS=value   # yes or no (default) :pre
+
+Setting BUILD_EXE=no will not produce an executable.  Setting
+BUILD_LIB=yes will produce a static library named liblammps.a.
+Setting both BUILD_LIB=yes and BUILD_SHARED_LIBS=yes will produce a
+shared library named liblammps.so.
+
+[Traditional make]:
+
+cd lammps/src
+make machine               # build LAMMPS executable lmp_machine
+make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so :pre
+
+The two library builds also create generic soft links, named
+liblammps.a and liblammps.so, which point to the liblammps_machine
+files.
+
+[CMake and make info]:
+
+Note that for a shared library to be usable by a calling program, all
+the auxiliary libraries it depends on must also exist as shared
+libraries.  This will be the case for libraries included with LAMMPS,
+such as the dummy MPI library in src/STUBS or any package libraries in
+the lib/packages directory, since they are always built as shared
+libraries using the -fPIC switch.  However, if a library like MPI or
+FFTW does not exist as a shared library, the shared library build will
+generate an error.  This means you will need to install a shared
+library version of the auxiliary library.  The build instructions for
+the library should tell you how to do this.
+
+As an example, here is how to build and install the "MPICH
+library"_mpich, a popular open-source version of MPI, distributed by
+Argonne National Lab, as a shared library in the default
+/usr/local/lib location:
+
+:link(mpich,http://www-unix.mcs.anl.gov/mpi)
+
+./configure --enable-shared
+make
+make install :pre
+
+You may need to use "sudo make install" in place of the last line if
+you do not have write privileges for /usr/local/lib.  The end result
+should be the file /usr/local/lib/libmpich.so.
+
+:line
+
+Build the LAMMPS documentation :h4,link(doc)
+
+[CMake variable]:
+
+-D BUILD_DOC=value       # yes or no (default) :pre
+
+This will create the HTML doc pages within the CMake build directory.
+The reason to do this is if you want to "install" LAMMPS on a system
+after the CMake build via "make install", and include the doc pages in
+the install.
+
+[Traditional make]:
+
+cd lammps/doc
+make html       # html doc pages
+make pdf        # single Manual.pdf file :pre
+
+This will create a lammps/doc/html dir with the HTML doc pages so that
+you can browse them locally on your system.  Type "make" from the
+lammps/doc dir to see other options.
+
+NOTE: You can also download a tarball of the documentation for the
+current LAMMPS version (HTML and PDF files), from the website
+"download page"_http://lammps.sandia.gov/download.html.
+
+:line
+
+Install LAMMPS after a build :h4,link(install)
+
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user privileges (e.g. sudo) if the directory
+you want to copy files to is protected.
+
+[CMake variable]:
+
+cmake -D CMAKE_INSTALL_PREFIX=path \[options ...\] ../cmake
+make                        # perform make after CMake command
+make install                # perform the installation into prefix :pre
+
+[Traditional make]:
+
+There is no "install" option in the src/Makefile for LAMMPS.  If you
+wish to do this you will need to first build LAMMPS, then manually
+copy the desired LAMMPS files to the appropriate system directories.

doc/src/Build_cmake.txt

@@ -0,0 +1,196 @@
+"Higher level section"_Build.html - "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
+
+Build LAMMPS with CMake :h3
+
+This page is a short summary of how to use CMake to build LAMMPS.
+Details on CMake variables that enable specific LAMMPS build options
+are given on the pages linked to from the "Build"_Build.html doc page.
+
+Richard Berger (Temple U) has also written a "more comprehensive
+guide"_https://github.com/lammps/lammps/blob/master/cmake/README.md
+for how to use CMake to build LAMMPS.  If you are new to CMake it is a
+good place to start.
+
+:line
+
+Building LAMMPS with CMake is a two-step process.  First you use CMake
+to create a build environment in a new directory.  On Linux systems,
+this will be based on makefiles for use with make.  Then you use the
+make command to build LAMMPS, which uses the created
+Makefile(s). Example:
+
+cd lammps                        # change to the LAMMPS distribution directory
+mkdir build; cd build            # create a new directory (folder) for build
+cmake ../cmake \[options ...\]   # configuration with (command-line) cmake
+make                             # compilation :pre
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment.  The make
+command will then compile and link LAMMPS, producing (by default) an
+executable called "lmp" and a library called "liblammps.a" in the
+"build" folder.
+
+If your machine has multiple CPU cores (most do these days), using a
+command like "make -jN" (with N being the number of available local
+CPU cores) can be much faster.  If you plan to do development on
+LAMMPS or need to re-compile LAMMPS repeatedly, installation of the
+ccache (= Compiler Cache) software may speed up compilation even more.
+
+After compilation, you can optionally copy the LAMMPS executable and
+library into your system folders (by default under $HOME/.local) with:
+
+make install    # optional, copy LAMMPS executable & library elsewhere :pre
+
+:line
+
+There are 3 variants of CMake: a command-line version (cmake), a text mode
+UI version (ccmake), and a graphical GUI version (cmake-GUI).  You can use
+any of them interchangeably to configure and create the LAMMPS build
+environment.  On Linux all the versions produce a Makefile as their
+output.  See more details on each below.
+
+You can specify a variety of options with any of the 3 versions, which
+affect how the build is performed and what is included in the LAMMPS
+executable.  Links to pages explaining all the options are listed on
+the "Build"_Build.html doc page.
+
+You must perform the CMake build system generation and compilation in
+a new directory you create.  It can be anywhere on your local machine.
+In these Build pages we assume that you are building in a directory
+called "lammps/build".  You can perform separate builds independently
+with different options, so long as you perform each of them in a
+separate directory you create.  All the auxiliary files created by one
+build process (executable, object files, log files, etc) are stored in
+this directory or sub-directories within it that CMake creates.
+
+NOTE: To perform a CMake build, no packages can be installed or a
+build been previously attempted in the LAMMPS src directory by using
+"make" commands to "perform a conventional LAMMPS
+build"_Build_make.html.  CMake detects if this is the case and
+generates an error, telling you to type "make no-all purge" in the src
+directory to un-install all packages.  The purge removes all the *.h
+files auto-generated by make.
+
+You must have CMake version 2.8 or later on your system to build
+LAMMPS.  A handful of LAMMPS packages (KOKKOS, LATTE, MSCG) require a
+later version.  CMake will print a message telling you if a later
+version is required.  Installation instructions for CMake are below.
+
+After the initial build, if you edit LAMMPS source files, or add your
+own new files to the source directory, you can just re-type make from
+your build directory and it will re-compile only the files that have
+changed.  If you want to change CMake options you can run cmake (or
+ccmake or cmake-gui) again from the same build directory and alter
+various options; see details below.  Or you can remove the entire build
+folder, recreate the directory and start over.
+
+:line
+
+[Command-line version of CMake]:
+
+cmake \[options ...\] /path/to/lammps/cmake  # build from any dir
+cmake \[options ...\] ../cmake               # build from lammps/build :pre
+
+The cmake command takes one required argument, which is the LAMMPS
+cmake directory which contains the CMakeLists.txt file.
+
+The argument can be preceeded or followed by various CMake
+command-line options.  Several useful ones are:
+
+-D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
+-D CMAKE_BUILD_TYPE=type      # type = Release or Debug
+-G output                     # style of output CMake generates
+-DVARIABLE=value              # setting for a LAMMPS feature to enable
+-D VARIABLE=value             # ditto, but cannot come after CMakeLists.txt dir :pre
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the "Build"_Build.html doc page.
+All of these variable names are upper-case and their values are
+lower-case, e.g. -D LAMMPS_SIZES=smallbig.  For boolean values, any of
+these forms can be used: yes/no, on/off, 1/0.
+
+On Unix/Linux machines, CMake generates a Makefile by default to
+perform the LAMMPS build.  Alternate forms of build info can be
+generated via the -G switch, e.g. Visual Studio on a Windows machine,
+Xcode on MacOS, or KDevelop on Linux.  Type "cmake --help" to see the
+"Generator" styles of output your system supports.
+
+NOTE: When CMake runs, it prints configuration info to the screen.
+You should review this to verify all the features you requested were
+enabled, including packages.  You can also see what compilers and
+compile options will be used for the build.  Any errors in CMake
+variable syntax will also be flagged, e.g. mis-typed variable names or
+variable values.
+
+CMake creates a CMakeCache.txt file when it runs.  This stores all the
+settings, so that when running CMake again you can use the current
+folder '.' instead of the path to the LAMMPS cmake folder as the
+required argument to the CMake command. Either way the existing
+settings will be inherited unless the CMakeCache.txt file is removed.
+
+If you later want to change a setting you can rerun cmake in the build
+directory with different setting. Please note that some automatically
+detected variables will not change their value when you rerun cmake.
+In these cases it is usually better to first remove all the
+files/directories in the build directory, or start with a fresh build
+directory.
+
+:line
+
+[Curses version (terminal-style menu) of CMake]:
+
+ccmake ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to type [c], for the second you
+have to type [g]. You may need to type [c] multiple times, and may be
+required to edit some of the entries of CMake configuration variables
+in between.  Please see the "ccmake
+manual"_https://cmake.org/cmake/help/latest/manual/ccmake.1.html for
+more information.
+
+:line
+
+[GUI version of CMake]:
+
+cmake-gui ../cmake :pre
+
+You initiate the configuration and build environment generation steps
+separately. For the first you have to click on the [Configure] button,
+for the second you have to click on the [Generate] button.  You may
+need to click on [Configure] multiple times, and may be required to
+edit some of the entries of CMake configuration variables in between.
+Please see the "cmake-gui
+manual"_https://cmake.org/cmake/help/latest/manual/cmake-gui.1.html
+for more information.
+
+:line
+
+[Installing CMake]
+
+Check if your machine already has CMake installed:
+
+which cmake             # do you have it?
+which cmake3            # version 3 may have this name
+cmake --version         # what specific version you have :pre
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+module list            # is a cmake module already loaded?
+module avail           # is a cmake module available?
+module load cmake3     # load cmake module with appropriate name :pre
+
+Most Linux distributions offer pre-compiled cmake packages through
+their package management system. If you do not have CMake or a new
+enough version, you can download the latest version at
+"https://cmake.org/download/"_https://cmake.org/download/.
+Instructions on how to install it on various platforms can be found
+"on this page"_https://cmake.org/install/.

doc/src/Build_link.txt

@@ -0,0 +1,85 @@
+"Higher level section"_Build.html - "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
+
+Link LAMMPS as a library to another code :h3
+
+LAMMPS can be used as a library by another application, including
+Python scripts.  The files src/library.cpp and library.h define the
+C-style API for using LAMMPS as a library.  See the "Howto
+library"_Howto_library.html doc page for a description of the
+interface and how to extend it for your needs.
+
+The "Build basics"_Build_basics.html doc page explains how to build
+LAMMPS as either a shared or static library.  This results in one of
+these 2 files:
+
+liblammps.so      # shared library
+liblammps.a       # static library
+
+:line
+
+[Link with LAMMPS as a static library]:
+
+The calling application can link to LAMMPS as a static library with a
+link command like this:
+
+g++ caller.o -L/home/sjplimp/lammps/src -llammps -o caller
+
+The -L argument is the path to where the liblammps.a file is.  The
+-llammps argument is shorthand for the file liblammps.a.
+
+:line
+
+[Link with LAMMPS as a shared library]:
+
+If you wish to link to liblammps.so, the operating system finds shared
+libraries to load at run-time using the environment variable
+LD_LIBRARY_PATH.  To enable this you can do one of two things:
+
+(1) Copy the liblammps.so file to a location the system can find it,
+such as /usr/local/lib.  I.e. a directory already listed in your
+LD_LIBRARY_PATH variable.  You can type
+
+printenv LD_LIBRARY_PATH :pre
+
+to see what directories are in that list.
+
+(2) Add the LAMMPS src directory (or the directory you perform CMake
+build in) to your LD_LIBRARY_PATH, so that the current version of the
+shared library is always available to programs that use it.
+
+For the csh or tcsh shells, you would add something like this to your
+~/.cshrc file:
+
+setenv LD_LIBRARY_PATH $\{LD_LIBRARY_PATH\}:/home/sjplimp/lammps/src :pre
+
+:line
+
+[Calling the LAMMPS library]:
+
+Either flavor of library (static or shared) allows one or more LAMMPS
+objects to be instantiated from the calling program.
+
+When used from a C++ program, all of LAMMPS is wrapped in a LAMMPS_NS
+namespace; you can safely use any of its classes and methods from
+within the calling code, as needed.
+
+When used from a C or Fortran program, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the "Python library"_Python_library.html doc page for a
+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 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_make.txt

@@ -0,0 +1,85 @@
+"Higher level section"_Build.html - "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
+
+Build LAMMPS with make :h3
+
+Building LAMMPS with traditional makefiles requires that you have a
+Makefile."machine" file appropriate for your system in the src/MAKE,
+src/MAKE/MACHINES, src/MAKE/OPTIONS, or src/MAKE/MINE directory (see
+below).  It can include various options for customizing your LAMMPS
+build with a number of global compilation options and features.
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must install them first, as discussed on the "Build
+package"_Build_package.html doc page.  If the packages require
+provided or external libraries, you must build those libraries before
+building LAMMPS.  Building "LAMMPS with CMake"_Build_cmake.html can
+automate all of this for many types of machines, especially
+workstations, desktops and laptops, so we suggest you try it first.
+
+These commands perform a default LAMMPS build, producing the LAMMPS
+executable lmp_serial or lmp_mpi in lammps/src:
+
+cd lammps/src
+make serial     # build a serial LAMMPS executable
+make mpi        # build a parallel LAMMPS executable with MPI
+make            # see a variety of make options :pre
+
+This initial compilation can take a long time, since LAMMPS is a large
+project with many features. If your machine has multiple CPU cores
+(most do these days), using a command like "make -jN mpi" (with N =
+the number of available CPU cores) can be much faster.  If you plan to
+do development on LAMMPS or need to re-compile LAMMPS repeatedly, the
+installation of the ccache (= Compiler Cache) software may speed up
+compilation even more.
+
+After the initial build, whenever you edit LAMMPS source files, or add
+or remove new files to the source directory (e.g. by installing or
+uninstalling packages), you must re-compile and relink the LAMMPS
+executable with the same "make" command.  This makefiles dependencies
+should insure that only the subset of files that need to be are
+re-compiled.
+
+NOTE: When you build LAMMPS for the first time, a long list of *.d
+files will be printed out rapidly.  This is not an error; it is the
+Makefile doing its normal creation of dependencies.
+
+:line
+
+The lammps/src/MAKE tree contains all the Makefile.machine files
+included in the LAMMPS distribution.  Typing "make machine" uses
+Makefile.machine.  Thus the "make serial" or "make mpi" lines above
+use Makefile.serial and Makefile.mpi.  Others are in these dirs:
+
+OPTIONS      # Makefiles which enable specific options
+MACHINES     # Makefiles for specific machines
+MINE         # customized Makefiles you create (you may need to create this folder) :pre
+
+Typing "make" lists all the available Makefile.machine files.  A file
+with the same name can appear in multiple folders (not a good idea).
+The order the dirs are searched is as follows: src/MAKE/MINE,
+src/MAKE, src/MAKE/OPTIONS, src/MAKE/MACHINES.  This gives preference
+to a customized file you put in src/MAKE/MINE.
+
+Makefiles you may wish to try include these (some require a package
+first be installed).  Many of these include specific compiler flags
+for optimized performance.  Please note, however, that some of these
+customized machine Makefile are contributed by users.  Since both
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
+
+make mac             # build serial LAMMPS on a Mac
+make mac_mpi         # build parallel LAMMPS on a Mac
+make intel_cpu       # build with the USER-INTEL package optimized for CPUs
+make knl             # build with the USER-INTEL package optimized for KNLs
+make opt             # build with the OPT package optimized for CPUs
+make omp             # build with the USER-OMP package optimized for OpenMP
+make kokkos_omp      # build with the KOKKOS package for OpenMP
+make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
+make kokkos_phi      # build with the KOKKOS package for KNLs :pre

doc/src/Build_package.txt

@@ -0,0 +1,226 @@
+"Higher level section"_Build.html - "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
+
+Include packages in build :h3
+
+In LAMMPS, a package is a group of files that enable a specific set of
+features.  For example, force fields for molecular systems or
+rigid-body constraints are in packages.  In the src directory, each
+package is a sub-directory with the package name in capital letters.
+
+An overview of packages is given on the "Packages"_Packages.html doc
+page.  Brief overviews of each package are on the "Packages
+details"_Packages_details.html doc page.
+
+When building LAMMPS, you can choose to include or exclude each
+package.  In general there is no need to include a package if you
+never plan to use its features.
+
+If you get a run-time error that a LAMMPS command or style is
+"Unknown", it is often because the command is contained in a package,
+and your build did not include that package.  Running LAMMPS with the
+"-h command-line switch"_Run_options.html will print all the included
+packages and commands for that executable.
+
+For the majority of packages, if you follow the single step below to
+include it, you can then build LAMMPS exactly the same as you would
+without any packages installed.  A few packages may require additional
+steps, as explained on the "Build extras"_Build_extras.html doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
+"COMPRESS"_Build_extras.html#compress,
+"GPU"_Build_extras.html#gpu,
+"KIM"_Build_extras.html#kim,
+"KOKKOS"_Build_extras.html#kokkos,
+"LATTE"_Build_extras.html#latte,
+"MEAM"_Build_extras.html#meam,
+"MESSAGE"_Build_extras.html#message,
+"MSCG"_Build_extras.html#mscg,
+"OPT"_Build_extras.html#opt,
+"POEMS"_Build_extras.html#poems,
+"PYTHON"_Build_extras.html#python,
+"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,
+"USER-H5MD"_Build_extras.html#user-h5md,
+"USER-INTEL"_Build_extras.html#user-intel,
+"USER-MOLFILE"_Build_extras.html#user-molfile,
+"USER-NETCDF"_Build_extras.html#user-netcdf,
+"USER-PLUMED"_Build_extras.html#user-plumed,
+"USER-OMP"_Build_extras.html#user-omp,
+"USER-QMMM"_Build_extras.html#user-qmmm,
+"USER-QUIP"_Build_extras.html#user-quip,
+"USER-SCAFACOS"_Build_extras.html#user-scafacos,
+"USER-SMD"_Build_extras.html#user-smd,
+"USER-VTK"_Build_extras.html#user-vtk :tb(c=6,ea=c,a=l)
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+[CMake variables]:
+
+-D PKG_NAME=value          # yes or no (default) :pre
+
+Examples:
+
+-D PKG_MANYBODY=yes
+-D PKG_USER-INTEL=yes :pre
+
+All standard and user packages are included the same way.  Note that
+USER packages have a hyphen between USER and the rest of the package
+name, not an underscore.
+
+See the shortcut section below for how to install many packages at
+once with CMake.
+
+NOTE: If you toggle back and forth between building with CMake vs
+make, no packages in the src directory can be installed when you
+invoke cmake.  CMake will give an error if that is not the case,
+indicating how you can un-install all packages in the src dir.
+
+[Traditional make]:
+
+cd lammps/src
+make ps                    # check which packages are currently installed
+make yes-name              # install a package with name
+make no-name               # un-install a package with name
+make mpi                   # build LAMMPS with whatever packages are now installed :pre
+
+Examples:
+
+make no-rigid
+make yes-user-intel :pre
+
+All standard and user packages are included the same way.
+
+See the shortcut section below for how to install many packages at
+once with make.
+
+NOTE: You must always re-build LAMMPS (via make) after installing or
+un-installing a package, for the action to take effect.
+
+NOTE: You cannot install or un-install packages and build LAMMPS in a
+single make command with multiple targets, e.g. make yes-colloid mpi.
+This is because the make procedure creates a list of source files that
+will be out-of-date for the build if the package configuration changes
+within the same command.  You can include or exclude multiple packages
+in a single make command, e.g. make yes-colloid no-manybody.
+
+[CMake and make info]:
+
+Any package can be included or excluded in a LAMMPS build, independent
+of all other packages.  However, some packages include files derived
+from files in other packages.  LAMMPS checks for this and does the
+right thing.  Individual files are only included if their dependencies
+are already included.  Likewise, if a package is excluded, other files
+dependent on that package are also excluded.
+
+When you download a LAMMPS tarball or download LAMMPS source files
+from the Git or SVN repositories, no packages are pre-installed in the
+src directory.
+
+NOTE: Prior to Aug 2018, if you downloaded a tarball, 3 packages
+(KSPACE, MANYBODY, MOLECULE) were pre-installed in the src directory.
+That is no longer the case, so that CMake will build as-is without the
+need to un-install those packages.
+
+:line
+
+[CMake shortcuts for installing many packages]:
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing the variable cache using script files. These
+are regular CMake files which can manipulate and set variables, and
+can also contain control flow constructs.
+
+LAMMPS includes several of these files to define configuration
+"presets", similar to the options that exist for the Make based
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
+
+cmake -C ../cmake/presets/all_on.cmake \[OPTIONS\] ../cmake | enable all packages
+cmake -C ../cmake/presets/all_off.cmake \[OPTIONS\] ../cmake | disable all packages
+cmake -C ../cmake/presets/std.cmake \[OPTIONS\] ../cmake | enable standard packages
+cmake -C ../cmake/presets/user.cmake \[OPTIONS\] ../cmake | enable user packages
+cmake -C ../cmake/presets/std_nolib.cmake \[OPTIONS\] ../cmake | enable standard packages that do not require extra libraries
+cmake -C ../cmake/presets/nolib.cmake \[OPTIONS\] ../cmake | disable all packages that do not require extra libraries
+cmake -C ../cmake/presets/manual_selection.cmake \[OPTIONS\] ../cmake | example of how to create a manual selection of packages :tb(s=|,a=l)
+
+NOTE: Running cmake this way manipulates the variable cache in your
+current build directory. You can combine presets and options with
+multiple cmake runs.
+
+[Example:]
+
+# build LAMMPS with all "standard" packages which don't
+# use libraries and enable GPU package
+mkdir build
+cd build
+cmake -C ../cmake/presets/std_nolib.cmake -D PKG_GPU=on ../cmake :pre
+
+:line
+
+[Make shortcuts for installing many packages]:
+
+The following commands are useful for managing package source files
+and their installation when building LAMMPS via traditional make.
+Just type "make" in lammps/src to see a one-line summary.
+
+These commands install/un-install sets of packages:
+
+make yes-all | install all packages
+make no-all | un-install all packages
+make yes-standard or make yes-std | install standard packages
+make no-standard or make no-std| un-install standard packages
+make yes-user | install user packages
+make no-user | un-install user packages
+make yes-lib | install packages that require extra libraries
+make no-lib | un-install packages that require extra libraries
+make yes-ext | install packages that require external libraries
+make no-ext | un-install packages that require external libraries :tb(s=|,a=l)
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+NOTE: Installing or un-installing a package works by simply copying
+files back and forth between the main src directory and
+sub-directories with the package name (e.g. src/KSPACE, src/USER-ATC),
+so that the files are included or excluded when LAMMPS is built.
+
+The following make commands help manage files that exist in both the
+src directory and in package sub-directories.  You do not normally
+need to use these commands unless you are editing LAMMPS files or are
+"installing a patch"_Install_patch.html downloaded from the LAMMPS web
+site.
+
+Type "make package-status" or "make ps" to show which packages are
+currently installed.  For those that are installed, it will list any
+files that are different in the src directory and package
+sub-directory.
+
+Type "make package-installed" or "make pi" to show which packages are
+currently installed, without listing the status of packages that are
+not installed.
+
+Type "make package-update" or "make pu" to overwrite src files with
+files from the package sub-directories if the package is installed.
+It should be used after a "patch has been applied"_Install_patch.html,
+since patches only update the files in the package sub-directory, but
+not the src files.
+
+Type "make package-overwrite" to overwrite files in the package
+sub-directories with src files.
+
+Type "make package-diff" to list all differences between pairs of
+files in both the src dir and a package dir.

doc/src/Build_settings.txt

@@ -0,0 +1,341 @@
+"Higher level section"_Build.html - "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
+
+Optional build settings :h3
+
+LAMMPS can be built with several optional settings.  Each sub-section
+explain how to do this for building both with CMake and make.
+
+"FFT library"_#fft for use with the "kspace_style pppm"_kspace_style.html command
+"Size of LAMMPS data types"_#size
+"Read or write compressed files"_#gzip
+"Output of JPG and PNG files"_#graphics via the "dump image"_dump_image.html command
+"Output of movie files"_#graphics via the "dump_movie"_dump_image.html command
+"Memory allocation alignment"_#align
+"Workaround for long long integers"_#longlong
+"Error handling exceptions"_#exceptions when using LAMMPS as a library :all(b)
+
+:line
+
+FFT library :h4,link(fft)
+
+When the KSPACE package is included in a LAMMPS build, the
+"kspace_style pppm"_kspace_style.html command performs 3d FFTs which
+require use of an FFT library to compute 1d FFTs.  The KISS FFT
+library is included with LAMMPS but other libraries can be faster.
+LAMMPS can use them if they are available on your system.
+
+[CMake variables]:
+
+-D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+-D FFT_SINGLE=value       # yes or no (default), no = double precision
+-D FFT_PACK=value         # array (default) or pointer or memcpy :pre
+
+NOTE: The values for the FFT variable must be in upper-case.  This is
+an exception to the rule that all CMake variables can be specified
+with lower-case values.
+
+Usually these settings are all that is needed.  If CMake cannot find
+the FFT library, you can set these variables:
+
+-D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
+-D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+-D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+-D MKL_LIBRARIES=path :pre
+
+[Makefile.machine settings]:
+
+FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                              # default is KISS if not specified
+FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY :pre
+                              # default is FFT_PACK_ARRAY if not specified
+
+FFT_INC =    	-I/usr/local/include
+FFT_PATH =      -L/usr/local/lib
+FFT_LIB =	-lfftw3             # FFTW3 double precision
+FFT_LIB =	-lfftw3 -lfftw3f    # FFTW3 single precision
+FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core  # MKL with Intel compiler
+FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core     # MKL with GNU compier :pre
+
+As with CMake, you do not need to set paths in FFT_INC or FFT_PATH, if
+make can find the FFT header and library files.  You must specify
+FFT_LIB with the appropriate FFT libraries to include in the link.
+
+[CMake and make info]:
+
+The "KISS FFT library"_http://kissfft.sf.net is included in the LAMMPS
+distribution.  It is portable across all platforms.  Depending on the
+size of the FFTs and the number of processors used, the other
+libraries listed here can be faster.
+
+However, note that long-range Coulombics are only a portion of the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly).  A breakdown of these timings is printed
+to the screen at the end of a run using the "kspace_style
+pppm"_kspace_style.html command.  The "Run output"_Run_output.html
+doc page gives more details.
+
+FFTW is a fast, portable FFT library that should also work on any
+platform and can be faster than the KISS FFT library.  You can
+download it from "www.fftw.org"_http://www.fftw.org.  LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
+
+Building FFTW for your box should be as simple as ./configure; make;
+make install.  The install command typically requires root privileges
+(e.g. invoke it via sudo), unless you specify a local directory with
+the "--prefix" option of configure.  Type "./configure --help" to see
+various options.
+
+The Intel MKL math library is part of the Intel compiler suite.  It
+can be used with the Intel or GNU compiler (see FFT_LIB setting above).
+
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication.  This cost can be reduced by
+performing single-precision FFTs instead of double precision.  Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats.  Double precision means they are 8-byte doubles.  Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the -DFFT_SINGLE
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
+
+When using -DFFT_SINGLE with FFTW3 you may need to build the FFTW
+library a second time with support for single-precision.
+
+For FFTW3, do the following, which should produce the additional
+library libfftw3f.a
+
+make clean
+./configure --enable-single; make; make install :pre
+
+Performing 3d FFTs requires communication to transpose the 3d FFT
+grid.  The data packing/unpacking for this can be done in one of 3
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
+Depending on the machine, the size of the FFT grid, the number of
+processors used, one option may be slightly faster.  The default is
+ARRAY mode.
+
+:line
+
+Size of LAMMPS data types :h4,link(size)
+
+LAMMPS has a few integer data types which can be defined as 4-byte or
+8-byte integers.  The default setting of "smallbig" is almost always
+adequate.
+
+[CMake variable]:
+
+-D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL :pre
+                               # default is LAMMPS_SMALLBIG if not specified
+[CMake and make info]:
+
+The default "smallbig" setting allows for simulations with:
+
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 :ul
+
+The "bigbig" setting increases the latter two limits.  It allows for:
+
+total atom count = 2^63 atoms (about 9e18)
+total timesteps = 2^63 (about 9e18)
+atom IDs = 2^63 (about 9e18)
+image flags = roll over at about 1 million (2^20) :ul
+
+The "smallsmall" setting is only needed if your machine does not
+support 8-byte integers.  It allows for:
+
+total atom count = 2^31 atoms (about 2 billion)
+total timesteps = 2^31 (about 2 billion)
+atom IDs = 2^31 (about 2 billion)
+image flags = roll over at 512 (2^9) :ul
+
+Atom IDs are not required for atomic systems which do not store bond
+topology information, though IDs are enabled by default.  The
+"atom_modify id no"_atom_modify.html command will turn them off.  Atom
+IDs are required for molecular systems with bond topology (bonds,
+angles, dihedrals, etc).  Thus if you model a molecular system with
+more than 2 billion atoms, you need the "bigbig" setting.
+
+Image flags store 3 values per atom which count the number of times an
+atom has moved through the periodic box in each dimension.  See the
+"dump"_dump.html doc page for a discussion.  If an atom moves through
+the periodic box more than this limit, the value will "roll over",
+e.g. from 511 to -512, which can cause diagnostics like the
+mean-squared displacement, as calculated by the "compute
+msd"_compute_msd.html command, to be faulty.
+
+Note that the USER-ATC package is not currently compatible with the
+"bigbig" setting.
+
+Also note that the GPU package requires its lib/gpu library to be
+compiled with the same size setting, or the link will fail.  A CMake
+build does this automatically.  When building with make, the setting
+in whichever lib/gpu/Makefile is used must be the same as above.
+
+:line
+
+Output of JPG, PNG, and movie files :h4,link(graphics)
+
+The "dump image"_dump_image.html command has options to output JPEG or
+PNG image files.  Likewise the "dump movie"_dump_image.html command
+outputs movie files in MPEG format.  Using these options requires the
+following settings:
+
+[CMake variables]:
+
+-D WITH_JPEG=value      # yes or no
+                          # default = yes if CMake finds JPEG files, else no
+-D WITH_PNG=value       # yes or no
+                          # default = yes if CMake finds PNG and ZLIB files, else no
+-D WITH_FFMPEG=value    # yes or no
+                          # default = yes if CMake can find ffmpeg, else no :pre
+
+Usually these settings are all that is needed.  If CMake cannot find
+the graphics header, library, executable files, you can set these
+variables:
+
+-D JPEG_INCLUDE_DIR=path    # path to jpeglib.h header file
+-D JPEG_LIBRARIES=path      # path to libjpeg.a (.so) file
+-D PNG_INCLUDE_DIR=path     # path to png.h header file
+-D PNG_LIBRARIES=path       # path to libpng.a (.so) file
+-D ZLIB_INCLUDE_DIR=path    # path to zlib.h header file
+-D ZLIB_LIBRARIES=path      # path to libz.a (.so) file
+-D FFMPEG_EXECUTABLE=path   # path to ffmpeg executable :pre
+
+[Makefile.machine settings]:
+
+LMP_INC = -DLAMMPS_JPEG
+LMP_INC = -DLAMMPS_PNG
+LMP_INC = -DLAMMPS_FFMPEG :pre
+
+JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+JPG_LIB = -ljpeg -lpng -lz       # library names :pre
+
+As with CMake, you do not need to set JPG_INC or JPG_PATH, if make can
+find the graphics header and library files.  You must specify JPG_LIB
+with a list of graphics libraries to include in the link.  You must
+insure ffmpeg is in a directory where LAMMPS can find it at runtime,
+i.e. a dir in your PATH environment variable.
+
+[CMake and make info]:
+
+Using ffmpeg to output movie files requires that your machine
+supports the "popen" function in the standard runtime library.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using ffmpeg to hang or
+crash.
+
+:line
+
+Read or write compressed files :h4,link(gzip)
+
+If this option is enabled, large files can be read or written with
+gzip compression by several LAMMPS commands, including
+"read_data"_read_data.html, "rerun"_rerun.html, and "dump"_dump.html.
+
+[CMake variables]:
+
+-D WITH_GZIP=value       # yes or no
+                         # default is yes if CMake can find gzip, else no
+-D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_GZIP :pre
+
+[CMake and make info]:
+
+This option requires that your machine supports the "popen()" function
+in the standard runtime library and that a gzip executable can be
+found by LAMMPS during a run.
+
+NOTE: On some clusters with high-speed networks, using the fork()
+library calls (required by popen()) can interfere with the fast
+communication library and lead to simulations using compressed output
+or input to hang or crash. For selected operations, compressed file
+I/O is also available using a compression library instead, which is
+what the "COMPRESS package"_Packages_details.html#PKG-COMPRESS enables.
+
+:line
+
+Memory allocation alignment :h4,link(align)
+
+This setting enables the use of the posix_memalign() call instead of
+malloc() when LAMMPS allocates large chunks or memory.  This can make
+vector instructions on CPUs more efficient, if dynamically allocated
+memory is aligned on larger-than-default byte boundaries.
+On most current systems, the malloc() implementation returns
+pointers that are aligned to 16-byte boundaries. Using SSE vector
+instructions efficiently, however, requires memory blocks being
+aligned on 64-byte boundaries.
+
+[CMake variable]:
+
+-D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default) :pre
+
+Use a LAMMPS_MEMALIGN value of 0 to disable using posix_memalign()
+and revert to using the malloc() C-library function instead.  When
+compiling LAMMPS for Windows systems, malloc() will always be used
+and this setting ignored.
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64 :pre
+
+Do not set -DLAMMPS_MEMALIGN, if you want to have memory allocated
+with the malloc() function call instead. -DLAMMPS_MEMALIGN [cannot]
+be used on Windows, as it does use different function calls for
+allocating aligned memory, that are not compatible with how LAMMPS
+manages its dynamical memory.
+
+:line
+
+Workaround for long long integers :h4,link(longlong)
+
+If your system or MPI version does not recognize "long long" data
+types, the following setting will be needed.  It converts "long long"
+to a "long" data type, which should be the desired 8-byte integer on
+those systems:
+
+[CMake variable]:
+
+-D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_LONGLONG_TO_LONG :pre
+
+:line
+
+Exception handling when using LAMMPS as a library :h4,link(exceptions)
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled LAMMPS errors do not kill the caller.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python.
+
+[CMake variable]:
+
+-D LAMMPS_EXCEPTIONS=value        # yes or no (default) :pre
+
+[Makefile.machine setting]:
+
+LMP_INC = -DLAMMPS_EXCEPTIONS :pre

doc/src/Build_windows.txt

@@ -0,0 +1,97 @@
+"Higher level section"_Build.html - "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
+
+Notes for building LAMMPS on Windows :h3
+
+"General remarks"_#generic
+"Running Linux on Windows"_#linux
+"Using GNU GCC ported to Windows"_#gnu
+"Using a cross-compiler"_#cross :ul
+
+:line
+
+General remarks :h4,link(generic)
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+Thus portability to other platforms is desired, but not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+
+Running Linux on Windows :h4,link(linux)
+
+So before trying to build LAMMPS on Windows, please consider if using
+the pre-compiled Windows binary packages are sufficient for your needs
+(as an aside, those packages themselves are build on a Linux machine
+using cross-compilers).  If it is necessary for your to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and run a Linux virtual machine,
+or - if have a recently updated Windows 10 installation - consider using
+the Windows subsystem for Linux, which allows to run a bash shell from
+Ubuntu and from there on, you can pretty much use that shell like you
+are running on an Ubuntu Linux machine (e.g. installing software via
+apt-get). For more details on that, please see "this tutorial"_Howto_bash.html
+
+
+Using GNU GCC ported to Windows :h4,link(gnu)
+
+One option for compiling LAMMPS on Windows natively, that has been known
+to work in the past is to install a bash shell, unix shell utilities,
+perl, GNU make, and a GNU compiler ported to Windows. The Cygwin package
+provides a unix/linux interface to low-level Windows functions, so LAMMPS
+can be compiled on Windows. The necessary (minor) modifications to LAMMPS
+are included, but may not always up-to-date for recently added functionality
+and the corresponding new code. A machine makefile for using cygwin for
+the old build system is provided. The CMake build system is untested
+for this; you will have to request that makefiles are generated and
+manually set the compiler.
+
+When compiling for Windows [not] set the -DLAMMPS_MEMALIGN define
+in the LMP_INC makefile variable and add -lwsock32 -lpsapi to the linker
+flags in LIB makefile variable. Try adding -static-libgcc or -static or
+both to the linker flags when your resulting LAMMPS Windows executable
+complains about missing .dll files. The CMake configuration should set
+this up automatically, but is untested.
+
+In case of problems, you are recommended to contact somebody with
+experience in using cygwin.  If you do come across portability problems
+requiring changes to the LAMMPS source code, or figure out corrections
+yourself, please report them on the lammps-users mailing list, or file
+them as an issue or pull request on the LAMMPS GitHub project.
+
+
+Using a cross-compiler :h4,link(cross)
+
+If you need to provide custom LAMMPS binaries for Windows, but do not
+need to do the compilation on Windows, please consider using a Linux
+to Windows cross-compiler. This is how currently the Windows binary
+packages are created by the LAMMPS developers. Because of that, this is
+probably the currently best tested and supported way to build LAMMPS
+executables for Windows.  There are makefiles provided for the
+traditional build system, but CMake has also been successfully tested
+using the mingw32-cmake and mingw64-cmake wrappers that are bundled
+with the cross-compiler environment on Fedora machines.
+
+Please keep in mind, though, that this only applies to compiling LAMMPS.
+Whether the resulting binaries do work correctly is no tested by the
+LAMMPS developers.  We instead rely on the feedback of the users
+of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
+issues to the best of our abilities if we become aware of them. However
+this is subject to time constraints and focus on HPC platforms.
+
+
+Native Visual C++ support :h4,link(native)
+
+Support for the Visual C++ compilers is currently not available. The
+CMake build system is capable of creating suitable a Visual Studio
+style build environment, but the LAMMPS code itself is not fully ported
+to support Visual C++. Volunteers to take on this task are welcome.

doc/src/Commands.txt

@@ -0,0 +1,53 @@
+"Previous Section"_Run_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Packages.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html#comm)
+
+:line
+
+Commands :h2
+
+These pages describe how a LAMMPS input script is formatted and the
+commands in it are used to define a LAMMPS simulation.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_input
+   Commands_parse
+   Commands_structure
+   Commands_category
+
+.. toctree::
+   :maxdepth: 1
+
+   Commands_all
+   Commands_fix
+   Commands_compute
+   Commands_pair
+   Commands_bond
+   Commands_kspace
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"LAMMPS input scripts"_Commands_input.html
+"Parsing rules for input scripts"_Commands_parse.html
+"Input script structure"_Commands_structure.html
+"Commands by category"_Commands_category.html :all(b)
+
+"General commands"_Commands_all.html
+"Fix commands"_Commands_fix.html
+"Compute commands"_Commands_compute.html
+"Pair commands"_Commands_pair.html
+"Bond, angle, dihedral, improper commands"_Commands_bond.html
+"KSpace solvers"_Commands_kspace.html  :all(b)
+
+<!-- END_HTML_ONLY -->
+

doc/src/Commands_all.txt

@@ -0,0 +1,133 @@
+"Higher level section"_Commands.html - "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
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+General commands :h3
+
+An alphabetic list of all general LAMMPS commands.
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"clear"_clear.html,
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"create_box"_create_box.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"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,
+"group"_group.html,
+"group2ndx"_group2ndx.html,
+"hyper"_hyper.html,
+"if"_if.html,
+"info"_info.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"include"_include.html,
+"jump"_jump.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"label"_label.html,
+"lattice"_lattice.html,
+"log"_log.html,
+"mass"_mass.html,
+"message"_message.html,
+"minimize"_minimize.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"molecule"_molecule.html,
+"ndx2group"_group2ndx.html,
+"neb"_neb.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"newton"_newton.html,
+"next"_next.html,
+"package"_package.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"partition"_partition.html,
+"prd"_prd.html,
+"print"_print.html,
+"processors"_processors.html,
+"python"_python.html,
+"quit"_quit.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"region"_region.html,
+"replicate"_replicate.html,
+"rerun"_rerun.html,
+"reset_ids"_reset_ids.html,
+"reset_timestep"_reset_timestep.html,
+"restart"_restart.html,
+"run"_run.html,
+"run_style"_run_style.html,
+"server"_server.html,
+"set"_set.html,
+"shell"_shell.html,
+"special_bonds"_special_bonds.html,
+"suffix"_suffix.html,
+"tad"_tad.html,
+"temper"_temper.html,
+"temper/grem"_temper_grem.html,
+"temper/npt"_temper_npt.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html,
+"uncompute"_uncompute.html,
+"undump"_undump.html,
+"unfix"_unfix.html,
+"units"_units.html,
+"variable"_variable.html,
+"velocity"_velocity.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :tb(c=6,ea=c)

doc/src/Commands_bond.txt

@@ -0,0 +1,132 @@
+"Higher level section"_Commands.html - "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)
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html#bond,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Bond, angle, dihedral, and improper commands :h3
+
+:line
+
+Bond_style potentials :h3,link(bond)
+
+All LAMMPS "bond_style"_bond_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_bond_none.html,
+"zero"_bond_zero.html,
+"hybrid"_bond_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_bond_class2.html,
+"fene (iko)"_bond_fene.html,
+"fene/expand (o)"_bond_fene_expand.html,
+"gromos (o)"_bond_gromos.html,
+"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,
+"oxdna2/fene"_bond_oxdna.html,
+"quartic (o)"_bond_quartic.html,
+"table (o)"_bond_table.html :tb(c=4,ea=c)
+
+:line
+
+Angle_style potentials :h3,link(angle)
+
+All LAMMPS "angle_style"_angle_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_angle_none.html,
+"zero"_angle_zero.html,
+"hybrid"_angle_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_angle_charmm.html,
+"class2 (ko)"_angle_class2.html,
+"class2/p6"_angle_class2.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)
+
+:line
+
+Dihedral_style potentials :h3,link(dihedral)
+
+All LAMMPS "dihedral_style"_dihedral_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_dihedral_none.html,
+"zero"_dihedral_zero.html,
+"hybrid"_dihedral_hybrid.html :tb(c=3,ea=c)
+
+"charmm (iko)"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
+"class2 (ko)"_dihedral_class2.html,
+"cosine/shift/exp (o)"_dihedral_cosine_shift_exp.html,
+"fourier (io)"_dihedral_fourier.html,
+"harmonic (io)"_dihedral_harmonic.html,
+"helix (o)"_dihedral_helix.html,
+"multi/harmonic (o)"_dihedral_multi_harmonic.html,
+"nharmonic (o)"_dihedral_nharmonic.html,
+"opls (iko)"_dihedral_opls.html,
+"quadratic (o)"_dihedral_quadratic.html,
+"spherical"_dihedral_spherical.html,
+"table (o)"_dihedral_table.html,
+"table/cut"_dihedral_table_cut.html :tb(c=4,ea=c)
+
+:line
+
+Improper_style potentials :h3,link(improper)
+
+All LAMMPS "improper_style"_improper_style.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_improper_none.html,
+"zero"_improper_zero.html,
+"hybrid"_improper_hybrid.html :tb(c=3,ea=c)
+
+"class2 (ko)"_improper_class2.html,
+"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_category.txt

@@ -0,0 +1,140 @@
+"Higher level section"_Commands.html - "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
+
+Commands by category :h3
+
+This page lists most of the LAMMPS commands, grouped by category.  The
+"General commands"_Commands_all.html doc page lists all general commands
+alphabetically.  Style options for entries like fix, compute, pair etc.
+have their own pages where they are listed alphabetically.
+
+Initialization:
+
+"newton"_newton.html,
+"package"_package.html,
+"processors"_processors.html,
+"suffix"_suffix.html,
+"units"_units.html :ul
+
+Setup simulation box:
+
+"boundary"_boundary.html,
+"box"_box.html,
+"change_box"_change_box.html,
+"create_box"_create_box.html,
+"dimension"_dimension.html,
+"lattice"_lattice.html,
+"region"_region.html :ul
+
+Setup atoms:
+
+"atom_modify"_atom_modify.html,
+"atom_style"_atom_style.html,
+"balance"_balance.html,
+"create_atoms"_create_atoms.html,
+"create_bonds"_create_bonds.html,
+"delete_atoms"_delete_atoms.html,
+"delete_bonds"_delete_bonds.html,
+"displace_atoms"_displace_atoms.html,
+"group"_group.html,
+"mass"_mass.html,
+"molecule"_molecule.html,
+"read_data"_read_data.html,
+"read_dump"_read_dump.html,
+"read_restart"_read_restart.html,
+"replicate"_replicate.html,
+"set"_set.html,
+"velocity"_velocity.html :ul
+
+Force fields:
+
+"angle_coeff"_angle_coeff.html,
+"angle_style"_angle_style.html,
+"bond_coeff"_bond_coeff.html,
+"bond_style"_bond_style.html,
+"bond_write"_bond_write.html,
+"dielectric"_dielectric.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"dihedral_style"_dihedral_style.html,
+"improper_coeff"_improper_coeff.html,
+"improper_style"_improper_style.html,
+"kspace_modify"_kspace_modify.html,
+"kspace_style"_kspace_style.html,
+"pair_coeff"_pair_coeff.html,
+"pair_modify"_pair_modify.html,
+"pair_style"_pair_style.html,
+"pair_write"_pair_write.html,
+"special_bonds"_special_bonds.html :ul
+
+Settings:
+
+"comm_modify"_comm_modify.html,
+"comm_style"_comm_style.html,
+"info"_info.html,
+"min_modify"_min_modify.html,
+"min_style"_min_style.html,
+"neigh_modify"_neigh_modify.html,
+"neighbor"_neighbor.html,
+"partition"_partition.html,
+"reset_timestep"_reset_timestep.html,
+"run_style"_run_style.html,
+"timer"_timer.html,
+"timestep"_timestep.html :ul
+
+Operations within timestepping (fixes) and diagnostics (computes):
+
+"compute"_compute.html,
+"compute_modify"_compute_modify.html,
+"fix"_fix.html,
+"fix_modify"_fix_modify.html,
+"uncompute"_uncompute.html,
+"unfix"_unfix.html :ul
+
+Output:
+
+"dump image"_dump_image.html,
+"dump movie"_dump_image.html,
+"dump"_dump.html,
+"dump_modify"_dump_modify.html,
+"restart"_restart.html,
+"thermo"_thermo.html,
+"thermo_modify"_thermo_modify.html,
+"thermo_style"_thermo_style.html,
+"undump"_undump.html,
+"write_coeff"_write_coeff.html,
+"write_data"_write_data.html,
+"write_dump"_write_dump.html,
+"write_restart"_write_restart.html :ul
+
+Actions:
+
+"minimize"_minimize.html,
+"neb"_neb.html,
+"prd"_prd.html,
+"rerun"_rerun.html,
+"run"_run.html,
+"tad"_tad.html,
+"temper"_temper.html :ul
+
+Input script control:
+
+"clear"_clear.html,
+"echo"_echo.html,
+"if"_if.html,
+"include"_include.html,
+"jump"_jump.html,
+"label"_label.html,
+"log"_log.html,
+"next"_next.html,
+"print"_print.html,
+"python"_python.html,
+"quit"_quit.html,
+"shell"_shell.html,
+"variable"_variable.html :ul
+

doc/src/Commands_compute.txt

@@ -0,0 +1,161 @@
+"Higher level section"_Commands.html - "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
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Compute commands :h3
+
+An alphabetic list of all LAMMPS "compute"_compute.html commands.
+Some styles have accelerated versions.  This is indicated by
+additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
+KOKKOS, o = USER-OMP, t = OPT.
+
+"ackland/atom"_compute_ackland_atom.html,
+"adf"_compute_adf.html,
+"aggregate/atom"_compute_cluster_atom.html,
+"angle"_compute_angle.html,
+"angle/local"_compute_angle_local.html,
+"angmom/chunk"_compute_angmom_chunk.html,
+"basal/atom"_compute_basal_atom.html,
+"body/local"_compute_body_local.html,
+"bond"_compute_bond.html,
+"bond/local"_compute_bond_local.html,
+"centro/atom"_compute_centro_atom.html,
+"chunk/atom"_compute_chunk_atom.html,
+"chunk/spread/atom"_compute_chunk_spread_atom.html,
+"cluster/atom"_compute_cluster_atom.html,
+"cna/atom"_compute_cna_atom.html,
+"cnp/atom"_compute_cnp_atom.html,
+"com"_compute_com.html,
+"com/chunk"_compute_com_chunk.html,
+"contact/atom"_compute_contact_atom.html,
+"coord/atom"_compute_coord_atom.html,
+"damage/atom"_compute_damage_atom.html,
+"dihedral"_compute_dihedral.html,
+"dihedral/local"_compute_dihedral_local.html,
+"dilatation/atom"_compute_dilatation_atom.html,
+"dipole/chunk"_compute_dipole_chunk.html,
+"displace/atom"_compute_displace_atom.html,
+"dpd"_compute_dpd.html,
+"dpd/atom"_compute_dpd_atom.html,
+"edpd/temp/atom"_compute_edpd_temp_atom.html,
+"entropy/atom"_compute_entropy_atom.html,
+"erotate/asphere"_compute_erotate_asphere.html,
+"erotate/rigid"_compute_erotate_rigid.html,
+"erotate/sphere"_compute_erotate_sphere.html,
+"erotate/sphere/atom"_compute_erotate_sphere_atom.html,
+"event/displace"_compute_event_displace.html,
+"fep"_compute_fep.html,
+"force/tally"_compute_tally.html,
+"fragment/atom"_compute_cluster_atom.html,
+"global/atom"_compute_global_atom.html,
+"group/group"_compute_group_group.html,
+"gyration"_compute_gyration.html,
+"gyration/chunk"_compute_gyration_chunk.html,
+"heat/flux"_compute_heat_flux.html,
+"heat/flux/tally"_compute_tally.html,
+"hexorder/atom"_compute_hexorder_atom.html,
+"improper"_compute_improper.html,
+"improper/local"_compute_improper_local.html,
+"inertia/chunk"_compute_inertia_chunk.html,
+"ke"_compute_ke.html,
+"ke/atom"_compute_ke_atom.html,
+"ke/atom/eff"_compute_ke_atom_eff.html,
+"ke/eff"_compute_ke_eff.html,
+"ke/rigid"_compute_ke_rigid.html,
+"meso/e/atom"_compute_meso_e_atom.html,
+"meso/rho/atom"_compute_meso_rho_atom.html,
+"meso/t/atom"_compute_meso_t_atom.html,
+"msd"_compute_msd.html,
+"msd/chunk"_compute_msd_chunk.html,
+"msd/nongauss"_compute_msd_nongauss.html,
+"omega/chunk"_compute_omega_chunk.html,
+"orientorder/atom"_compute_orientorder_atom.html,
+"pair"_compute_pair.html,
+"pair/local"_compute_pair_local.html,
+"pe"_compute_pe.html,
+"pe/atom"_compute_pe_atom.html,
+"pe/mol/tally"_compute_tally.html,
+"pe/tally"_compute_tally.html,
+"plasticity/atom"_compute_plasticity_atom.html,
+"pressure"_compute_pressure.html,
+"pressure/cylinder"_compute_pressure_cylinder.html,
+"pressure/uef"_compute_pressure_uef.html,
+"property/atom"_compute_property_atom.html,
+"property/chunk"_compute_property_chunk.html,
+"property/local"_compute_property_local.html,
+"ptm/atom"_compute_ptm_atom.html,
+"rdf"_compute_rdf.html,
+"reduce"_compute_reduce.html,
+"reduce/chunk"_compute_reduce_chunk.html,
+"reduce/region"_compute_reduce.html,
+"rigid/local"_compute_rigid_local.html,
+"saed"_compute_saed.html,
+"slice"_compute_slice.html,
+"smd/contact/radius"_compute_smd_contact_radius.html,
+"smd/damage"_compute_smd_damage.html,
+"smd/hourglass/error"_compute_smd_hourglass_error.html,
+"smd/internal/energy"_compute_smd_internal_energy.html,
+"smd/plastic/strain"_compute_smd_plastic_strain.html,
+"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html,
+"smd/rho"_compute_smd_rho.html,
+"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html,
+"smd/tlsph/dt"_compute_smd_tlsph_dt.html,
+"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html,
+"smd/tlsph/shape"_compute_smd_tlsph_shape.html,
+"smd/tlsph/strain"_compute_smd_tlsph_strain.html,
+"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html,
+"smd/tlsph/stress"_compute_smd_tlsph_stress.html,
+"smd/triangle/vertices"_compute_smd_triangle_vertices.html,
+"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html,
+"smd/ulsph/strain"_compute_smd_ulsph_strain.html,
+"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html,
+"smd/ulsph/stress"_compute_smd_ulsph_stress.html,
+"smd/vol"_compute_smd_vol.html,
+"sna/atom"_compute_sna_atom.html,
+"snad/atom"_compute_sna_atom.html,
+"snav/atom"_compute_sna_atom.html,
+"spin"_compute_spin.html,
+"stress/atom"_compute_stress_atom.html,
+"stress/mop"_compute_stress_mop.html,
+"stress/mop/profile"_compute_stress_mop.html,
+"stress/tally"_compute_tally.html,
+"tdpd/cc/atom"_compute_tdpd_cc_atom.html,
+"temp (k)"_compute_temp.html,
+"temp/asphere"_compute_temp_asphere.html,
+"temp/body"_compute_temp_body.html,
+"temp/chunk"_compute_temp_chunk.html,
+"temp/com"_compute_temp_com.html,
+"temp/cs"_compute_temp_cs.html,
+"temp/deform"_compute_temp_deform.html,
+"temp/deform/eff"_compute_temp_deform_eff.html,
+"temp/drude"_compute_temp_drude.html,
+"temp/eff"_compute_temp_eff.html,
+"temp/partial"_compute_temp_partial.html,
+"temp/profile"_compute_temp_profile.html,
+"temp/ramp"_compute_temp_ramp.html,
+"temp/region"_compute_temp_region.html,
+"temp/region/eff"_compute_temp_region_eff.html,
+"temp/rotate"_compute_temp_rotate.html,
+"temp/sphere"_compute_temp_sphere.html,
+"temp/uef"_compute_temp_uef.html,
+"ti"_compute_ti.html,
+"torque/chunk"_compute_torque_chunk.html,
+"vacf"_compute_vacf.html,
+"vcm/chunk"_compute_vcm_chunk.html,
+"voronoi/atom"_compute_voronoi_atom.html,
+"xrd"_compute_xrd.html :tb(c=6,ea=c)

doc/src/Commands_fix.txt

@@ -0,0 +1,237 @@
+"Higher level section"_Commands.html - "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
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Fix commands :h3
+
+An alphabetic list of all LAMMPS "fix"_fix.html commands.  Some styles
+have accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"adapt"_fix_adapt.html,
+"adapt/fep"_fix_adapt_fep.html,
+"addforce"_fix_addforce.html,
+"addtorque"_fix_addtorque.html,
+"append/atoms"_fix_append_atoms.html,
+"atc"_fix_atc.html,
+"atom/swap"_fix_atom_swap.html,
+"ave/atom"_fix_ave_atom.html,
+"ave/chunk"_fix_ave_chunk.html,
+"ave/correlate"_fix_ave_correlate.html,
+"ave/correlate/long"_fix_ave_correlate_long.html,
+"ave/histo"_fix_ave_histo.html,
+"ave/histo/weight"_fix_ave_histo.html,
+"ave/time"_fix_ave_time.html,
+"aveforce"_fix_aveforce.html,
+"balance"_fix_balance.html,
+"bocs"_fix_bocs.html,
+"bond/break"_fix_bond_break.html,
+"bond/create"_fix_bond_create.html,
+"bond/react"_fix_bond_react.html,
+"bond/swap"_fix_bond_swap.html,
+"box/relax"_fix_box_relax.html,
+"client/md"_fix_client_md.html,
+"cmap"_fix_cmap.html,
+"colvars"_fix_colvars.html,
+"controller"_fix_controller.html,
+"deform (k)"_fix_deform.html,
+"deposit"_fix_deposit.html,
+"dpd/energy (k)"_fix_dpd_energy.html,
+"drag"_fix_drag.html,
+"drude"_fix_drude.html,
+"drude/transform/direct"_fix_drude_transform.html,
+"drude/transform/inverse"_fix_drude_transform.html,
+"dt/reset"_fix_dt_reset.html,
+"edpd/source"_fix_dpd_source.html,
+"efield"_fix_efield.html,
+"ehex"_fix_ehex.html,
+"enforce2d (k)"_fix_enforce2d.html,
+"eos/cv"_fix_eos_cv.html,
+"eos/table"_fix_eos_table.html,
+"eos/table/rx (k)"_fix_eos_table_rx.html,
+"evaporate"_fix_evaporate.html,
+"external"_fix_external.html,
+"ffl"_fix_ffl.html,
+"filter/corotate"_fix_filter_corotate.html,
+"flow/gauss"_fix_flow_gauss.html,
+"freeze (k)"_fix_freeze.html,
+"gcmc"_fix_gcmc.html,
+"gld"_fix_gld.html,
+"gle"_fix_gle.html,
+"gravity (ko)"_fix_gravity.html,
+"grem"_fix_grem.html,
+"halt"_fix_halt.html,
+"heat"_fix_heat.html,
+"hyper/global"_fix_hyper_global.html,
+"hyper/local"_fix_hyper_local.html,
+"imd"_fix_imd.html,
+"indent"_fix_indent.html,
+"ipi"_fix_ipi.html,
+"langevin (k)"_fix_langevin.html,
+"langevin/drude"_fix_langevin_drude.html,
+"langevin/eff"_fix_langevin_eff.html,
+"langevin/spin"_fix_langevin_spin.html,
+"latte"_fix_latte.html,
+"lb/fluid"_fix_lb_fluid.html,
+"lb/momentum"_fix_lb_momentum.html,
+"lb/pc"_fix_lb_pc.html,
+"lb/rigid/pc/sphere"_fix_lb_rigid_pc_sphere.html,
+"lb/viscous"_fix_lb_viscous.html,
+"lineforce"_fix_lineforce.html,
+"manifoldforce"_fix_manifoldforce.html,
+"meso"_fix_meso.html,
+"meso/move"_fix_meso_move.html,
+"meso/stationary"_fix_meso_stationary.html,
+"momentum (k)"_fix_momentum.html,
+"move"_fix_move.html,
+"mscg"_fix_mscg.html,
+"msst"_fix_msst.html,
+"mvv/dpd"_fix_mvv_dpd.html,
+"mvv/edpd"_fix_mvv_dpd.html,
+"mvv/tdpd"_fix_mvv_dpd.html,
+"neb"_fix_neb.html,
+"nph (ko)"_fix_nh.html,
+"nph/asphere (o)"_fix_nph_asphere.html,
+"nph/body"_fix_nph_body.html,
+"nph/eff"_fix_nh_eff.html,
+"nph/sphere (o)"_fix_nph_sphere.html,
+"nphug (o)"_fix_nphug.html,
+"npt (iko)"_fix_nh.html,
+"npt/asphere (o)"_fix_npt_asphere.html,
+"npt/body"_fix_npt_body.html,
+"npt/eff"_fix_nh_eff.html,
+"npt/sphere (o)"_fix_npt_sphere.html,
+"npt/uef"_fix_nh_uef.html,
+"nve (iko)"_fix_nve.html,
+"nve/asphere (i)"_fix_nve_asphere.html,
+"nve/asphere/noforce"_fix_nve_asphere_noforce.html,
+"nve/awpmd"_fix_nve_awpmd.html,
+"nve/body"_fix_nve_body.html,
+"nve/dot"_fix_nve_dot.html,
+"nve/dotc/langevin"_fix_nve_dotc_langevin.html,
+"nve/eff"_fix_nve_eff.html,
+"nve/limit"_fix_nve_limit.html,
+"nve/line"_fix_nve_line.html,
+"nve/manifold/rattle"_fix_nve_manifold_rattle.html,
+"nve/noforce"_fix_nve_noforce.html,
+"nve/sphere (ko)"_fix_nve_sphere.html,
+"nve/spin"_fix_nve_spin.html,
+"nve/tri"_fix_nve_tri.html,
+"nvk"_fix_nvk.html,
+"nvt (iko)"_fix_nh.html,
+"nvt/asphere (o)"_fix_nvt_asphere.html,
+"nvt/body"_fix_nvt_body.html,
+"nvt/eff"_fix_nh_eff.html,
+"nvt/manifold/rattle"_fix_nvt_manifold_rattle.html,
+"nvt/sllod (io)"_fix_nvt_sllod.html,
+"nvt/sllod/eff"_fix_nvt_sllod_eff.html,
+"nvt/sphere (o)"_fix_nvt_sphere.html,
+"nvt/uef"_fix_nh_uef.html,
+"oneway"_fix_oneway.html,
+"orient/bcc"_fix_orient.html,
+"orient/fcc"_fix_orient.html,
+"phonon"_fix_phonon.html,
+"pimd"_fix_pimd.html,
+"planeforce"_fix_planeforce.html,
+"plumed"_fix_plumed.html,
+"poems"_fix_poems.html,
+"pour"_fix_pour.html,
+"precession/spin"_fix_precession_spin.html,
+"press/berendsen"_fix_press_berendsen.html,
+"print"_fix_print.html,
+"property/atom (k)"_fix_property_atom.html,
+"python/invoke"_fix_python_invoke.html,
+"python/move"_fix_python_move.html,
+"qbmsst"_fix_qbmsst.html,
+"qeq/comb (o)"_fix_qeq_comb.html,
+"qeq/dynamic"_fix_qeq.html,
+"qeq/fire"_fix_qeq.html,
+"qeq/point"_fix_qeq.html,
+"qeq/reax (ko)"_fix_qeq_reax.html,
+"qeq/shielded"_fix_qeq.html,
+"qeq/slater"_fix_qeq.html,
+"qmmm"_fix_qmmm.html,
+"qtb"_fix_qtb.html,
+"rattle"_fix_shake.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,
+"rhok"_fix_rhok.html,
+"rigid (o)"_fix_rigid.html,
+"rigid/meso"_fix_rigid_meso.html,
+"rigid/nph (o)"_fix_rigid.html,
+"rigid/nph/small"_fix_rigid.html,
+"rigid/npt (o)"_fix_rigid.html,
+"rigid/npt/small"_fix_rigid.html,
+"rigid/nve (o)"_fix_rigid.html,
+"rigid/nve/small"_fix_rigid.html,
+"rigid/nvt (o)"_fix_rigid.html,
+"rigid/nvt/small"_fix_rigid.html,
+"rigid/small (o)"_fix_rigid.html,
+"rx (k)"_fix_rx.html,
+"saed/vtk"_fix_saed_vtk.html,
+"setforce (k)"_fix_setforce.html,
+"shake"_fix_shake.html,
+"shardlow (k)"_fix_shardlow.html,
+"smd"_fix_smd.html,
+"smd/adjust_dt"_fix_smd_adjust_dt.html,
+"smd/integrate_tlsph"_fix_smd_integrate_tlsph.html,
+"smd/integrate_ulsph"_fix_smd_integrate_ulsph.html,
+"smd/move_tri_surf"_fix_smd_move_triangulated_surface.html,
+"smd/setvel"_fix_smd_setvel.html,
+"smd/wall_surface"_fix_smd_wall_surface.html,
+"spring"_fix_spring.html,
+"spring/chunk"_fix_spring_chunk.html,
+"spring/rg"_fix_spring_rg.html,
+"spring/self"_fix_spring_self.html,
+"srd"_fix_srd.html,
+"store/force"_fix_store_force.html,
+"store/state"_fix_store_state.html,
+"tdpd/source"_fix_dpd_source.html,
+"temp/berendsen"_fix_temp_berendsen.html,
+"temp/csld"_fix_temp_csvr.html,
+"temp/csvr"_fix_temp_csvr.html,
+"temp/rescale"_fix_temp_rescale.html,
+"temp/rescale/eff"_fix_temp_rescale_eff.html,
+"tfmc"_fix_tfmc.html,
+"thermal/conductivity"_fix_thermal_conductivity.html,
+"ti/spring"_fix_ti_spring.html,
+"tmd"_fix_tmd.html,
+"ttm"_fix_ttm.html,
+"ttm/mod"_fix_ttm.html,
+"tune/kspace"_fix_tune_kspace.html,
+"vector"_fix_vector.html,
+"viscosity"_fix_viscosity.html,
+"viscous"_fix_viscous.html,
+"wall/body/polygon"_fix_wall_body_polygon.html,
+"wall/body/polyhedron"_fix_wall_body_polyhedron.html,
+"wall/colloid"_fix_wall.html,
+"wall/ees"_fix_wall_ees.html,
+"wall/gran (o)"_fix_wall_gran.html,
+"wall/gran/region"_fix_wall_gran_region.html,
+"wall/harmonic"_fix_wall.html,
+"wall/lj1043"_fix_wall.html,
+"wall/lj126"_fix_wall.html,
+"wall/lj93 (k)"_fix_wall.html,
+"wall/piston"_fix_wall_piston.html,
+"wall/reflect (k)"_fix_wall_reflect.html,
+"wall/region"_fix_wall_region.html,
+"wall/region/ees"_fix_wall_ees.html,
+"wall/srd"_fix_wall_srd.html :tb(c=6,ea=c)

doc/src/Commands_input.txt

@@ -0,0 +1,60 @@
+"Higher level section"_Commands.html - "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
+
+LAMMPS input scripts :h3
+
+LAMMPS executes by reading commands from a input script (text file),
+one line at a time.  When the input script ends, LAMMPS exits.  Each
+command causes LAMMPS to take some action.  It may set an internal
+variable, read in a file, or run a simulation.  Most commands have
+default settings, which means you only need to use the command if you
+wish to change the default.
+
+In many cases, the ordering of commands in an input script is not
+important.  However the following rules apply:
+
+(1) LAMMPS does not read your entire input script and then perform a
+simulation with all the settings.  Rather, the input script is read
+one line at a time and each command takes effect when it is read.
+Thus this sequence of commands:
+
+timestep 0.5
+run      100
+run      100 :pre
+
+does something different than this sequence:
+
+run      100
+timestep 0.5
+run      100 :pre
+
+In the first case, the specified timestep (0.5 fs) is used for two
+simulations of 100 timesteps each.  In the 2nd case, the default
+timestep (1.0 fs) is used for the 1st 100 step simulation and a 0.5 fs
+timestep is used for the 2nd one.
+
+(2) Some commands are only valid when they follow other commands.  For
+example you cannot set the temperature of a group of atoms until atoms
+have been defined and a group command is used to define which atoms
+belong to the group.
+
+(3) Sometimes command B will use values that can be set by command A.
+This means command A must precede command B in the input script if it
+is to have the desired effect.  For example, the
+"read_data"_read_data.html command initializes the system by setting
+up the simulation box and assigning atoms to processors.  If default
+values are not desired, the "processors"_processors.html and
+"boundary"_boundary.html commands need to be used before read_data to
+tell LAMMPS how to map processors to the simulation box.
+
+Many input script errors are detected by LAMMPS and an ERROR or
+WARNING message is printed.  The "Errors"_Errors.html doc page gives
+more information on what errors mean.  The documentation for each
+command lists restrictions on how the command can be used.
+

doc/src/Commands_kspace.txt

@@ -0,0 +1,37 @@
+"Higher level section"_Commands.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands.html)
+
+:line
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+KSpace solvers :h3
+
+All LAMMPS "kspace_style"_kspace_style.html solvers.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"ewald (o)"_kspace_style.html,
+"ewald/disp"_kspace_style.html,
+"msm (o)"_kspace_style.html,
+"msm/cg (o)"_kspace_style.html,
+"pppm (gok)"_kspace_style.html,
+"pppm/cg (o)"_kspace_style.html,
+"pppm/disp (i)"_kspace_style.html,
+"pppm/disp/tip4p"_kspace_style.html,
+"pppm/stagger"_kspace_style.html,
+"pppm/tip4p (o)"_kspace_style.html,
+"scafacos"_kspace_style.html :tb(c=4,ea=c)

doc/src/Commands_pair.txt

@@ -0,0 +1,243 @@
+"Higher level section"_Commands.html - "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
+
+"General commands"_Commands_all.html,
+"Fix styles"_Commands_fix.html,
+"Compute styles"_Commands_compute.html,
+"Pair styles"_Commands_pair.html,
+"Bond styles"_Commands_bond.html,
+"Angle styles"_Commands_bond.html#angle,
+"Dihedral styles"_Commands_bond.html#dihedral,
+"Improper styles"_Commands_bond.html#improper,
+"KSpace styles"_Commands_kspace.html :tb(c=3,ea=c)
+
+Pair_style potentials :h3
+
+All LAMMPS "pair_style"_pair_style.html commands.  Some styles have
+accelerated versions.  This is indicated by additional letters in
+parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+OPT.
+
+"none"_pair_none.html,
+"zero"_pair_zero.html,
+"hybrid (k)"_pair_hybrid.html,
+"hybrid/overlay (k)"_pair_hybrid.html :tb(c=4,ea=c)
+
+"adp (o)"_pair_adp.html,
+"agni (o)"_pair_agni.html,
+"airebo (io)"_pair_airebo.html,
+"airebo/morse (io)"_pair_airebo.html,
+"atm"_pair_atm.html,
+"awpmd/cut"_pair_awpmd.html,
+"beck (go)"_pair_beck.html,
+"body/nparticle"_pair_body_nparticle.html,
+"body/rounded/polygon"_pair_body_rounded_polygon.html,
+"body/rounded/polyhedron"_pair_body_rounded_polyhedron.html,
+"bop"_pair_bop.html,
+"born (go)"_pair_born.html,
+"born/coul/dsf"_pair_born.html,
+"born/coul/dsf/cs"_pair_cs.html,
+"born/coul/long (go)"_pair_born.html,
+"born/coul/long/cs (g)"_pair_cs.html,
+"born/coul/msm (o)"_pair_born.html,
+"born/coul/wolf (go)"_pair_born.html,
+"born/coul/wolf/cs (g)"_pair_cs.html,
+"brownian (o)"_pair_brownian.html,
+"brownian/poly (o)"_pair_brownian.html,
+"buck (giko)"_pair_buck.html,
+"buck/coul/cut (giko)"_pair_buck.html,
+"buck/coul/long (giko)"_pair_buck.html,
+"buck/coul/long/cs"_pair_cs.html,
+"buck/coul/msm (o)"_pair_buck.html,
+"buck/long/coul/long (o)"_pair_buck_long.html,
+"buck/mdf"_pair_mdf.html,
+"buck6d/coul/gauss/dsf"_pair_buck6d_coul_gauss.html,
+"buck6d/coul/gauss/long"_pair_buck6d_coul_gauss.html,
+"colloid (go)"_pair_colloid.html,
+"comb (o)"_pair_comb.html,
+"comb3"_pair_comb.html,
+"coul/cut (gko)"_pair_coul.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_fep_soft.html,
+"coul/msm (o)"_pair_coul.html,
+"coul/shield"_pair_coul_shield.html,
+"coul/streitz"_pair_coul.html,
+"coul/wolf (ko)"_pair_coul.html,
+"coul/wolf/cs"_pair_cs.html,
+"dpd (gio)"_pair_dpd.html,
+"dpd/fdt"_pair_dpd_fdt.html,
+"dpd/fdt/energy (k)"_pair_dpd_fdt.html,
+"dpd/tstat (go)"_pair_dpd.html,
+"dsmc"_pair_dsmc.html,
+"eam (gikot)"_pair_eam.html,
+"eam/alloy (gikot)"_pair_eam.html,
+"eam/cd (o)"_pair_eam.html,
+"eam/cd/old (o)"_pair_eam.html,
+"eam/fs (gikot)"_pair_eam.html,
+"edip (o)"_pair_edip.html,
+"edip/multi"_pair_edip.html,
+"edpd"_pair_meso.html,
+"eff/cut"_pair_eff.html,
+"eim (o)"_pair_eim.html,
+"exp6/rx (k)"_pair_exp6_rx.html,
+"extep"_pair_extep.html,
+"gauss (go)"_pair_gauss.html,
+"gauss/cut (o)"_pair_gauss.html,
+"gayberne (gio)"_pair_gayberne.html,
+"gran/hertz/history (o)"_pair_gran.html,
+"gran/hooke (o)"_pair_gran.html,
+"gran/hooke/history (ko)"_pair_gran.html,
+"gw"_pair_gw.html,
+"gw/zbl"_pair_gw.html,
+"hbond/dreiding/lj (o)"_pair_hbond_dreiding.html,
+"hbond/dreiding/morse (o)"_pair_hbond_dreiding.html,
+"ilp/graphene/hbn"_pair_ilp_graphene_hbn.html,
+"kim"_pair_kim.html,
+"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_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_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_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_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_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,
+"lj/gromacs/coul/gromacs (ko)"_pair_gromacs.html,
+"lj/long/coul/long (iot)"_pair_lj_long.html,
+"lj/long/dipole/long"_pair_dipole.html,
+"lj/long/tip4p/long (o)"_pair_lj_long.html,
+"lj/mdf"_pair_mdf.html,
+"lj/sdk (gko)"_pair_sdk.html,
+"lj/sdk/coul/long (go)"_pair_sdk.html,
+"lj/sdk/coul/msm (o)"_pair_sdk.html,
+"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,
+"lubricateU"_pair_lubricateU.html,
+"lubricateU/poly"_pair_lubricateU.html,
+"mdpd"_pair_meso.html,
+"mdpd/rhosum"_pair_meso.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,
+"mie/cut (g)"_pair_mie.html,
+"momb"_pair_momb.html,
+"morse (gkot)"_pair_morse.html,
+"morse/smooth/linear (o)"_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,
+"nm/cut (o)"_pair_nm.html,
+"nm/cut/coul/cut (o)"_pair_nm.html,
+"nm/cut/coul/long (o)"_pair_nm.html,
+"oxdna/coaxstk"_pair_oxdna.html,
+"oxdna/excv"_pair_oxdna.html,
+"oxdna/hbond"_pair_oxdna.html,
+"oxdna/stk"_pair_oxdna.html,
+"oxdna/xstk"_pair_oxdna.html,
+"oxdna2/coaxstk"_pair_oxdna2.html,
+"oxdna2/dh"_pair_oxdna2.html,
+"oxdna2/excv"_pair_oxdna2.html,
+"oxdna2/hbond"_pair_oxdna2.html,
+"oxdna2/stk"_pair_oxdna2.html,
+"oxdna2/xstk"_pair_oxdna2.html,
+"peri/eps"_pair_peri.html,
+"peri/lps (o)"_pair_peri.html,
+"peri/pmb (o)"_pair_peri.html,
+"peri/ves"_pair_peri.html,
+"polymorphic"_pair_polymorphic.html,
+"python"_pair_python.html,
+"quip"_pair_quip.html,
+"reax/c (ko)"_pair_reaxc.html,
+"rebo (io)"_pair_airebo.html,
+"resquared (go)"_pair_resquared.html,
+"sdpd/taitwater/isothermal"_pair_sdpd_taitwater_isothermal.html,
+"smd/hertz"_pair_smd_hertz.html,
+"smd/tlsph"_pair_smd_tlsph.html,
+"smd/tri_surface"_pair_smd_triangulated_surface.html,
+"smd/ulsph"_pair_smd_ulsph.html,
+"smtbq"_pair_smtbq.html,
+"snap (k)"_pair_snap.html,
+"snap (k)"_pair_snap.html,
+"soft (go)"_pair_soft.html,
+"sph/heatconduction"_pair_sph_heatconduction.html,
+"sph/idealgas"_pair_sph_idealgas.html,
+"sph/lj"_pair_sph_lj.html,
+"sph/rhosum"_pair_sph_rhosum.html,
+"sph/taitwater"_pair_sph_taitwater.html,
+"sph/taitwater/morris"_pair_sph_taitwater_morris.html,
+"spin/dmi"_pair_spin_dmi.html,
+"spin/exchange"_pair_spin_exchange.html,
+"spin/magelec"_pair_spin_magelec.html,
+"spin/neel"_pair_spin_neel.html,
+"srp"_pair_srp.html,
+"sw (giko)"_pair_sw.html,
+"table (gko)"_pair_table.html,
+"table/rx (k)"_pair_table_rx.html,
+"tdpd"_pair_meso.html,
+"tersoff (giko)"_pair_tersoff.html,
+"tersoff/mod (gko)"_pair_tersoff_mod.html,
+"tersoff/mod/c (o)"_pair_tersoff_mod.html,
+"tersoff/table (o)"_pair_tersoff.html,
+"tersoff/zbl (gko)"_pair_tersoff_zbl.html,
+"thole"_pair_thole.html,
+"tip4p/cut (o)"_pair_coul.html,
+"tip4p/long (o)"_pair_coul.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,
+"vashishta/table (o)"_pair_vashishta.html,
+"yukawa (gko)"_pair_yukawa.html,
+"yukawa/colloid (go)"_pair_yukawa_colloid.html,
+"zbl (gko)"_pair_zbl.html :tb(c=4,ea=c)

doc/src/Commands_parse.txt

@@ -0,0 +1,136 @@
+"Higher level section"_Commands.html - "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
+
+Parsing rules for input scripts :h3
+
+Each non-blank line in the input script is treated as a command.
+LAMMPS commands are case sensitive.  Command names are lower-case, as
+are specified command arguments.  Upper case letters may be used in
+file names or user-chosen ID strings.
+
+Here are 6 rules for how each line in the input script is parsed by
+LAMMPS:
+
+(1) If the last printable character on the line is a "&" character,
+the command is assumed to continue on the next line.  The next line is
+concatenated to the previous line by removing the "&" character and
+line break.  This allows long commands to be continued across two or
+more lines.  See the discussion of triple quotes in (6) for how to
+continue a command across multiple line without using "&" characters.
+
+(2) All characters from the first "#" character onward are treated as
+comment and discarded.  See an exception in (6).  Note that a
+comment after a trailing "&" character will prevent the command from
+continuing on the next line.  Also note that for multi-line commands a
+single leading "#" will comment out the entire command.
+
+(3) The line is searched repeatedly for $ characters, which indicate
+variables that are replaced with a text string.  See an exception in
+(6).
+
+If the $ is followed by curly brackets, then the variable name is the
+text inside the curly brackets.  If no curly brackets follow the $,
+then the variable name is the single character immediately following
+the $.  Thus $\{myTemp\} and $x refer to variable names "myTemp" and
+"x".
+
+How the variable is converted to a text string depends on what style
+of variable it is; see the "variable"_variable.html doc page for details.
+It can be a variable that stores multiple text strings, and return one
+of them.  The returned text string can be multiple "words" (space
+separated) which will then be interpreted as multiple arguments in the
+input command.  The variable can also store a numeric formula which
+will be evaluated and its numeric result returned as a string.
+
+As a special case, if the $ is followed by parenthesis, then the text
+inside the parenthesis is treated as an "immediate" variable and
+evaluated as an "equal-style variable"_variable.html.  This is a way
+to use numeric formulas in an input script without having to assign
+them to variable names.  For example, these 3 input script lines:
+
+variable X equal (xlo+xhi)/2+sqrt(v_area)
+region 1 block $X 2 INF INF EDGE EDGE
+variable X delete :pre
+
+can be replaced by
+
+region 1 block $((xlo+xhi)/2+sqrt(v_area)) 2 INF INF EDGE EDGE :pre
+
+so that you do not have to define (or discard) a temporary variable X.
+
+Additionally, the "immediate" variable expression may be followed by a
+colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
+The format string must be appropriate for a double-precision
+floating-point value.  The format string is used to output the result
+of the variable expression evaluation.  If a format string is not
+specified a high-precision "%.20g" is used as the default.
+
+This can be useful for formatting print output to a desired precision:
+
+print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom" :pre
+
+Note that neither the curly-bracket or immediate form of variables can
+contain nested $ characters for other variables to substitute for.
+Thus you cannot do this:
+
+variable        a equal 2
+variable        b2 equal 4
+print           "B2 = $\{b$a\}" :pre
+
+Nor can you specify this $($x-1.0) for an immediate variable, but
+you could use $(v_x-1.0), since the latter is valid syntax for an
+"equal-style variable"_variable.html.
+
+See the "variable"_variable.html command for more details of how
+strings are assigned to variables and evaluated, and how they can be
+used in input script commands.
+
+(4) The line is broken into "words" separated by white-space (tabs,
+spaces).  Note that words can thus contain letters, digits,
+underscores, or punctuation characters.
+
+(5) The first word is the command name.  All successive words in the
+line are arguments.
+
+(6) If you want text with spaces to be treated as a single argument,
+it can be enclosed in either single or double or triple quotes.  A
+long single argument enclosed in single or double quotes can span
+multiple lines if the "&" character is used, as described above.  When
+the lines are concatenated together (and the "&" characters and line
+breaks removed), the text will become a single line.  If you want
+multiple lines of an argument to retain their line breaks, the text
+can be enclosed in triple quotes, in which case "&" characters are not
+needed.  For example:
+
+print "Volume = $v"
+print 'Volume = $v'
+if "$\{steps\} > 1000" then quit
+variable a string "red green blue &
+                   purple orange cyan"
+print """
+System volume = $v
+System temperature = $t
+""" :pre
+
+In each case, the single, double, or triple quotes are removed when
+the single argument they enclose is stored internally.
+
+See the "dump modify format"_dump_modify.html, "print"_print.html,
+"if"_if.html, and "python"_python.html commands for examples.
+
+A "#" or "$" character that is between quotes will not be treated as a
+comment indicator in (2) or substituted for as a variable in (3).
+
+NOTE: If the argument is itself a command that requires a quoted
+argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then single, double, or
+triple quotes can be nested in the usual manner.  See the doc pages
+for those commands for examples.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
+

doc/src/Commands_structure.txt

@@ -0,0 +1,95 @@
+"Higher level section"_Commands.html - "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
+
+Input script structure :h3
+
+This page describes the structure of a typical LAMMPS input script.
+The examples directory in the LAMMPS distribution contains many sample
+input scripts; it is discussed on the "Examples"_Examples.html doc
+page.
+
+A LAMMPS input script typically has 4 parts:
+
+Initialization
+Atom definition
+Settings
+Run a simulation :ol
+
+The last 2 parts can be repeated as many times as desired.  I.e. run a
+simulation, change some settings, run some more, etc.  Each of the 4
+parts is now described in more detail.  Remember that almost all
+commands need only be used if a non-default value is desired.
+
+(1) Initialization
+
+Set parameters that need to be defined before atoms are created or
+read-in from a file.
+
+The relevant commands are "units"_units.html,
+"dimension"_dimension.html, "newton"_newton.html,
+"processors"_processors.html, "boundary"_boundary.html,
+"atom_style"_atom_style.html, "atom_modify"_atom_modify.html.
+
+If force-field parameters appear in the files that will be read, these
+commands tell LAMMPS what kinds of force fields are being used:
+"pair_style"_pair_style.html, "bond_style"_bond_style.html,
+"angle_style"_angle_style.html, "dihedral_style"_dihedral_style.html,
+"improper_style"_improper_style.html.
+
+(2) Atom definition
+
+There are 3 ways to define atoms in LAMMPS.  Read them in from a data
+or restart file via the "read_data"_read_data.html or
+"read_restart"_read_restart.html commands.  These files can contain
+molecular topology information.  Or create atoms on a lattice (with no
+molecular topology), using these commands: "lattice"_lattice.html,
+"region"_region.html, "create_box"_create_box.html,
+"create_atoms"_create_atoms.html.  The entire set of atoms can be
+duplicated to make a larger simulation using the
+"replicate"_replicate.html command.
+
+(3) Settings
+
+Once atoms and molecular topology are defined, a variety of settings
+can be specified: force field coefficients, simulation parameters,
+output options, etc.
+
+Force field coefficients are set by these commands (they can also be
+set in the read-in files): "pair_coeff"_pair_coeff.html,
+"bond_coeff"_bond_coeff.html, "angle_coeff"_angle_coeff.html,
+"dihedral_coeff"_dihedral_coeff.html,
+"improper_coeff"_improper_coeff.html,
+"kspace_style"_kspace_style.html, "dielectric"_dielectric.html,
+"special_bonds"_special_bonds.html.
+
+Various simulation parameters are set by these commands:
+"neighbor"_neighbor.html, "neigh_modify"_neigh_modify.html,
+"group"_group.html, "timestep"_timestep.html,
+"reset_timestep"_reset_timestep.html, "run_style"_run_style.html,
+"min_style"_min_style.html, "min_modify"_min_modify.html.
+
+Fixes impose a variety of boundary conditions, time integration, and
+diagnostic options.  The "fix"_fix.html command comes in many flavors.
+
+Various computations can be specified for execution during a
+simulation using the "compute"_compute.html,
+"compute_modify"_compute_modify.html, and "variable"_variable.html
+commands.
+
+Output options are set by the "thermo"_thermo.html, "dump"_dump.html,
+and "restart"_restart.html commands.
+
+(4) Run a simulation
+
+A molecular dynamics simulation is run using the "run"_run.html
+command.  Energy minimization (molecular statics) is performed using
+the "minimize"_minimize.html command.  A parallel tempering
+(replica-exchange) simulation can be run using the
+"temper"_temper.html command.
+

doc/src/Developer/.gitignore

@@ -0,0 +1,3 @@
+/developer.aux
+/developer.log
+/developer.toc

doc/src/Developer/developer.tex

@@ -22,10 +22,10 @@ users.
 LAMMPS source files are in two directories of the distribution
 tarball.  The src directory has the majority of them, all of which are
 C++ files (*.cpp and *.h).  Many of these files are in the src
-directory itself.  There are also dozens of "packages", which can be
+directory itself.  There are also dozens of ``packages'', which can be
 included or excluded when LAMMPS is built.  See the
 doc/Section\_build.html section of the manual for more information
-about packages, or type "make" from within the src directory, which
+about packages, or type ``make'' from within the src directory, which
 lists package-related commands, such as ``make package-status''.  The
 source files for each package are in an all-uppercase sub-directory of
 src, like src/MOLECULE or src/USER-CUDA.  If the package is currently
@@ -38,17 +38,17 @@ The lib directory also contains source code for external libraries,
 used by a few of the packages.  Each sub-directory, like meam or gpu,
 contains the source files, some of which are in different languages
 such as Fortran.  The files are compiled into libraries from within
-each sub-directory, e.g. performing a "make" in the lib/meam directory
+each sub-directory, e.g. performing a ``make'' in the lib/meam directory
 creates a libmeam.a file.  These libraries are linked to during a
 LAMMPS build, if the corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as run.cpp
 and run.h.  The pair of files defines a C++ class, the Run class in
-this case, which contains the code invoked by the "run" command in a
+this case, which contains the code invoked by the ``run'' command in a
 LAMMPS input script.  As this example illustrates, source file and
 class names often have a one-to-one correspondence with a command used
 in a LAMMPS input script.  Some source files and classes do not have a
-corresponding input script command, e.g. force.cpp and the Force
+corresponding input script command, e.g. ``force.cpp'' and the Force
 class.  They are discussed in the next section.
 
 \pagebreak
@@ -57,12 +57,12 @@ class.  They are discussed in the next section.
 Though LAMMPS has a lot of source files and classes, its class
 hierarchy is quite simple, as outlined in Fig \ref{fig:classes}.  Each
 boxed name refers to a class and has a pair of associated source files
-in lammps/src, e.g. memory.cpp and memory.h.  More details on the
+in lammps/src, e.g. ``memory.cpp'' and ``memory.h''.  More details on the
 class and its methods and data structures can be found by examining
 its *.h file.
 
 LAMMPS (lammps.cpp/h) is the top-level class for the entire code.  It
-holds an "instance" of LAMMPS and can be instantiated one or more
+holds an ``instance'' of LAMMPS and can be instantiated one or more
 times by a calling code.  For example, the file src/main.cpp simply
 instantiates one instance of LAMMPS and passes it the input script.
 
@@ -81,7 +81,7 @@ enabled by a bit of cleverness in the Pointers class (see
 src/pointers.h) which every class inherits from.
 
 There are a handful of virtual parent classes in LAMMPS that define
-what LAMMPS calls "styles".  They are shaded red in Fig
+what LAMMPS calls ``styles''.  They are shaded red in Fig
 \ref{fig:classes}.  Each of these are parents of a number of child
 classes that implement the interface defined by the parent class.  For
 example, the fix style has around 100 child classes.  They are the
@@ -89,17 +89,17 @@ possible fixes that can be specified by the fix command in an input
 script, e.g. fix nve, fix shake, fix ave/time, etc.  The corresponding
 classes are Fix (for the parent class), FixNVE, FixShake, FixAveTime,
 etc.  The source files for these classes are easy to identify in the
-src directory, since they begin with the word "fix", e,g,
+src directory, since they begin with the word ``fix'', e,g,
 fix\_nve.cpp, fix\_shake,cpp, fix\_ave\_time.cpp, etc.
 
-The one exception is child class files for the "command" style.  These
+The one exception is child class files for the ``command'' style.  These
 implement specific commands in the input script that can be invoked
 before/after/between runs or which launch a simulation.  Examples are
 the create\_box, minimize, run, and velocity commands which encode the
 CreateBox, Minimize, Run, and Velocity classes.  The corresponding
 files are create\_box,cpp, minimize.cpp, run.cpp, and velocity.cpp.
-The list of command style files can be found by typing "grep
-COMMAND\_CLASS *.h" from within the src directory, since that word in
+The list of command style files can be found by typing ``grep
+COMMAND\_CLASS *.h'' from within the src directory, since that word in
 the header file identifies the class as an input script command.
 Similar words can be grepped to list files for the other LAMMPS
 styles.  E.g. ATOM\_CLASS, PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS,
@@ -471,13 +471,13 @@ FixStyle(your/fix/name,FixMine)
   \end{verbatim}
  \end{center}
 
-Where "your/fix/name" is a name of your fix in the script and FixMine
+Where ``your/fix/name'' is a name of your fix in the script and FixMine
 is the name of the class. This code allows LAMMPS to find your fix
 when it parses input script. In addition, your fix header must be
-included in the file "style\_fix.h". In case if you use LAMMPS make,
+included in the file ``style\_fix.h''. In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
-fix\_ are included, so call your header the same way. Otherwise, don<EFBFBD>t
-forget to add your include into "style\_fix.h".
+fix\_ are included, so call your header the same way. Otherwise, don't
+forget to add your include into ``style\_fix.h''.
 
 Let's write a simple fix which will print average velocity at the end
 of each timestep. First of all, implement a constructor:
@@ -567,11 +567,11 @@ void FixPrintVel::end_of_step()
 \end{center}
 
 In the code above, we use MathExtra routines defined in
-"math\_extra.h".  There are bunch of math functions to work with
+``math\_extra.h''.  There are bunch of math functions to work with
 arrays of doubles as with math vectors.
 
 In this code we use an instance of Atom class. This object is stored
-in the Pointers class (see "pointers.h"). This object contains all
+in the Pointers class (see ``pointers.h''). This object contains all
 global information about the simulation system. Data from Pointers
 class available to all classes inherited from it using protected
 inheritance. Hence when you write you own class, which is going to use
@@ -689,7 +689,7 @@ int FixSavePos::unpack_exchange(int nlocal, double *buf)
 
 Now, a little bit about memory allocation. We used Memory class which
 is just a bunch of template functions for allocating 1D and 2D
-arrays. So you need to add include "memory.h" to have access to them.
+arrays. So you need to add include ``memory.h'' to have access to them.
 
 Finally, if you need to write/read some global information used in
 your fix to the restart file, you might do it by setting flag

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_atm.tex

@@ -0,0 +1,9 @@
+\documentclass[12pt]{article}
+
+\begin{document}
+
+\begin{equation}
+E=\nu\frac{1+3\cos\gamma_1\cos\gamma_2\cos\gamma_3}{r_{12}^3r_{23}^3r_{31}^3}
+\end{equation}
+
+\end{document}

doc/src/Eqs/pair_body_rounded.tex

@@ -0,0 +1,13 @@
+\documentstyle[12pt]{article}
+
+\begin{document}
+
+\begin{eqnarray*}
+ F_n &=& k_n \delta_n - c_n v_n, \qquad \delta_n \le 0 \\
+     &=& -k_{na} \delta_n - c_n v_n, \qquad 0 < \delta_n \le r_c \\
+     &=& 0 \qquad \qquad \qquad \qquad \delta_n > r_c \\
+ F_t &=& \mu k_n \delta_n - c_t v_t, \qquad \delta_n \le 0 \\
+     &=& 0 \qquad \qquad \qquad \qquad \delta_n > 0
+\end{eqnarray*}
+
+\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_spin_dmi_forces.tex

@@ -0,0 +1,14 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \vec{\omega}_i = -\frac{1}{\hbar} \sum_{j}^{Neighb} \vec{s}_{j}\times \left(\vec{e}_{ij}\times \vec{D} \right) 
+    ~~{\rm and}~~
+    \vec{F}_i = -\sum_{j}^{Neighb} \frac{1}{r_{ij}} \vec{D} \times \left( \vec{s}_{i}\times \vec{s}_{j} \right) 
+    , \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/pair_spin_dmi_interaction.tex

@@ -5,7 +5,7 @@
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \bm{H}_{dm} = -\sum_{{ i,j}=1,i\neq j}^{N} 
+    \bm{H}_{dm} = \sum_{{ i,j}=1,i\neq j}^{N} 
     \left( \vec{e}_{ij} \times \vec{D} \right)
     \cdot\left(\vec{s}_{i}\times \vec{s}_{j}\right), 
     \nonumber

doc/src/Eqs/pair_spin_exchange_forces.tex

@@ -5,10 +5,12 @@
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \vec{F}^{i} = \sum_{j}^{Neighbor} \frac{\partial {J} \left(r_{ij} \right)}{
-    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{r}_{ij}  
-    ~~{\rm and}~~ \vec{\omega}^{i} = \frac{1}{\hbar} \sum_{j}^{Neighbor} {J} 
-    \left(r_{ij} \right)\,\vec{s}_{j} \nonumber
+    \vec{\omega}_{i} = \frac{1}{\hbar} \sum_{j}^{Neighb} {J} 
+    \left(r_{ij} \right)\,\vec{s}_{j} 
+    ~~{\rm and}~~ 
+    \vec{F}_{i} = \sum_{j}^{Neighb} \frac{\partial {J} \left(r_{ij} \right)}{
+    \partial r_{ij}} \left( \vec{s}_{i}\cdot \vec{s}_{j} \right) \vec{e}_{ij}  
+    \nonumber
   \end{equation}
 \end{varwidth}
 \end{document}

doc/src/Eqs/pair_spin_exchange_interaction.tex

@@ -5,7 +5,7 @@
 \begin{document}
 \begin{varwidth}{50in}
   \begin{equation}
-    \bm{H}_{exchange} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
+    \bm{H}_{ex} ~=~ -\sum_{i,j,i\neq j}^{N} {J} \left(r_{ij} \right)\, \vec{s}_{i}\cdot \vec{s}_{j} \nonumber
   \end{equation}
 \end{varwidth}
 \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/Eqs/ptm_rmsd.tex

@@ -0,0 +1,21 @@
+\documentclass[12pt,article]{article}
+
+\usepackage{indentfirst}
+\usepackage{amsmath}
+
+\newcommand{\set}[1]{\ensuremath{\mathbf{#1}}}
+\newcommand{\mean}[1]{\ensuremath{\overline{#1}}}
+\newcommand{\norm}[1]{\ensuremath{\left|\left|{#1}\right|\right|}}
+
+\begin{document}
+
+\begin{equation*}
+\text{RMSD}(\set{u}, \set{v}) = \min_{s, \set{Q}} \sqrt{\frac{1}{N} \sum\limits_{i=1}^{N}
+\norm{
+s[\vec{u_i} - \mean{\set{u}}]
+-
+\set{Q} \vec{v_i}
+}^2}
+\end{equation*}
+
+\end{document}

doc/src/Errors.txt

@@ -0,0 +1,38 @@
+"Previous Section"_Python_head.html - "LAMMPS WWW Site"_lws -
+"LAMMPS Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Manual.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Errors :h2
+
+These doc pages describe the errors you can encounter when using
+LAMMPS.  The common problems include conceptual issues.  The messages
+and warnings doc pages give complete lists of all the messages the
+code may generate (except those generated by USER packages), with
+additional details for many of them.
+
+<!-- RST
+
+.. toctree::
+   :maxdepth: 1
+
+   Errors_common
+   Errors_bugs
+   Errors_messages
+   Errors_warnings
+
+END_RST -->
+
+<!-- HTML_ONLY -->
+
+"Common problems"_Errors_common.html
+"Reporting bugs"_Errors_bugs.html
+"Error messages"_Errors_messages.html
+"Warning messages"_Errors_warnings.html :all(b)
+
+<!-- END_HTML_ONLY -->

doc/src/Errors_bugs.txt

@@ -0,0 +1,35 @@
+"Higher level section"_Errors.html - "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
+
+Reporting bugs :h3
+
+If you are confident that you have found a bug in LAMMPS, follow these
+steps.
+
+Check the "New features and bug
+fixes"_http://lammps.sandia.gov/bug.html section of the "LAMMPS WWW
+site"_lws to see if the bug has already been reported or fixed or the
+"Unfixed bug"_http://lammps.sandia.gov/unbug.html to see if a fix is
+pending.
+
+Check the "mailing list"_http://lammps.sandia.gov/mail.html to see if
+it has been discussed before.
+
+If not, send an email to the mailing list describing the problem with
+any ideas you have as to what is causing it or where in the code the
+problem might be.  The developers will ask for more info if needed,
+such as an input script or data files.
+
+The most useful thing you can do to help us fix the bug is to isolate
+the problem.  Run it on the smallest number of atoms and fewest number
+of processors and with the simplest input script that reproduces the
+bug and try to identify what command or combination of commands is
+causing the problem.
+
+NOTE: this page needs to have GitHub issues info added

doc/src/Errors_common.txt

@@ -0,0 +1,126 @@
+"Higher level section"_Errors.html - "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
+
+Common problems :h3
+
+If two LAMMPS runs do not produce the exact same answer on different
+machines or different numbers of processors, this is typically not a
+bug.  In theory you should get identical answers on any number of
+processors and on any machine.  In practice, numerical round-off can
+cause slight differences and eventual divergence of molecular dynamics
+phase space trajectories within a few 100s or few 1000s of timesteps.
+However, the statistical properties of the two runs (e.g. average
+energy or temperature) should still be the same.
+
+If the "velocity"_velocity.html command is used to set initial atom
+velocities, a particular atom can be assigned a different velocity
+when the problem is run on a different number of processors or on
+different machines.  If this happens, the phase space trajectories of
+the two simulations will rapidly diverge.  See the discussion of the
+{loop} option in the "velocity"_velocity.html command for details and
+options that avoid this issue.
+
+Similarly, the "create_atoms"_create_atoms.html command generates a
+lattice of atoms.  For the same physical system, the ordering and
+numbering of atoms by atom ID may be different depending on the number
+of processors.
+
+Some commands use random number generators which may be setup to
+produce different random number streams on each processor and hence
+will produce different effects when run on different numbers of
+processors.  A commonly-used example is the "fix
+langevin"_fix_langevin.html command for thermostatting.
+
+A LAMMPS simulation typically has two stages, setup and run.  Most
+LAMMPS errors are detected at setup time; others like a bond
+stretching too far may not occur until the middle of a run.
+
+LAMMPS tries to flag errors and print informative error messages so
+you can fix the problem.  For most errors it will also print the last
+input script command that it was processing.  Of course, LAMMPS cannot
+figure out your physics or numerical mistakes, like choosing too big a
+timestep, specifying erroneous force field coefficients, or putting 2
+atoms on top of each other!  If you run into errors that LAMMPS
+doesn't catch that you think it should flag, please send an email to
+the "developers"_http://lammps.sandia.gov/authors.html.
+
+If you get an error message about an invalid command in your input
+script, you can determine what command is causing the problem by
+looking in the log.lammps file or using the "echo command"_echo.html
+to see it on the screen.  If you get an error like "Invalid ...
+style", with ... being fix, compute, pair, etc, it means that you
+mistyped the style name or that the command is part of an optional
+package which was not compiled into your executable.  The list of
+available styles in your executable can be listed by using "the -h
+command-line swith"_Run_options.html.  The installation and
+compilation of optional packages is explained on the "Build
+packages"_Build_package.html doc page.
+
+For a given command, LAMMPS expects certain arguments in a specified
+order.  If you mess this up, LAMMPS will often flag the error, but it
+may also simply read a bogus argument and assign a value that is
+valid, but not what you wanted.  E.g. trying to read the string "abc"
+as an integer value of 0.  Careful reading of the associated doc page
+for the command should allow you to fix these problems. In most cases,
+where LAMMPS expects to read a number, either integer or floating point,
+it performs a stringent test on whether the provided input actually
+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 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
+course of a run.  This is typically done with the syntax {v_name} for a
+parameter, where name is the name of the variable. On the other hand,
+immediate variable expansion with the syntax ${name} is performed while
+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
+print a WARNING to the screen and logfile and continue on; you can
+decide if the WARNING is important or not.  A WARNING message that is
+generated in the middle of a run is only printed to the screen, not to
+the logfile, to avoid cluttering up thermodynamic output.  If LAMMPS
+crashes or hangs without spitting out an error message first then it
+could be a bug (see "this section"_Errors_bugs.html) or one of the following
+cases:
+
+LAMMPS runs in the available memory a processor allows to be
+allocated.  Most reasonable MD runs are compute limited, not memory
+limited, so this shouldn't be a bottleneck on most platforms.  Almost
+all large memory allocations in the code are done via C-style malloc's
+which will generate an error message if you run out of memory.
+Smaller chunks of memory are allocated via C++ "new" statements.  If
+you are unlucky you could run out of memory just when one of these
+small requests is made, in which case the code will crash or hang (in
+parallel), since LAMMPS doesn't trap on those errors.
+
+Illegal arithmetic can cause LAMMPS to run slow or crash.  This is
+typically due to invalid physics and numerics that your simulation is
+computing.  If you see wild thermodynamic values or NaN values in your
+LAMMPS output, something is wrong with your simulation.  If you
+suspect this is happening, it is a good idea to print out
+thermodynamic info frequently (e.g. every timestep) via the
+"thermo"_thermo.html so you can monitor what is happening.
+Visualizing the atom movement is also a good idea to insure your model
+is behaving as you expect.
+
+In parallel, one way LAMMPS can hang is due to how different MPI
+implementations handle buffering of messages.  If the code hangs
+without an error message, it may be that you need to specify an MPI
+setting or two (usually via an environment variable) to enable
+buffering or boost the sizes of messages that can be buffered.

doc/src/Errors_warnings.txt

@@ -0,0 +1,910 @@
+"Higher level section"_Errors.html - "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
+
+Warning messages :h3
+
+This is an alphabetic list of the WARNING messages LAMMPS prints out
+and the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  Warning messages
+also list the source file and line number where the warning was
+generated.  For example, a message like this:
+
+WARNING: Bond atom missing in box size check (domain.cpp:187) :pre
+
+means that line #187 in the file src/domain.cpp generated the error.
+Looking in the source code may help you figure out what went wrong.
+
+Note that warning messages from "user-contributed
+packages"_Packages_user.html are not listed here.  If such a warning
+occurs and is not self-explanatory, you'll need to look in the source
+code or contact the author of the package.
+
+Doc page with "ERROR messages"_Errors_messages.html
+
+:line
+
+:dlb
+
+{Adjusting Coulombic cutoff for MSM, new cutoff = %g} :dt
+
+The adjust/cutoff command is turned on and the Coulombic cutoff has been
+adjusted to match the user-specified accuracy. :dd
+
+{Angle atoms missing at step %ld} :dt
+
+One or more of 3 atoms needed to compute a particular angle are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the angle has blown apart and an atom is
+too far away. :dd
+
+{Angle style in data file differs from currently defined angle style} :dt
+
+Self-explanatory. :dd
+
+{Atom style in data file differs from currently defined atom style} :dt
+
+Self-explanatory. :dd
+
+{Bond atom missing in box size check} :dt
+
+The 2nd atoms needed to compute a particular bond is missing on this
+processor.  Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away. :dd
+
+{Bond atom missing in image check} :dt
+
+The 2nd atom in a particular bond is missing on this processor.
+Typically this is because the pairwise cutoff is set too short or the
+bond has blown apart and an atom is too far away. :dd
+
+{Bond atoms missing at step %ld} :dt
+
+The 2nd atom needed to compute a particular bond is missing on this
+processor.  Typically this is because the pairwise cutoff is set too
+short or the bond has blown apart and an atom is too far away. :dd
+
+{Bond style in data file differs from currently defined bond style} :dt
+
+Self-explanatory. :dd
+
+{Bond/angle/dihedral extent > half of periodic box length} :dt
+
+This is a restriction because LAMMPS can be confused about which image
+of an atom in the bonded interaction is the correct one to use.
+"Extent" in this context means the maximum end-to-end length of the
+bond/angle/dihedral.  LAMMPS computes this by taking the maximum bond
+length, multiplying by the number of bonds in the interaction (e.g. 3
+for a dihedral) and adding a small amount of stretch. :dd
+
+{Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero} :dt
+
+Self-explanatory. :dd
+
+{Calling write_dump before a full system init.} :dt
+
+The write_dump command is used before the system has been fully
+initialized as part of a 'run' or 'minimize' command. Not all dump
+styles and features are fully supported at this point and thus the
+command may fail or produce incomplete or incorrect output. Insert
+a "run 0" command, if a full system init is required. :dd
+
+{Cannot count rigid body degrees-of-freedom before bodies are fully initialized} :dt
+
+This means the temperature associated with the rigid bodies may be
+incorrect on this timestep. :dd
+
+{Cannot count rigid body degrees-of-freedom before bodies are initialized} :dt
+
+This means the temperature associated with the rigid bodies may be
+incorrect on this timestep. :dd
+
+{Cannot include log terms without 1/r terms; setting flagHI to 1} :dt
+
+Self-explanatory. :dd
+
+{Cannot include log terms without 1/r terms; setting flagHI to 1.} :dt
+
+Self-explanatory. :dd
+
+{Charges are set, but coulombic solver is not used} :dt
+
+Self-explanatory. :dd
+
+{Charges did not converge at step %ld: %lg} :dt
+
+Self-explanatory. :dd
+
+{Communication cutoff is too small for SNAP micro load balancing, increased to %lf} :dt
+
+Self-explanatory. :dd
+
+{Compute cna/atom cutoff may be too large to find ghost atom neighbors} :dt
+
+The neighbor cutoff used may not encompass enough ghost atoms
+to perform this operation correctly. :dd
+
+{Computing temperature of portions of rigid bodies} :dt
+
+The group defined by the temperature compute does not encompass all
+the atoms in one or more rigid bodies, so the change in
+degrees-of-freedom for the atoms in those partial rigid bodies will
+not be accounted for. :dd
+
+{Create_bonds max distance > minimum neighbor cutoff} :dt
+
+This means atom pairs for some atom types may not be in the neighbor
+list and thus no bond can be created between them. :dd
+
+{Delete_atoms cutoff > minimum neighbor cutoff} :dt
+
+This means atom pairs for some atom types may not be in the neighbor
+list and thus an atom in that pair cannot be deleted. :dd
+
+{Dihedral atoms missing at step %ld} :dt
+
+One or more of 4 atoms needed to compute a particular dihedral are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the dihedral has blown apart and an atom is
+too far away. :dd
+
+{Dihedral problem} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Dihedral problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Dihedral style in data file differs from currently defined dihedral style} :dt
+
+Self-explanatory. :dd
+
+{Dump dcd/xtc timestamp may be wrong with fix dt/reset} :dt
+
+If the fix changes the timestep, the dump dcd file will not
+reflect the change. :dd
+
+{Energy due to X extra global DOFs will be included in minimizer energies} :dt
+
+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
+
+{Estimated error in splitting of dispersion coeffs is %g} :dt
+
+Error is greater than 0.0001 percent. :dd
+
+{Ewald/disp Newton solver failed, using old method to estimate g_ewald} :dt
+
+Self-explanatory. Choosing a different cutoff value may help. :dd
+
+{FENE bond too long} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{FENE bond too long: %ld %d %d %g} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{FENE bond too long: %ld %g} :dt
+
+A FENE bond has stretched dangerously far.  It's interaction strength
+will be truncated to attempt to prevent the bond from blowing up. :dd
+
+{Fix SRD walls overlap but fix srd overlap not set} :dt
+
+You likely want to set this in your input script. :dd
+
+{Fix bond/swap will ignore defined angles} :dt
+
+See the doc page for fix bond/swap for more info on this
+restriction. :dd
+
+{Fix deposit near setting < possible overlap separation %g} :dt
+
+This test is performed for finite size particles with a diameter, not
+for point particles.  The near setting is smaller than the particle
+diameter which can lead to overlaps. :dd
+
+{Fix evaporate may delete atom with non-zero molecule ID} :dt
+
+This is probably an error, since you should not delete only one atom
+of a molecule. :dd
+
+{Fix gcmc using full_energy option} :dt
+
+Fix gcmc has automatically turned on the full_energy option since it
+is required for systems like the one specified by the user. User input
+included one or more of the following: kspace, triclinic, a hybrid
+pair style, an eam pair style, or no "single" function for the pair
+style. :dd
+
+{Fix property/atom mol or charge w/out ghost communication} :dt
+
+A model typically needs these properties defined for ghost atoms. :dd
+
+{Fix qeq CG convergence failed (%g) after %d iterations at %ld step} :dt
+
+Self-explanatory. :dd
+
+{Fix qeq has non-zero lower Taper radius cutoff} :dt
+
+Absolute value must be <= 0.01. :dd
+
+{Fix qeq has very low Taper radius cutoff} :dt
+
+Value should typically be >= 5.0. :dd
+
+{Fix qeq/dynamic tolerance may be too small for damped dynamics} :dt
+
+Self-explanatory. :dd
+
+{Fix qeq/fire tolerance may be too small for damped fires} :dt
+
+Self-explanatory. :dd
+
+{Fix rattle should come after all other integration fixes} :dt
+
+This fix is designed to work after all other integration fixes change
+atom positions.  Thus it should be the last integration fix specified.
+If not, it will not satisfy the desired constraints as well as it
+otherwise would. :dd
+
+{Fix recenter should come after all other integration fixes} :dt
+
+Other fixes may change the position of the center-of-mass, so
+fix recenter should come last. :dd
+
+{Fix srd SRD moves may trigger frequent reneighboring} :dt
+
+This is because the SRD particles may move long distances. :dd
+
+{Fix srd grid size > 1/4 of big particle diameter} :dt
+
+This may cause accuracy problems. :dd
+
+{Fix srd particle moved outside valid domain} :dt
+
+This may indicate a problem with your simulation parameters. :dd
+
+{Fix srd particles may move > big particle diameter} :dt
+
+This may cause accuracy problems. :dd
+
+{Fix srd viscosity < 0.0 due to low SRD density} :dt
+
+This may cause accuracy problems. :dd
+
+{Fixes cannot send data in Kokkos communication, switching to classic communication} :dt
+
+This is current restriction with Kokkos. :dd
+
+{For better accuracy use 'pair_modify table 0'} :dt
+
+The user-specified force accuracy cannot be achieved unless the table
+feature is disabled by using 'pair_modify table 0'. :dd
+
+{Geometric mixing assumed for 1/r^6 coefficients} :dt
+
+Self-explanatory. :dd
+
+{Group for fix_modify temp != fix group} :dt
+
+The fix_modify command is specifying a temperature computation that
+computes a temperature on a different group of atoms than the fix
+itself operates on.  This is probably not what you want to do. :dd
+
+{H matrix size has been exceeded: m_fill=%d H.m=%d\n} :dt
+
+This is the size of the matrix. :dd
+
+{Ignoring unknown or incorrect info command flag} :dt
+
+Self-explanatory.  An unknown argument was given to the info command.
+Compare your input with the documentation. :dd
+
+{Improper atoms missing at step %ld} :dt
+
+One or more of 4 atoms needed to compute a particular improper are
+missing on this processor.  Typically this is because the pairwise
+cutoff is set too short or the improper has blown apart and an atom is
+too far away. :dd
+
+{Improper problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed improper atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Improper style in data file differs from currently defined improper style} :dt
+
+Self-explanatory. :dd
+
+{Inconsistent image flags} :dt
+
+The image flags for a pair on bonded atoms appear to be inconsistent.
+Inconsistent means that when the coordinates of the two atoms are
+unwrapped using the image flags, the two atoms are far apart.
+Specifically they are further apart than half a periodic box length.
+Or they are more than a box length apart in a non-periodic dimension.
+This is usually due to the initial data file not having correct image
+flags for the 2 atoms in a bond that straddles a periodic boundary.
+They should be different by 1 in that case.  This is a warning because
+inconsistent image flags will not cause problems for dynamics or most
+LAMMPS simulations.  However they can cause problems when such atoms
+are used with the fix rigid or replicate commands.  Note that if you
+have an infinite periodic crystal with bonds then it is impossible to
+have fully consistent image flags, since some bonds will cross
+periodic boundaries and connect two atoms with the same image
+flag. :dd
+
+{KIM Model does not provide 'energy'; Potential energy will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'forces'; Forces will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'particleEnergy'; energy per atom will be zero} :dt
+
+Self-explanatory. :dd
+
+{KIM Model does not provide 'particleVirial'; virial per atom will be zero} :dt
+
+Self-explanatory. :dd
+
+{Kspace_modify slab param < 2.0 may cause unphysical behavior} :dt
+
+The kspace_modify slab parameter should be larger to insure periodic
+grids padded with empty space do not overlap. :dd
+
+{Less insertions than requested} :dt
+
+The fix pour command was unsuccessful at finding open space
+for as many particles as it tried to insert. :dd
+
+{Library error in lammps_gather_atoms} :dt
+
+This library function cannot be used if atom IDs are not defined
+or are not consecutively numbered. :dd
+
+{Library error in lammps_scatter_atoms} :dt
+
+This library function cannot be used if atom IDs are not defined or
+are not consecutively numbered, or if no atom map is defined.  See the
+atom_modify command for details about atom maps. :dd
+
+{Lost atoms via change_box: original %ld current %ld} :dt
+
+The command options you have used caused atoms to be lost. :dd
+
+{Lost atoms via displace_atoms: original %ld current %ld} :dt
+
+The command options you have used caused atoms to be lost. :dd
+
+{Lost atoms: original %ld current %ld} :dt
+
+Lost atoms are checked for each time thermo output is done.  See the
+thermo_modify lost command for options.  Lost atoms usually indicate
+bad dynamics, e.g. atoms have been blown far out of the simulation
+box, or moved further than one processor's sub-domain away before
+reneighboring. :dd
+
+{MSM mesh too small, increasing to 2 points in each direction} :dt
+
+Self-explanatory. :dd
+
+{Mismatch between velocity and compute groups} :dt
+
+The temperature computation used by the velocity command will not be
+on the same group of atoms that velocities are being set for. :dd
+
+{Mixing forced for lj coefficients} :dt
+
+Self-explanatory. :dd
+
+{Molecule attributes do not match system attributes} :dt
+
+An attribute is specified (e.g. diameter, charge) that is
+not defined for the specified atom style. :dd
+
+{Molecule has bond topology but no special bond settings} :dt
+
+This means the bonded atoms will not be excluded in pair-wise
+interactions. :dd
+
+{Molecule template for create_atoms has multiple molecules} :dt
+
+The create_atoms command will only create molecules of a single type,
+i.e. the first molecule in the template. :dd
+
+{Molecule template for fix gcmc has multiple molecules} :dt
+
+The fix gcmc command will only create molecules of a single type,
+i.e. the first molecule in the template. :dd
+
+{Molecule template for fix shake has multiple molecules} :dt
+
+The fix shake command will only recognize molecules of a single
+type, i.e. the first molecule in the template. :dd
+
+{More than one compute centro/atom} :dt
+
+It is not efficient to use compute centro/atom more than once. :dd
+
+{More than one compute cluster/atom} :dt
+
+It is not efficient to use compute cluster/atom  more than once. :dd
+
+{More than one compute cna/atom defined} :dt
+
+It is not efficient to use compute cna/atom  more than once. :dd
+
+{More than one compute contact/atom} :dt
+
+It is not efficient to use compute contact/atom more than once. :dd
+
+{More than one compute coord/atom} :dt
+
+It is not efficient to use compute coord/atom more than once. :dd
+
+{More than one compute damage/atom} :dt
+
+It is not efficient to use compute ke/atom more than once. :dd
+
+{More than one compute dilatation/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute erotate/sphere/atom} :dt
+
+It is not efficient to use compute erorate/sphere/atom more than once. :dd
+
+{More than one compute hexorder/atom} :dt
+
+It is not efficient to use compute hexorder/atom more than once. :dd
+
+{More than one compute ke/atom} :dt
+
+It is not efficient to use compute ke/atom more than once. :dd
+
+{More than one compute orientorder/atom} :dt
+
+It is not efficient to use compute orientorder/atom more than once. :dd
+
+{More than one compute plasticity/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute sna/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute snad/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one compute snav/atom} :dt
+
+Self-explanatory. :dd
+
+{More than one fix poems} :dt
+
+It is not efficient to use fix poems more than once. :dd
+
+{More than one fix rigid} :dt
+
+It is not efficient to use fix rigid more than once. :dd
+
+{Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies} :dt
+
+This is because excluding specific pair interactions also excludes
+them from long-range interactions which may not be the desired effect.
+The special_bonds command handles this consistently by insuring
+excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
+consistently by both the short-range pair style and the long-range
+solver.  This is not done for exclusions of charged atom pairs via the
+neigh_modify exclude command. :dd
+
+{New thermo_style command, previous thermo_modify settings will be lost} :dt
+
+If a thermo_style command is used after a thermo_modify command, the
+settings changed by the thermo_modify command will be reset to their
+default values.  This is because the thermo_modify command acts on
+the currently defined thermo style, and a thermo_style command creates
+a new style. :dd
+
+{No Kspace calculation with verlet/split} :dt
+
+The 2nd partition performs a kspace calculation so the kspace_style
+command must be used. :dd
+
+{No automatic unit conversion to XTC file format conventions possible for units lj} :dt
+
+This means no scaling will be performed. :dd
+
+{No fixes defined, atoms won't move} :dt
+
+If you are not using a fix like nve, nvt, npt then atom velocities and
+coordinates will not be updated during timestepping. :dd
+
+{No joints between rigid bodies, use fix rigid instead} :dt
+
+The bodies defined by fix poems are not connected by joints.  POEMS
+will integrate the body motion, but it would be more efficient to use
+fix rigid. :dd
+
+{Not using real units with pair reax} :dt
+
+This is most likely an error, unless you have created your own ReaxFF
+parameter file in a different set of units. :dd
+
+{Number of MSM mesh points changed to be a multiple of 2} :dt
+
+MSM requires that the number of grid points in each direction be a multiple
+of two and the number of grid points in one or more directions have been
+adjusted to meet this requirement. :dd
+
+{OMP_NUM_THREADS environment is not set.} :dt
+
+This environment variable must be set appropriately to use the
+USER-OMP package. :dd
+
+{One or more atoms are time integrated more than once} :dt
+
+This is probably an error since you typically do not want to
+advance the positions or velocities of an atom more than once
+per timestep. :dd
+
+{One or more chunks do not contain all atoms in molecule} :dt
+
+This may not be what you intended. :dd
+
+{One or more dynamic groups may not be updated at correct point in timestep} :dt
+
+If there are other fixes that act immediately after the initial stage
+of time integration within a timestep (i.e. after atoms move), then
+the command that sets up the dynamic group should appear after those
+fixes.  This will insure that dynamic group assignments are made
+after all atoms have moved. :dd
+
+{One or more respa levels compute no forces} :dt
+
+This is computationally inefficient. :dd
+
+{Pair COMB charge %.10f with force %.10f hit max barrier} :dt
+
+Something is possibly wrong with your model. :dd
+
+{Pair COMB charge %.10f with force %.10f hit min barrier} :dt
+
+Something is possibly wrong with your model. :dd
+
+{Pair brownian needs newton pair on for momentum conservation} :dt
+
+Self-explanatory. :dd
+
+{Pair dpd needs newton pair on for momentum conservation} :dt
+
+Self-explanatory. :dd
+
+{Pair dsmc: num_of_collisions > number_of_A} :dt
+
+Collision model in DSMC is breaking down. :dd
+
+{Pair dsmc: num_of_collisions > number_of_B} :dt
+
+Collision model in DSMC is breaking down. :dd
+
+{Pair style in data file differs from currently defined pair style} :dt
+
+Self-explanatory. :dd
+
+{Pair style restartinfo set but has no restart support} :dt
+
+This pair style has a bug, where it does not support reading and
+writing information to a restart file, but does not set the member
+variable "restartinfo" to 0 as required in that case. :dd
+
+{Particle deposition was unsuccessful} :dt
+
+The fix deposit command was not able to insert as many atoms as
+needed.  The requested volume fraction may be too high, or other atoms
+may be in the insertion region. :dd
+
+{Proc sub-domain size < neighbor skin, could lead to lost atoms} :dt
+
+The decomposition of the physical domain (likely due to load
+balancing) has led to a processor's sub-domain being smaller than the
+neighbor skin in one or more dimensions.  Since reneighboring is
+triggered by atoms moving the skin distance, this may lead to lost
+atoms, if an atom moves all the way across a neighboring processor's
+sub-domain before reneighboring is triggered. :dd
+
+{Reducing PPPM order b/c stencil extends beyond nearest neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Reducing PPPMDisp Coulomb order b/c stencil extends beyond neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Reducing PPPMDisp dispersion order b/c stencil extends beyond neighbor processor} :dt
+
+This may lead to a larger grid than desired.  See the kspace_modify overlap
+command to prevent changing of the PPPM order. :dd
+
+{Replacing a fix, but new group != old group} :dt
+
+The ID and style of a fix match for a fix you are changing with a fix
+command, but the new group you are specifying does not match the old
+group. :dd
+
+{Replicating in a non-periodic dimension} :dt
+
+The parameters for a replicate command will cause a non-periodic
+dimension to be replicated; this may cause unwanted behavior. :dd
+
+{Resetting reneighboring criteria during PRD} :dt
+
+A PRD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes.  Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation. :dd
+
+{Resetting reneighboring criteria during TAD} :dt
+
+A TAD simulation requires that neigh_modify settings be delay = 0,
+every = 1, check = yes.  Since these settings were not in place,
+LAMMPS changed them and will restore them to their original values
+after the PRD simulation. :dd
+
+{Resetting reneighboring criteria during minimization} :dt
+
+Minimization requires that neigh_modify settings be delay = 0, every =
+1, check = yes.  Since these settings were not in place, LAMMPS
+changed them and will restore them to their original values after the
+minimization. :dd
+
+{Restart file used different # of processors} :dt
+
+The restart file was written out by a LAMMPS simulation running on a
+different number of processors.  Due to round-off, the trajectories of
+your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors. :dd
+
+{Restart file used different 3d processor grid} :dt
+
+The restart file was written out by a LAMMPS simulation running on a
+different 3d grid of processors.  Due to round-off, the trajectories
+of your restarted simulation may diverge a little more quickly than if
+you ran on the same # of processors. :dd
+
+{Restart file used different boundary settings, using restart file values} :dt
+
+Your input script cannot change these restart file settings. :dd
+
+{Restart file used different newton bond setting, using restart file value} :dt
+
+The restart file value will override the setting in the input script. :dd
+
+{Restart file used different newton pair setting, using input script value} :dt
+
+The input script value will override the setting in the restart file. :dd
+
+{Restrain problem: %d %ld %d %d %d %d} :dt
+
+Conformation of the 4 listed dihedral atoms is extreme; you may want
+to check your simulation geometry. :dd
+
+{Running PRD with only one replica} :dt
+
+This is allowed, but you will get no parallel speed-up. :dd
+
+{SRD bin shifting turned on due to small lamda} :dt
+
+This is done to try to preserve accuracy. :dd
+
+{SRD bin size for fix srd differs from user request} :dt
+
+Fix SRD had to adjust the bin size to fit the simulation box.  See the
+cubic keyword if you want this message to be an error vs warning. :dd
+
+{SRD bins for fix srd are not cubic enough} :dt
+
+The bin shape is not within tolerance of cubic.  See the cubic
+keyword if you want this message to be an error vs warning. :dd
+
+{SRD particle %d started inside big particle %d on step %ld bounce %d} :dt
+
+See the inside keyword if you want this message to be an error vs
+warning. :dd
+
+{SRD particle %d started inside wall %d on step %ld bounce %d} :dt
+
+See the inside keyword if you want this message to be an error vs
+warning. :dd
+
+{Shake determinant < 0.0} :dt
+
+The determinant of the quadratic equation being solved for a single
+cluster specified by the fix shake command is numerically suspect.  LAMMPS
+will set it to 0.0 and continue. :dd
+
+{Shell command '%s' failed with error '%s'} :dt
+
+Self-explanatory. :dd
+
+{Shell command returned with non-zero status} :dt
+
+This may indicate the shell command did not operate as expected. :dd
+
+{Should not allow rigid bodies to bounce off reflecting walls} :dt
+
+LAMMPS allows this, but their dynamics are not computed correctly. :dd
+
+{Should not use fix nve/limit with fix shake or fix rattle} :dt
+
+This will lead to invalid constraint forces in the SHAKE/RATTLE
+computation. :dd
+
+{Simulations might be very slow because of large number of structure factors} :dt
+
+Self-explanatory. :dd
+
+{Slab correction not needed for MSM} :dt
+
+Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM. :dd
+
+{System is not charge neutral, net charge = %g} :dt
+
+The total charge on all atoms on the system is not 0.0.
+For some KSpace solvers this is only a warning. :dd
+
+{Table inner cutoff >= outer cutoff} :dt
+
+You specified an inner cutoff for a Coulombic table that is longer
+than the global cutoff.  Probably not what you wanted. :dd
+
+{Temperature for MSST is not for group all} :dt
+
+User-assigned temperature to MSST fix does not compute temperature for
+all atoms.  Since MSST computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by MSST could be inaccurate. :dd
+
+{Temperature for NPT is not for group all} :dt
+
+User-assigned temperature to NPT fix does not compute temperature for
+all atoms.  Since NPT computes a global pressure, the kinetic energy
+contribution from the temperature is assumed to also be for all atoms.
+Thus the pressure used by NPT could be inaccurate. :dd
+
+{Temperature for fix modify is not for group all} :dt
+
+The temperature compute is being used with a pressure calculation
+which does operate on group all, so this may be inconsistent. :dd
+
+{Temperature for thermo pressure is not for group all} :dt
+
+User-assigned temperature to thermo via the thermo_modify command does
+not compute temperature for all atoms.  Since thermo computes a global
+pressure, the kinetic energy contribution from the temperature is
+assumed to also be for all atoms.  Thus the pressure printed by thermo
+could be inaccurate. :dd
+
+{The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015} :dt
+
+Self-explanatory. :dd
+
+{The minimizer does not re-orient dipoles when using fix efield} :dt
+
+This means that only the atom coordinates will be minimized,
+not the orientation of the dipoles. :dd
+
+{Too many common neighbors in CNA %d times} :dt
+
+More than the maximum # of neighbors was found multiple times.  This
+was unexpected. :dd
+
+{Too many inner timesteps in fix ttm} :dt
+
+Self-explanatory. :dd
+
+{Too many neighbors in CNA for %d atoms} :dt
+
+More than the maximum # of neighbors was found multiple times.  This
+was unexpected. :dd
+
+{Triclinic box skew is large} :dt
+
+The displacement in a skewed direction is normally required to be less
+than half the box length in that dimension.  E.g. the xy tilt must be
+between -half and +half of the x box length.  You have relaxed the
+constraint using the box tilt command, but the warning means that a
+LAMMPS simulation may be inefficient as a result. :dd
+
+{Use special bonds = 0,1,1 with bond style fene} :dt
+
+Most FENE models need this setting for the special_bonds command. :dd
+
+{Use special bonds = 0,1,1 with bond style fene/expand} :dt
+
+Most FENE models need this setting for the special_bonds command. :dd
+
+{Using a many-body potential with bonds/angles/dihedrals and special_bond exclusions} :dt
+
+This is likely not what you want to do.  The exclusion settings will
+eliminate neighbors in the neighbor list, which the many-body potential
+needs to calculated its terms correctly. :dd
+
+{Using compute temp/deform with inconsistent fix deform remap option} :dt
+
+Fix nvt/sllod assumes deforming atoms have a velocity profile provided
+by "remap v" or "remap none" as a fix deform option. :dd
+
+{Using compute temp/deform with no fix deform defined} :dt
+
+This is probably an error, since it makes little sense to use
+compute temp/deform in this case. :dd
+
+{Using fix srd with box deformation but no SRD thermostat} :dt
+
+The deformation will heat the SRD particles so this can
+be dangerous. :dd
+
+{Using kspace solver on system with no charge} :dt
+
+Self-explanatory. :dd
+
+{Using largest cut-off for lj/long/dipole/long long long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for buck/long/coul/long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for lj/long/coul/long} :dt
+
+Self-explanatory. :dd
+
+{Using largest cutoff for pair_style lj/long/tip4p/long} :dt
+
+Self-explanatory. :dd
+
+{Using package gpu without any pair style defined} :dt
+
+Self-explanatory. :dd
+
+{Using pair potential shift with pair_modify compute no} :dt
+
+The shift effects will thus not be computed. :dd
+
+{Using pair tail corrections with nonperiodic system} :dt
+
+This is probably a bogus thing to do, since tail corrections are
+computed by integrating the density of a periodic system out to
+infinity. :dd
+
+{Using pair tail corrections with pair_modify compute no} :dt
+
+The tail corrections will thus not be computed. :dd
+
+{pair style reax is now deprecated and will soon be retired. Users should switch to pair_style reax/c} :dt
+
+Self-explanatory. :dd
+
+:dle

doc/src/Examples.txt

@@ -0,0 +1,147 @@
+"Previous Section"_Howto.html - "LAMMPS WWW Site"_lws - "LAMMPS
+Documentation"_ld - "LAMMPS Commands"_lc - "Next
+Section"_Tools.html :c
+
+:link(lws,http://lammps.sandia.gov)
+:link(ld,Manual.html)
+:link(lc,Commands_all.html)
+
+:line
+
+Example scripts :h3
+
+The LAMMPS distribution includes an examples sub-directory with many
+sample problems.  Many are 2d models that run quickly are are
+straightforward to visualize, requiring at most a couple of minutes to
+run on a desktop machine.  Each problem has an input script (in.*) and
+produces a log file (log.*) when it runs.  Some use a data file
+(data.*) of initial coordinates as additional input.  A few sample log
+file run on different machines and different numbers of processors are
+included in the directories to compare your answers to.  E.g. a log
+file like log.date.crack.foo.P means the "crack" example was run on P
+processors of machine "foo" on that date (i.e. with that version of
+LAMMPS).
+
+Many of the input files have commented-out lines for creating dump
+files and image files.
+
+If you uncomment the "dump"_dump.html command in the input script, a
+text dump file will be produced, which can be animated by various
+"visualization programs"_http://lammps.sandia.gov/viz.html.
+
+If you uncomment the "dump image"_dump.html command in the input
+script, and assuming you have built LAMMPS with a JPG library, JPG
+snapshot images will be produced when the simulation runs.  They can
+be quickly post-processed into a movie using commands described on the
+"dump image"_dump_image.html doc page.
+
+Animations of many of the examples can be viewed on the Movies section
+of the "LAMMPS web site"_lws.
+
+There are two kinds of sub-directories in the examples dir.  Lowercase
+dirs contain one or a few simple, quick-to-run problems.  Uppercase
+dirs contain up to several complex scripts that illustrate a
+particular kind of simulation method or model.  Some of these run for
+longer times, e.g. to measure a particular quantity.
+
+Lists of both kinds of directories are given below.
+
+:line
+
+Lowercase directories :h4
+
+accelerate: run with various acceleration options (OpenMP, GPU, Phi)
+airebo:   polyethylene with AIREBO potential
+balance:  dynamic load balancing, 2d system
+body:     body particles, 2d system
+cmap:     CMAP 5-body contributions to CHARMM force field
+colloid:  big colloid particles in a small particle solvent, 2d system
+comb:     models using the COMB potential
+coreshell: core/shell model using CORESHELL package
+controller: use of fix controller as a thermostat
+crack:    crack propagation in a 2d solid
+deposit:  deposit atoms and molecules on a surface
+dipole:   point dipolar particles, 2d system
+dreiding: methanol via Dreiding FF
+eim:      NaCl using the EIM potential
+ellipse:  ellipsoidal particles in spherical solvent, 2d system
+flow:     Couette and Poiseuille flow in a 2d channel
+friction: frictional contact of spherical asperities between 2d surfaces
+gcmc:     Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
+granregion: use of fix wall/region/gran as boundary on granular particles
+hugoniostat: Hugoniostat shock dynamics
+indent:   spherical indenter into a 2d solid
+kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
+meam:     MEAM test for SiC and shear (same as shear examples)
+melt:     rapid melt of 3d LJ system
+micelle:  self-assembly of small lipid-like molecules into 2d bilayers
+min:      energy minimization of 2d LJ melt
+mscg:     parameterize a multi-scale coarse-graining (MSCG) model
+msst:     MSST shock dynamics
+nb3b:     use of non-bonded 3-body harmonic pair style
+neb:      nudged elastic band (NEB) calculation for barrier finding
+nemd:     non-equilibrium MD of 2d sheared system
+obstacle: flow around two voids in a 2d channel
+peptide:  dynamics of a small solvated peptide chain (5-mer)
+peri:     Peridynamic model of cylinder impacted by indenter
+pour:     pouring of granular particles into a 3d box, then chute flow
+prd:      parallel replica dynamics of vacancy diffusion in bulk Si
+python:   using embedded Python in a LAMMPS input script
+qeq:      use of the QEQ package for charge equilibration
+reax:     RDX and TATB models using the ReaxFF
+rigid:    rigid bodies modeled as independent or coupled
+shear:    sideways shear applied to 2d solid, with and without a void
+snap:     NVE dynamics for BCC tantalum crystal using SNAP potential
+srd:      stochastic rotation dynamics (SRD) particles as solvent
+streitz:  use of Streitz/Mintmire potential with charge equilibration
+tad:      temperature-accelerated dynamics of vacancy diffusion in bulk Si
+vashishta: use of the Vashishta potential
+voronoi:  Voronoi tesselation via compute voronoi/atom command :tb(s=:)
+
+Here is how you can run and visualize one of the sample problems:
+
+cd indent
+cp ../../src/lmp_linux .           # copy LAMMPS executable to this dir
+lmp_linux -in in.indent            # run the problem :pre
+
+Running the simulation produces the files {dump.indent} and
+{log.lammps}.  You can visualize the dump file of snapshots with a
+variety of 3rd-party tools highlighted on the
+"Visualization"_http://lammps.sandia.gov/viz.html page of the LAMMPS
+web site.
+
+If you uncomment the "dump image"_dump_image.html line(s) in the input
+script a series of JPG images will be produced by the run (assuming
+you built LAMMPS with JPG support; see the
+"Build_settings"_Build_settings.html doc page for details).  These can
+be viewed individually or turned into a movie or animated by tools
+like ImageMagick or QuickTime or various Windows-based tools.  See the
+"dump image"_dump_image.html doc page for more details.  E.g. this
+Imagemagick command would create a GIF file suitable for viewing in a
+browser.
+
+% convert -loop 1 *.jpg foo.gif :pre
+
+:line
+
+Uppercase directories :h4
+
+ASPHERE: various aspherical particle models, using ellipsoids, rigid bodies, line/triangle particles, etc
+COUPLE: examples of how to use LAMMPS as a library
+DIFFUSE: compute diffusion coefficients via several methods
+ELASTIC: compute elastic constants at zero temperature
+ELASTIC_T: compute elastic constants at finite temperature
+KAPPA: compute thermal conductivity via several methods
+MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
+USER: examples for USER packages and USER-contributed commands
+VISCOSITY: compute viscosity via several methods :tb(s=:)
+
+Nearly all of these directories have README files which give more
+details on how to understand and use their contents.
+
+The USER directory has a large number of sub-directories which
+correspond by name to a USER package.  They contain scripts that
+illustrate how to use the command(s) provided in that package.  Many
+of the sub-directories have their own README files which give further
+instructions.  See the "Packages_details"_Packages_details.html doc
+page for more info on specific USER packages.