Merge pull request #1914 from akohlmey/next_lammps_version

Step version string for next patch and stable version

.github/CODEOWNERS

@@ -9,13 +9,124 @@ lib/kokkos/*          @stanmoore1
 lib/molfile/*         @akohlmey
 lib/qmmm/*            @akohlmey
 lib/vtk/*             @rbberger
+lib/kim/*             @ellio167
 
-# packages
-src/KOKKOS            @stanmoore1
-src/USER-CGSDK        @akohlmey
-src/USER-COLVARS      @giacomofiorin
-src/USER-OMP          @akohlmey
-src/USER-QMMM         @akohlmey
+# whole packages
+src/COMPRESS/*        @akohlmey
+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
+src/USER-DPD/*        @timattox
+src/USER-INTEL/*      @wmbrownintel
+src/USER-MANIFOLD/*   @Pakketeretet2
+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
+src/min*                  @sjplimp @stanmoore1
 
 # tools
 tools/msi2lmp/*       @akohlmey
+tools/emacs/*         @HaoZeke
+
+# cmake
+cmake/*               @junghans @rbberger
+
+# python
+python/*              @rbberger
+
+# docs
+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).
@@ -62,17 +62,18 @@ 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 trailing whitespace, 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, 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.
+* Source, style name, and documentation file should follow the following naming convention: style names should be lowercase and words separated by a forward slash; for a new fix style 'foo/bar', the class should be named FixFooBar, the name of the source files should be 'fix_foo_bar.h' and 'fix_foo_bar.cpp' and the corresponding documentation should be in a file 'fix_foo_bar.rst'.
 * 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.
-* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are simple text files with a specific markup language, that are then auto-converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.txt` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. A description of the markup can also be found in `lammps/doc/utils/txt2html/README.html` As appropriate, the text files can include links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.txt for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv, the requirement for generating the PDF format manual is the htmldoc software. Please run at least "make html" and carefully inspect and proofread the resulting HTML format doc page before submitting your code.
+* You **must** also create or extend a documentation file for each new command or style you are adding to LAMMPS. For simplicity and convenience, the documentation of groups of closely related commands or styles may be combined into a single file. This will be one file for a single-file feature. For a package, it might be several files. These are files in the [reStructuredText](https://docutils.sourceforge.io/rst.html) markup language, that are then converted to HTML and PDF. The tools for this conversion are included in the source distribution, and the translation can be as simple as doing "make html pdf" in the doc folder. Thus the documentation source files must be in the same format and style as other `<name>.rst` files in the lammps/doc/src directory for similar commands and styles; use one or more of them as a starting point. An introduction to reStructuredText can be found at [https://docutils.sourceforge.io/docs/user/rst/quickstart.html](https://docutils.sourceforge.io/docs/user/rst/quickstart.html). As appropriate, the text files can include mathematical expressions in MathJAX markup or links to equations (see doc/Eqs/*.tex for examples, we auto-create the associated JPG files), or figures (see doc/JPG for examples), or even additional PDF files with further details (see doc/PDF for examples). The doc page should also include literature citations as appropriate; see the bottom of doc/fix_nh.rst for examples and the earlier part of the same file for how to format the cite itself. The "Restrictions" section of the doc page should indicate that your command is only available if LAMMPS is built with the appropriate USER-MISC or USER-FOO package. See other user package doc files for examples of how to do this. The prerequisite for building the HTML format files are Python 3.x and virtualenv. Please run at least `make html` and `make spelling` and carefully inspect and proofread the resulting HTML format doc page as well as the output produced to the screen. Make sure that all spelling errors are fixed or the necessary false positives are added to the `doc/utils/sphinx-config/false_positives.txt` file.  For new styles, those usually also need to be added to lists on the respective overview pages. This can be checked for also with `make style_check`.
 * For a new package (or even a single command) you should include one or more example scripts demonstrating its use. These should run in no more than a couple minutes, even on a single processor, and not require large data files as input. See directories under examples/USER for examples of input scripts other users provided for their packages. These example inputs are also required for validating memory accesses and testing for memory leaks with valgrind
 * If there is a paper of yours describing your feature (either the algorithm/science behind the feature itself, or its initial usage, or its implementation in LAMMPS), you can add the citation to the *.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
 
@@ -102,11 +103,11 @@ 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 for this project, please mention the issue number here, and describe the relation. Use the phrases `fixes #221` or `closes #135`, when you want an issue to be automatically closed when the pull request is merged_
 
-## Backward Compatibility
+**Author(s)**
 
-_Please state whether any changes in the pull request break backward compatibility for inputs, and - if yes - explain what has been changed and why_
+_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._
 
-## Implementation Notes
+**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 will 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
+**Post Submission Checklist**
+
+_Please check the fields below as they are completed **after** the pull request has been submitted. Delete lines that don't apply_
 
-_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
@@ -21,9 +22,11 @@ log.cite
 .*.swp
 *.orig
 *.rej
+vgcore.*
 .vagrant
 \#*#
 .#*
+.vscode
 
 .DS_Store
 .DS_Store?
@@ -32,6 +35,7 @@ log.cite
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 
 #cmake
 /build*

README

@@ -25,7 +25,7 @@ The LAMMPS distribution includes the following files and directories:
 README			   this file
 LICENSE			   the GNU General Public License (GPL)
 bench			   benchmark problems
-couple			   code coupling examples using LAMMPS as a library
+cmake			   CMake build system
 doc			   documentation
 examples		   simple test problems
 lib			   libraries LAMMPS can be linked with
@@ -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

bench/POTENTIALS/CH.airebo

@@ -0,0 +1 @@
+../../potentials/CH.airebo

bench/POTENTIALS/CdTe.bop.table

@@ -0,0 +1 @@
+../../potentials/CdTe.bop.table

bench/POTENTIALS/Cu_u3.eam

@@ -1,305 +0,0 @@
-Cu functions (universal 3), SM Foiles et al, PRB, 33, 7983 (1986)
-   29     63.550         3.6150    FCC
-  500  5.0100200400801306e-04  500  1.0000000000000009e-02  4.9499999999999886e+00
-  0.                     -3.1561636903424350e-01 -5.2324876182494506e-01 -6.9740831416804383e-01 -8.5202525457518519e-01
- -9.9329216586042435e-01 -1.1246331970890324e+00 -1.2481882647347859e+00 -1.3654054700363645e+00 -1.4773214276236644e+00
- -1.5847099936904741e+00 -1.6865851873526410e+00 -1.7843534091637920e+00 -1.8790616476576076e+00 -1.9710188604521761e+00
- -2.0604838665854572e+00 -2.1476762477372944e+00 -2.2327843595560068e+00 -2.3159713409697673e+00 -2.3973797031286352e+00
- -2.4771348895887826e+00 -2.5553480773272810e+00 -2.6321184083774227e+00 -2.7075347880408458e+00 -2.7816773487592030e+00
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- -6.3201485619430571e+00 -6.3639791729330000e+00 -6.4076819904493902e+00 -6.4512607272098990e+00 -6.4947190123648113e+00
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- -7.9918504090315139e+00 -8.0323942861870705e+00 -8.0729086739704030e+00 -8.1133952464140293e+00 -8.1538556491162808e+00
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- -8.3961572227176475e+00 -8.4364782502312892e+00 -8.4767853193496308e+00 -8.5170798454139458e+00 -8.5573632207473906e+00
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-  3.3961263062063513e-04  3.3158640950565685e-04  3.2373154119109092e-04  3.1604468762060252e-04  3.0852256784754707e-04
-  3.0116195723081836e-04  2.9395968663908575e-04  2.8691264166377101e-04  2.8001776184017647e-04  2.7327203987681688e-04
-  2.6667252089326854e-04  2.6021630166557681e-04  2.5390052988028163e-04  2.4772240339593181e-04  2.4167916951265550e-04
-  2.3576812424967210e-04  2.2998661163024531e-04  2.2433202297460642e-04  2.1880179620031078e-04  2.1339341513026532e-04
-  2.0810440880823181e-04  2.0293235082175821e-04  1.9787485863260665e-04  1.9292959291436311e-04  1.8809425689761319e-04
-  1.8336659572205580e-04  1.7874439579616125e-04  1.7422548416372047e-04  1.6980772787763936e-04  1.6548903338088530e-04
-  1.6126734589430591e-04  1.5714064881157744e-04  1.5310696310104604e-04  1.4916434671449329e-04  1.4531089400280153e-04
-  1.4154473513841234e-04  1.3786403554466153e-04  1.3426699533172857e-04  1.3075184873951283e-04  1.2731686358694039e-04
-  1.2396034072819674e-04  1.2068061351527565e-04  1.1747604726729168e-04  1.1434503874632306e-04  1.1128601563955686e-04
-  1.0829743604811193e-04  1.0537778798212988e-04  1.0252558886227753e-04  9.9739385027582898e-05  9.7017751249615057e-05
-  9.4359290252773662e-05  9.1762632240957511e-05  8.9226434430383569e-05  8.6749380588361721e-05  8.4330180578390864e-05
-  8.1967569911181246e-05  7.9660309301724484e-05  7.7407184232279429e-05  7.5207004521348451e-05  7.3058603898526649e-05
-  7.0960839585107720e-05  6.8912591880629977e-05  6.6912763755002085e-05  6.4960280446513426e-05  6.3054089065330086e-05
-  6.1193158202771814e-05  5.9376477546041213e-05  5.7603057498502742e-05  5.5871928805544500e-05  5.4182142185708361e-05
-  5.2532767967318744e-05  5.0922895730446966e-05  4.9351633954125953e-05  4.7818109668823321e-05  4.6321468114150300e-05
-  4.4860872401664663e-05  4.3435503182825573e-05  4.2044558321957873e-05  4.0687252574273750e-05  3.9362817268785450e-05
-  3.8070499996214428e-05  3.6809564301621984e-05  3.5579289382025496e-05  3.4378969788611451e-05  3.3207915133769052e-05
-  3.2065449802711312e-05  3.0950912669766876e-05  2.9863656819185611e-05  2.8803049270468119e-05  2.7768470708167169e-05
-  2.6759315216115260e-05  2.5774990015931323e-05  2.4814915209964844e-05  2.3878523528387922e-05  2.2965260080560611e-05
-  2.2074582110528148e-05  2.1205958756658535e-05  2.0358870815317476e-05  1.9532810508535560e-05  1.8727281255713447e-05
-  1.7941797449145505e-05  1.7175884233475961e-05  1.6429077288930018e-05  1.5700922618341645e-05  1.4990976337865471e-05
-  1.4298804471386687e-05  1.3623982748522034e-05  1.2966096406226424e-05  1.2324739993882115e-05  1.1699517181902770e-05
-  1.1090040573734860e-05  1.0495931521266495e-05  9.9168199435395021e-06  9.3523441487842465e-06  8.8021506596591475e-06
-  8.2658940417265321e-06  7.7432367350197678e-06  7.2338488887770244e-06  6.7374081991923703e-06  6.2535997501888662e-06
-  5.7821158571569505e-06  5.3226559136389283e-06  4.8749262408651290e-06  4.4386399401326240e-06  4.0135167480073166e-06
-  3.5992828942305738e-06  3.1956709623667747e-06  2.8024197531120341e-06  2.4192741502208947e-06  2.0459849890155880e-06
-  1.6823089274468580e-06  1.3280083196495871e-06  9.8285109196557868e-07  6.4661062138351467e-07  3.1906561636122974e-07
-  0.                      0.                      0.                      0.                      0.
-
-

bench/POTENTIALS/Cu_u3.eam

@@ -0,0 +1 @@
+../../potentials/Cu_u3.eam

bench/POTENTIALS/Ni.adp

@@ -0,0 +1 @@
+../../potentials/Ni.adp

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/CodeCoverage.cmake

@@ -0,0 +1,28 @@
+###############################################################################
+# Coverage
+#
+# Requires latest gcovr (for GCC 8.1 support):#
+# pip install git+https://github.com/gcovr/gcovr.git
+###############################################################################
+if(ENABLE_COVERAGE)
+    find_program(GCOVR_BINARY gcovr)
+    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+
+    if(GCOVR_FOUND)
+        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+
+        add_custom_target(
+            gen_coverage_xml
+            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating XML Coverage Report..."
+        )
+
+        add_custom_target(
+            gen_coverage_html
+            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.html
+            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+            COMMENT "Generating HTML Coverage Report..."
+        )
+    endif()
+endif()

cmake/Modules/Documentation.cmake

@@ -0,0 +1,42 @@
+###############################################################################
+# Build documentation
+###############################################################################
+option(BUILD_DOC "Build LAMMPS documentation" OFF)
+if(BUILD_DOC)
+  include(ProcessorCount)
+  ProcessorCount(NPROCS)
+  find_package(PythonInterp 3 REQUIRED)
+
+  set(VIRTUALENV ${PYTHON_EXECUTABLE} -m virtualenv)
+
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+
+  add_custom_command(
+    OUTPUT docenv
+    COMMAND ${VIRTUALENV} docenv
+  )
+
+  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+
+  add_custom_command(
+    OUTPUT requirements.txt
+    DEPENDS docenv
+    COMMAND ${CMAKE_COMMAND} -E copy ${LAMMPS_DOC_DIR}/utils/requirements.txt requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip install -r requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+  )
+
+  add_custom_command(
+    OUTPUT html
+    DEPENDS ${DOC_SOURCES} docenv requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build -j ${NPROCS} -b html -c ${LAMMPS_DOC_DIR}/utils/sphinx-config -d ${CMAKE_BINARY_DIR}/doctrees ${LAMMPS_DOC_DIR}/src html
+  )
+
+  add_custom_target(
+    doc ALL
+    DEPENDS html
+    SOURCES ${LAMMPS_DOC_DIR}/utils/requirements.txt ${DOC_SOURCES}
+  )
+
+  install(DIRECTORY ${CMAKE_BINARY_DIR}/html DESTINATION ${CMAKE_INSTALL_DOCDIR})
+endif()

cmake/Modules/FindFFTW2.cmake

@@ -1,22 +0,0 @@
-# - Find fftw2
-# Find the native FFTW2 headers and libraries.
-#
-#  FFTW2_INCLUDE_DIRS - where to find fftw2.h, etc.
-#  FFTW2_LIBRARIES    - List of libraries when using fftw2.
-#  FFTW2_FOUND        - True if fftw2 found.
-#
-
-find_path(FFTW2_INCLUDE_DIR fftw.h)
-
-find_library(FFTW2_LIBRARY NAMES fftw)
-
-set(FFTW2_LIBRARIES ${FFTW2_LIBRARY})
-set(FFTW2_INCLUDE_DIRS ${FFTW2_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set FFTW2_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(FFTW2 DEFAULT_MSG FFTW2_LIBRARY FFTW2_INCLUDE_DIR)
-
-mark_as_advanced(FFTW2_INCLUDE_DIR FFTW2_LIBRARY )

cmake/Modules/FindFFTW3.cmake

@@ -1,20 +1,22 @@
 # - Find fftw3
-# Find the native FFTW3 headers and libraries.
+# Find the native double precision FFTW3 headers and libraries.
 #
-#  FFTW3_INCLUDE_DIRS - where to find fftw3.h, etc.
-#  FFTW3_LIBRARIES    - List of libraries when using fftw3.
-#  FFTW3_FOUND        - True if fftw3 found.
+#  FFTW3_INCLUDE_DIRS  - where to find fftw3.h, etc.
+#  FFTW3_LIBRARIES     - List of libraries when using fftw3.
+#  FFTW3_OMP_LIBRARIES - List of libraries when using fftw3.
+#  FFTW3_FOUND         - True if fftw3 found.
 #
 
 find_package(PkgConfig)
 
 pkg_check_modules(PC_FFTW3 fftw3)
 find_path(FFTW3_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3_INCLUDE_DIRS})
-
 find_library(FFTW3_LIBRARY NAMES fftw3 HINTS ${PC_FFTW3_LIBRARY_DIRS})
+find_library(FFTW3_OMP_LIBRARY NAMES fftw3_omp HINTS ${PC_FFTW3_LIBRARY_DIRS})
 
-set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
 set(FFTW3_INCLUDE_DIRS ${FFTW3_INCLUDE_DIR})
+set(FFTW3_LIBRARIES ${FFTW3_LIBRARY})
+set(FFTW3_OMP_LIBRARIES ${FFTW3_OMP_LIBRARY})
 
 include(FindPackageHandleStandardArgs)
 # handle the QUIETLY and REQUIRED arguments and set FFTW3_FOUND to TRUE
@@ -22,4 +24,4 @@ include(FindPackageHandleStandardArgs)
 
 find_package_handle_standard_args(FFTW3 DEFAULT_MSG FFTW3_LIBRARY FFTW3_INCLUDE_DIR)
 
-mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY )
+mark_as_advanced(FFTW3_INCLUDE_DIR FFTW3_LIBRARY FFTW3_OMP_LIBRARY)

cmake/Modules/FindFFTW3F.cmake

@@ -0,0 +1,26 @@
+# Find the native single precision FFTW3 headers and libraries.
+#
+#  FFTW3F_INCLUDE_DIRS - where to find fftw3f.h, etc.
+#  FFTW3F_LIBRARIES    - List of libraries when using fftw3f.
+#  FFTW3F_OMP_LIBRARIES - List of libraries when using fftw3.
+#  FFTW3F_FOUND        - True if fftw3f found.
+#
+
+find_package(PkgConfig)
+
+pkg_check_modules(PC_FFTW3F fftw3f)
+find_path(FFTW3F_INCLUDE_DIR fftw3.h HINTS ${PC_FFTW3F_INCLUDE_DIRS})
+find_library(FFTW3F_LIBRARY NAMES fftw3f HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+find_library(FFTW3F_OMP_LIBRARY NAMES fftw3f_omp HINTS ${PC_FFTW3F_LIBRARY_DIRS})
+
+set(FFTW3F_INCLUDE_DIRS ${FFTW3F_INCLUDE_DIR})
+set(FFTW3F_LIBRARIES ${FFTW3F_LIBRARY})
+set(FFTW3F_OMP_LIBRARIES ${FFTW3F_OMP_LIBRARY})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set FFTW3F_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(FFTW3F DEFAULT_MSG FFTW3F_LIBRARY FFTW3F_INCLUDE_DIR)
+
+mark_as_advanced(FFTW3F_INCLUDE_DIR FFTW3F_LIBRARY)

cmake/Modules/FindKIM-API.cmake

@@ -0,0 +1,85 @@
+#
+# 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--2019, Regents of the University of Minnesota.
+# All rights reserved.
+#
+# Contributors:
+#    Richard Berger
+#    Christoph Junghans
+#    Ryan S. Elliott
+#
+
+# - Find KIM-API
+#
+# sets standard pkg_check_modules variables plus:
+#
+# KIM-API-CMAKE_C_COMPILER
+# KIM-API-CMAKE_CXX_COMPILER
+# KIM-API-CMAKE_Fortran_COMPILER
+#
+
+function(_KIMAPI_GET_VERSION _OUT_ver _version_hdr)
+  if(NOT EXISTS ${_version_hdr})
+    message(FATAL_ERROR "Header file ${_version_hdr} not found (check value of KIM-API_INCLUDE_DIR)")
+  endif()
+  foreach(_var KIM_VERSION_MAJOR KIM_VERSION_MINOR KIM_VERSION_PATCH)  
+    file(STRINGS ${_version_hdr} _contents REGEX "#define ${_var}[ \t]+")
+    if(_contents)
+      string(REGEX REPLACE ".*#define ${_var}[ \t]+([0-9]+).*" "\\1" _${_var} "${_contents}")
+      if(${_${_var}} STREQUAL "")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, got empty return!")
+      elseif(NOT ${_${_var}} MATCHES "^[0-9]+$")
+        message(FATAL_ERROR "Version parsing failed for ${_var} in ${_version_hdr}, excepted a number but got ${_${_var}}!")
+      endif()
+    else()
+      message(FATAL_ERROR "No ${_var} line found in include file ${_version_hdr}")
+    endif()
+  endforeach()
+  set(${_OUT_ver} ${_KIM_VERSION_MAJOR}.${_KIM_VERSION_MINOR}.${_KIM_VERSION_PATCH} PARENT_SCOPE)
+endfunction()
+
+if(KIM-API_FIND_QUIETLY)
+  set(REQ_OR_QUI "QUIET")
+else()
+  set(REQ_OR_QUI "REQUIRED")
+endif()
+
+find_package(PkgConfig ${REQ_OR_QUI})
+include(FindPackageHandleStandardArgs)
+
+pkg_check_modules(KIM-API ${REQ_OR_QUI} libkim-api>=2.0)
+
+if(KIM-API_FOUND)
+  pkg_get_variable(KIM-API-CMAKE_C_COMPILER libkim-api CMAKE_C_COMPILER)
+  pkg_get_variable(KIM-API-CMAKE_CXX_COMPILER libkim-api CMAKE_CXX_COMPILER)
+  pkg_get_variable(KIM-API_CMAKE_Fortran_COMPILER libkim-api CMAKE_Fortran_COMPILER)
+endif()
+
+if(KIM-API_INCLUDEDIR)
+  _KIMAPI_GET_VERSION(KIM-API_VERSION ${KIM-API_INCLUDEDIR}/KIM_Version.h)
+else()
+  set(KIM-API_VERSION 0)
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set KIM-API_FOUND to TRUE
+# if all listed variables are TRUE
+find_package_handle_standard_args(KIM-API REQUIRED_VARS KIM-API_LIBRARIES VERSION_VAR KIM-API_VERSION)

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/FindMSCG.cmake

@@ -0,0 +1,22 @@
+# - Find mscg
+# Find the native MSCG headers and libraries.
+#
+#  MSCG_INCLUDE_DIRS - where to find mscg.h, etc.
+#  MSCG_LIBRARIES    - List of libraries when using mscg.
+#  MSCG_FOUND        - True if mscg found.
+#
+
+find_path(MSCG_INCLUDE_DIR mscg.h PATH_SUFFIXES mscg)
+
+find_library(MSCG_LIBRARY NAMES mscg)
+
+set(MSCG_LIBRARIES ${MSCG_LIBRARY})
+set(MSCG_INCLUDE_DIRS ${MSCG_INCLUDE_DIR})
+
+include(FindPackageHandleStandardArgs)
+# handle the QUIETLY and REQUIRED arguments and set MSCG_FOUND to TRUE
+# if all listed variables are TRUE
+
+find_package_handle_standard_args(MSCG DEFAULT_MSG MSCG_LIBRARY MSCG_INCLUDE_DIR)
+
+mark_as_advanced(MSCG_INCLUDE_DIR MSCG_LIBRARY )

cmake/Modules/FindNetCDF.cmake

@@ -46,10 +46,14 @@ endif()
 find_path (NETCDF_INCLUDE_DIR netcdf.h
   HINTS "${NETCDF_DIR}/include")
 mark_as_advanced (NETCDF_INCLUDE_DIR)
+
 set (NETCDF_C_INCLUDE_DIRS ${NETCDF_INCLUDE_DIR})
 
+string(REGEX REPLACE "/include/?$" ""
+  NETCDF_LIB_HINT ${NETCDF_INCLUDE_DIR})
+
 find_library (NETCDF_LIBRARY NAMES netcdf
-  HINTS "${NETCDF_DIR}/lib")
+  HINTS "${NETCDF_DIR}" "${NETCDF_LIB_HINT}" PATH_SUFFIXES lib lib64)
 mark_as_advanced (NETCDF_LIBRARY)
 
 set (NETCDF_C_LIBRARIES ${NETCDF_LIBRARY})

cmake/Modules/FindPNetCDF.cmake

@@ -0,0 +1,55 @@
+# source: https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/CMake/FindPNetCDF.cmake
+# license: GPL v3 (https://ftp.space.dtu.dk/pub/Ioana/pism0.6.1-10/COPYING)
+#
+# - Find PNetCDF
+# Find the native PNetCDF includes and library
+#
+#  PNETCDF_INCLUDES    - where to find netcdf.h, etc
+#  PNETCDF_LIBRARIES   - Link these libraries when using NetCDF
+#  PNETCDF_FOUND       - True if PNetCDF was found
+#
+# Normal usage would be:
+#  find_package (PNetCDF REQUIRED)
+#  target_link_libraries (uses_pnetcdf ${PNETCDF_LIBRARIES})
+
+if (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+  # Already in cache, be silent
+  set (PNETCDF_FIND_QUIETLY TRUE)
+endif (PNETCDF_INCLUDES AND PNETCDF_LIBRARIES)
+
+find_path (PNETCDF_INCLUDES pnetcdf.h
+  HINTS "${PNETCDF_ROOT}/include" "$ENV{PNETCDF_ROOT}/include")
+
+string(REGEX REPLACE "/include/?$" ""
+  PNETCDF_LIB_HINT ${PNETCDF_INCLUDES})
+
+find_library (PNETCDF_LIBRARIES
+  NAMES pnetcdf
+  HINTS ${PNETCDF_LIB_HINT} PATH_SUFFIXES lib lib64)
+
+if ((NOT PNETCDF_LIBRARIES) OR (NOT PNETCDF_INCLUDES))
+  message(STATUS "Trying to find PNetCDF using LD_LIBRARY_PATH (we're desperate)...")
+
+  file(TO_CMAKE_PATH "$ENV{LD_LIBRARY_PATH}" LD_LIBRARY_PATH)
+
+  find_library(PNETCDF_LIBRARIES
+    NAMES pnetcdf
+    HINTS ${LD_LIBRARY_PATH})
+
+  if (PNETCDF_LIBRARIES)
+    get_filename_component(PNETCDF_LIB_DIR ${PNETCDF_LIBRARIES} PATH)
+    string(REGEX REPLACE "/(lib|lib64)/?$" "/include"
+      PNETCDF_H_HINT ${PNETCDF_LIB_DIR})
+
+    find_path (PNETCDF_INCLUDES pnetcdf.h
+      HINTS ${PNETCDF_H_HINT}
+      DOC "Path to pnetcdf.h")
+  endif()
+endif()
+
+# handle the QUIETLY and REQUIRED arguments and set PNETCDF_FOUND to TRUE if
+# all listed variables are TRUE
+include (FindPackageHandleStandardArgs)
+find_package_handle_standard_args (PNetCDF DEFAULT_MSG PNETCDF_LIBRARIES PNETCDF_INCLUDES)
+
+mark_as_advanced (PNETCDF_LIBRARIES PNETCDF_INCLUDES)

cmake/Modules/FindQE.cmake

@@ -1,29 +0,0 @@
-# - Find quantum-espresso
-# Find the native QE headers and libraries.
-#
-#  QE_INCLUDE_DIRS - where to find quantum-espresso.h, etc.
-#  QE_LIBRARIES    - List of libraries when using quantum-espresso.
-#  QE_FOUND        - True if quantum-espresso found.
-#
-
-find_path(QE_INCLUDE_DIR libqecouple.h PATH_SUFFIXES COUPLE/include)
-
-find_library(QECOUPLE_LIBRARY NAMES qecouple)
-find_library(PW_LIBRARY NAMES pw)
-find_library(QEMOD_LIBRARY NAMES qemod)
-find_library(QEFFT_LIBRARY NAMES qefft)
-find_library(QELA_LIBRARY NAMES qela)
-find_library(CLIB_LIBRARY NAMES clib)
-find_library(IOTK_LIBRARY NAMES iotk)
-
-
-set(QE_LIBRARIES ${QECOUPLE_LIBRARY} ${PW_LIBRARY} ${QEMOD_LIBRARY} ${QEFFT_LIBRARY} ${QELA_LIBRARY} ${CLIB_LIBRARY} ${IOTK_LIBRARY})
-set(QE_INCLUDE_DIRS ${QE_INCLUDE_DIR})
-
-include(FindPackageHandleStandardArgs)
-# handle the QUIETLY and REQUIRED arguments and set QE_FOUND to TRUE
-# if all listed variables are TRUE
-
-find_package_handle_standard_args(QE DEFAULT_MSG QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_LIBRARY QE_INCLUDE_DIR)
-
-mark_as_advanced(QE_INCLUDE_DIR QECOUPLE_LIBRARY PW_LIBRARY QEMOD_LIBRARY QEFFT_LIBRARY QELA_LIBRARY CLIB_LIBRARY IOTK_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/LAMMPSUtils.cmake

@@ -0,0 +1,71 @@
+# Utility functions
+function(list_to_bulletpoints result)
+    list(REMOVE_AT ARGV 0)
+    set(temp "")
+    foreach(item ${ARGV})
+        set(temp "${temp}* ${item}\n")
+    endforeach()
+    set(${result} "${temp}" PARENT_SCOPE)
+endfunction(list_to_bulletpoints)
+
+function(validate_option name values)
+    string(TOLOWER ${${name}} needle_lower)
+    string(TOUPPER ${${name}} needle_upper)
+    list(FIND ${values} ${needle_lower} IDX_LOWER)
+    list(FIND ${values} ${needle_upper} IDX_UPPER)
+    if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+        list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+        message(FATAL_ERROR "\n########################################################################\n"
+                            "Invalid value '${${name}}' for option ${name}\n"
+                            "\n"
+                            "Possible values are:\n"
+                            "${POSSIBLE_VALUE_LIST}"
+                            "########################################################################")
+    endif()
+endfunction(validate_option)
+
+function(get_lammps_version version_header variable)
+    file(READ ${version_header} line)
+    set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\3" year "${line}")
+    string(STRIP ${day} day)
+    string(STRIP ${month} month)
+    string(STRIP ${year} year)
+    list(FIND MONTHS "${month}" month)
+    string(LENGTH ${day} day_length)
+    string(LENGTH ${month} month_length)
+    if(day_length EQUAL 1)
+        set(day "0${day}")
+    endif()
+    if(month_length EQUAL 1)
+        set(month "0${month}")
+    endif()
+    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+endfunction()
+
+function(check_for_autogen_files source_dir)
+    message(STATUS "Running check for auto-generated files from make-based build system")
+    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
+    foreach(_SRC ${SRC_AUTOGEN_FILES})
+      get_filename_component(FILENAME "${_SRC}" NAME)
+      if(EXISTS ${source_dir}/${FILENAME})
+        message(FATAL_ERROR "\n########################################################################\n"
+                              "Found header file(s) generated by the make-based build system\n"
+                              "\n"
+                              "Please run\n"
+                              "make -C ${source_dir} purge\n"
+                              "to remove\n"
+                              "########################################################################")
+      endif()
+    endforeach()
+endfunction()
+
+macro(pkg_depends PKG1 PKG2)
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
+    message(FATAL_ERROR "${PKG1} package needs LAMMPS to be build with ${PKG2}")
+  endif()
+endmacro()

cmake/Modules/OpenCLUtils.cmake

@@ -6,7 +6,7 @@ function(GenerateOpenCLHeader varname outfile files)
     foreach(IDX RANGE 2 ${ARG_END})
         list(GET ARGV ${IDX} filename)
         file(READ ${filename} content)
-        string(REGEX REPLACE "\\s*//[^\n]*\n" "" content "${content}")
+        string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
         string(REGEX REPLACE "\"" "\\\\\"" content "${content}")
         string(REGEX REPLACE "([^\n]+)\n" "\"\\1\\\\n\"\n" content "${content}")

cmake/Modules/Packages/COMPRESS.cmake

@@ -0,0 +1,5 @@
+if(PKG_COMPRESS)
+  find_package(ZLIB REQUIRED)
+  include_directories(${ZLIB_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${ZLIB_LIBRARIES})
+endif()

cmake/Modules/Packages/CORESHELL.cmake

@@ -0,0 +1,13 @@
+if(PKG_CORESHELL)
+    set(CORESHELL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/CORESHELL)
+    set(CORESHELL_SOURCES)
+    set_property(GLOBAL PROPERTY "CORESHELL_SOURCES" "${CORESHELL_SOURCES}")
+
+    # detects styles which have a CORESHELL version
+    RegisterStylesExt(${CORESHELL_SOURCES_DIR} cs CORESHELL_SOURCES)
+
+    get_property(CORESHELL_SOURCES GLOBAL PROPERTY CORESHELL_SOURCES)
+
+    list(APPEND LIB_SOURCES ${CORESHELL_SOURCES})
+    include_directories(${CORESHELL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/GPU.cmake

@@ -0,0 +1,194 @@
+if(PKG_GPU)
+    if (CMAKE_VERSION VERSION_LESS "3.1")
+      message(FATAL_ERROR "For the GPU package you need at least cmake-3.1")
+    endif()
+    set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
+    set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.h
+                    ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+
+    set(GPU_API "opencl" CACHE STRING "API used by GPU package")
+    set(GPU_API_VALUES opencl cuda)
+    set_property(CACHE GPU_API PROPERTY STRINGS ${GPU_API_VALUES})
+    validate_option(GPU_API GPU_API_VALUES)
+    string(TOUPPER ${GPU_API} GPU_API)
+
+    set(GPU_PREC "mixed" CACHE STRING "LAMMPS GPU precision")
+    set(GPU_PREC_VALUES double mixed single)
+    set_property(CACHE GPU_PREC PROPERTY STRINGS ${GPU_PREC_VALUES})
+    validate_option(GPU_PREC GPU_PREC_VALUES)
+    string(TOUPPER ${GPU_PREC} GPU_PREC)
+
+    if(GPU_PREC STREQUAL "DOUBLE")
+      set(GPU_PREC_SETTING "DOUBLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "MIXED")
+      set(GPU_PREC_SETTING "SINGLE_DOUBLE")
+    elseif(GPU_PREC STREQUAL "SINGLE")
+      set(GPU_PREC_SETTING "SINGLE_SINGLE")
+    endif()
+
+    file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+    file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+    if(GPU_API STREQUAL "CUDA")
+      find_package(CUDA REQUIRED)
+      find_program(BIN2C bin2c)
+      if(NOT BIN2C)
+        message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
+      endif()
+      option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+      option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
+      if(CUDA_MPS_SUPPORT)
+        set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+      endif()
+
+      set(GPU_ARCH "sm_30" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
+
+      cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
+
+      if(CUDPP_OPT)
+        cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+        file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+      endif()
+
+      # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
+      # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
+      set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH} ")
+      # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+      if((CUDA_VERSION VERSION_GREATER "3.1") AND (CUDA_VERSION VERSION_LESS "9.0"))
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_20,code=[sm_20,compute_20] ")
+      endif()
+      # Kepler (GPU Arch 3.x) is supported by CUDA 5 and later
+      if(CUDA_VERSION VERSION_GREATER "4.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_30,code=[sm_30,compute_30] -gencode arch=compute_35,code=[sm_35,compute_35] ")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER "5.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52] ")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER "7.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61] ")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER "8.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_70,code=[sm_70,compute_70] ")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER "9.9")
+        string(APPEND GPU_CUDA_GENCODE "-gencode arch=compute_75,code=[sm_75,compute_75] ")
+      endif()
+
+      cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
+              -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+
+      foreach(CU_OBJ ${GPU_GEN_OBJS})
+        get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
+        string(REGEX REPLACE "^.*_lal_" "" CU_NAME "${CU_NAME}")
+        add_custom_command(OUTPUT ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          COMMAND ${BIN2C} -c -n ${CU_NAME} ${CU_OBJ} > ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h
+          DEPENDS ${CU_OBJ}
+          COMMENT "Generating ${CU_NAME}_cubin.h")
+        list(APPEND GPU_LIB_SOURCES ${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h)
+      endforeach()
+      set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h")
+
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
+      target_link_libraries(gpu ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+      if(CUDPP_OPT)
+        target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
+        target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
+      endif()
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+      target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
+      target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
+
+
+    elseif(GPU_API STREQUAL "OPENCL")
+      find_package(OpenCL REQUIRED)
+      set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
+      set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
+      set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
+      validate_option(OCL_TUNE OCL_TUNE_VALUES)
+      string(TOUPPER ${OCL_TUNE} OCL_TUNE)
+
+      include(OpenCLUtils)
+      set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
+
+      file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+      list(REMOVE_ITEM GPU_LIB_CU
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
+        ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
+      )
+
+      foreach(GPU_KERNEL ${GPU_LIB_CU})
+          get_filename_component(basename ${GPU_KERNEL} NAME_WE)
+          string(SUBSTRING ${basename} 4 -1 KERNEL_NAME)
+          GenerateOpenCLHeader(${KERNEL_NAME} ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h ${OCL_COMMON_HEADERS} ${GPU_KERNEL})
+          list(APPEND GPU_LIB_SOURCES ${CMAKE_CURRENT_BINARY_DIR}/gpu/${KERNEL_NAME}_cl.h)
+      endforeach()
+
+      GenerateOpenCLHeader(gayberne ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu)
+      GenerateOpenCLHeader(gayberne_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu)
+      GenerateOpenCLHeader(re_squared ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared.cu)
+      GenerateOpenCLHeader(re_squared_lj ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_ellipsoid_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_re_squared_lj.cu)
+      GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
+      GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
+      GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
+
+      list(APPEND GPU_LIB_SOURCES
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/re_squared_lj_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
+        ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
+      )
+
+      add_library(gpu STATIC ${GPU_LIB_SOURCES})
+      target_link_libraries(gpu ${OpenCL_LIBRARIES})
+      target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu ${OpenCL_INCLUDE_DIRS})
+      target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+      target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
+      list(APPEND LAMMPS_LINK_LIBS gpu)
+
+      add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+      target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
+      target_link_libraries(ocl_get_devices PRIVATE ${OpenCL_LIBRARIES})
+      target_include_directories(ocl_get_devices PRIVATE ${OpenCL_INCLUDE_DIRS})
+    endif()
+
+    # GPU package
+    FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
+
+    set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
+
+    # detects styles which have GPU version
+    RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+
+    get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
+
+    list(APPEND LIB_SOURCES ${GPU_SOURCES})
+    include_directories(${GPU_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KIM.cmake

@@ -0,0 +1,67 @@
+if(PKG_KIM)
+  set(KIM-API_MIN_VERSION 2.1)
+  find_package(CURL)
+  if(CURL_FOUND)
+    include_directories(${CURL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${CURL_LIBRARIES})
+    add_definitions(-DLMP_KIM_CURL)
+    set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
+    mark_as_advanced(LMP_DEBUG_CURL)
+    if(LMP_DEBUG_CURL)
+      add_definitions(-DLMP_DEBUG_CURL)
+    endif()
+    set(LMP_NO_SSL_CHECK OFF CACHE STRING "Tell libcurl to not verify the peer. If on, the connection succeeds regardless of the names in the certificate. Insecure - Use with caution!")
+    mark_as_advanced(LMP_NO_SSL_CHECK)
+    if(LMP_NO_SSL_CHECK)
+      add_definitions(-DLMP_NO_SSL_CHECK)
+    endif()
+  endif()
+  find_package(KIM-API QUIET)
+  if(KIM-API_FOUND)
+    if (KIM-API_VERSION VERSION_LESS ${KIM-API_MIN_VERSION})
+      if ("${DOWNLOAD_KIM}" STREQUAL "")
+        message(WARNING "Unsuitable KIM-API version \"${KIM-API_VERSION}\" found, but required is at least \"${KIM-API_MIN_VERSION}\".  Default behavior set to download and build our own.")
+      endif()
+      set(DOWNLOAD_KIM_DEFAULT ON)
+    else()
+      set(DOWNLOAD_KIM_DEFAULT OFF)
+    endif()
+  else()
+    if ("${DOWNLOAD_KIM}" STREQUAL "")
+      message(WARNING "KIM-API package not found.  Default behavior set to download and build our own")
+    endif()
+    set(DOWNLOAD_KIM_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_KIM "Download KIM-API from OpenKIM instead of using an already installed one" ${DOWNLOAD_KIM_DEFAULT})
+  if(DOWNLOAD_KIM)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded KIM-API library with Ninja build tool")
+    endif()
+    message(STATUS "KIM-API download requested - we will build our own")
+    include(CheckLanguage)
+    include(ExternalProject)
+    enable_language(C)
+    check_language(Fortran)
+    if(NOT CMAKE_Fortran_COMPILER)
+      message(FATAL_ERROR "Compiling the KIM-API library requires a Fortran compiler")
+    endif()
+    ExternalProject_Add(kim_build
+      URL https://s3.openkim.org/kim-api/kim-api-2.1.3.txz
+      URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
+      BINARY_DIR build
+      CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+                 -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                 -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}
+                 -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+      )
+    ExternalProject_get_property(kim_build INSTALL_DIR)
+    set(KIM-API_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api)
+    set(KIM-API_LDFLAGS ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX})
+    list(APPEND LAMMPS_DEPS kim_build)
+  else()
+    find_package(KIM-API ${KIM-API_MIN_VERSION} REQUIRED)
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS "${KIM-API_LDFLAGS}")
+  include_directories(${KIM-API_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -0,0 +1,74 @@
+if(PKG_KOKKOS)
+  # TODO: this option needs to be documented when this works with a
+  # regular release version of KOKKOS, and a version compatibility check
+  # of external KOKKOS lib versus what the KOKKOS package needs is required.
+  option(EXTERNAL_KOKKOS "Build against external kokkos library")
+  if(EXTERNAL_KOKKOS)
+    find_package(Kokkos REQUIRED)
+    list(APPEND LAMMPS_LINK_LIBS Kokkos::kokkos)
+  else()
+    set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
+    set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
+    add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+
+    set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
+                            ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
+                            ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+    include_directories(${Kokkos_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS kokkos)
+  endif()
+  add_definitions(-DLMP_KOKKOS)
+
+  set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
+  set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_list_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/neigh_bond_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/fix_nh_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
+                         ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
+
+  if(PKG_KSPACE)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
+                                   ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
+    if(KOKKOS_ENABLE_CUDA)
+      if(NOT ${FFT} STREQUAL "KISS")
+        add_definitions(-DFFT_CUFFT)
+        list(APPEND LAMMPS_LINK_LIBS cufft)
+      endif()
+    endif()
+  endif()
+
+  set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+
+  # detects styles which have KOKKOS version
+  RegisterStylesExt(${KOKKOS_PKG_SOURCES_DIR} kokkos KOKKOS_PKG_SOURCES)
+
+  # register kokkos-only styles
+  RegisterNBinStyle(${KOKKOS_PKG_SOURCES_DIR}/nbin_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_kokkos.h)
+  RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_halffull_kokkos.h)
+
+  if(PKG_USER-DPD)
+    get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+    list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.cpp)
+    RegisterNPairStyle(${KOKKOS_PKG_SOURCES_DIR}/npair_ssa_kokkos.h)
+    set_property(GLOBAL PROPERTY "KOKKOS_PKG_SOURCES" "${KOKKOS_PKG_SOURCES}")
+  endif()
+
+  get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
+
+  list(APPEND LIB_SOURCES ${KOKKOS_PKG_SOURCES})
+  include_directories(${KOKKOS_PKG_SOURCES_DIR})
+endif()

cmake/Modules/Packages/KSPACE.cmake

@@ -0,0 +1,60 @@
+if(PKG_KSPACE)
+  option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
+  set(FFTW "FFTW3")
+  if(FFT_SINGLE)
+    set(FFTW "FFTW3F")
+    add_definitions(-DFFT_SINGLE)
+  endif()
+  find_package(${FFTW} QUIET)
+  if(${FFTW}_FOUND)
+    set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
+  else()
+    set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
+  endif()
+  set(FFT_VALUES KISS FFTW3 MKL)
+  set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
+  validate_option(FFT FFT_VALUES)
+  string(TOUPPER ${FFT} FFT)
+
+  if(FFT STREQUAL "FFTW3")
+    find_package(${FFTW} REQUIRED)
+    add_definitions(-DFFT_FFTW3)
+    include_directories(${${FFTW}_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
+    if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+      option(FFT_FFTW_THREADS "Use threaded FFTW library" ON)
+    else()
+      option(FFT_FFTW_THREADS "Use threaded FFT library" OFF)
+    endif()
+
+    if(FFT_FFTW_THREADS)
+      if(FFTW3_OMP_LIBRARY OR FFTW3F_OMP_LIBRARY)
+        add_definitions(-DFFT_FFTW_THREADS)
+        list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_OMP_LIBRARIES})
+      else()
+        message(FATAL_ERROR "Need OpenMP enabled FFTW3 library for FFT_THREADS")
+      endif()
+    endif()
+  elseif(FFT STREQUAL "MKL")
+    find_package(MKL REQUIRED)
+    add_definitions(-DFFT_MKL)
+    option(FFT_MKL_THREADS "Use threaded MKL FFT" ON)
+    if(FFT_MKL_THREADS)
+      add_definitions(-DFFT_MKL_THREADS)
+    endif()
+    include_directories(${MKL_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    # last option is KISSFFT
+    add_definitions(-DFFT_KISS)
+  endif()
+
+  set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
+  set(FFT_PACK_VALUES array pointer memcpy)
+  set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
+  validate_option(FFT_PACK FFT_PACK_VALUES)
+  if(NOT FFT_PACK STREQUAL "array")
+    string(TOUPPER ${FFT_PACK} FFT_PACK)
+    add_definitions(-DFFT_PACK_${FFT_PACK})
+  endif()
+endif()

cmake/Modules/Packages/LATTE.cmake

@@ -0,0 +1,38 @@
+if(PKG_LATTE)
+  enable_language(Fortran)
+  find_package(LATTE)
+  if(LATTE_FOUND)
+    set(DOWNLOAD_LATTE_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_LATTE_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
+  if(DOWNLOAD_LATTE)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading LATTE you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded LATTE library with Ninja build tool")
+    endif()
+    message(STATUS "LATTE download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(latte_build
+      URL https://github.com/lanl/LATTE/archive/v1.2.1.tar.gz
+      URL_MD5 85ac414fdada2d04619c8f936344df14
+      SOURCE_SUBDIR cmake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC}
+      -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
+      -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
+      -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    )
+    ExternalProject_get_property(latte_build INSTALL_DIR)
+    set(LATTE_LIBRARIES ${INSTALL_DIR}/${CMAKE_INSTALL_LIBDIR}/liblatte.a)
+    list(APPEND LAMMPS_DEPS latte_build)
+  else()
+    find_package(LATTE)
+    if(NOT LATTE_FOUND)
+      message(FATAL_ERROR "LATTE library not found, help CMake to find it by setting LATTE_LIBRARY, or set DOWNLOAD_LATTE=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${LATTE_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/MESSAGE.cmake

@@ -0,0 +1,32 @@
+if(PKG_MESSAGE)
+  if(LAMMPS_SIZES STREQUAL BIGBIG)
+    message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
+  endif()
+  option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
+  file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
+      ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+
+  add_library(cslib STATIC ${cslib_SOURCES})
+  if(BUILD_MPI)
+    target_compile_definitions(cslib PRIVATE -DMPI_YES)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csmpi")
+  else()
+    target_compile_definitions(cslib PRIVATE -DMPI_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_MPI)
+    set_target_properties(cslib PROPERTIES OUTPUT_NAME "csnompi")
+  endif()
+
+  if(MESSAGE_ZMQ)
+    target_compile_definitions(cslib PRIVATE -DZMQ_YES)
+    find_package(ZMQ REQUIRED)
+    target_include_directories(cslib PRIVATE ${ZMQ_INCLUDE_DIRS})
+    target_link_libraries(cslib PUBLIC ${ZMQ_LIBRARIES})
+  else()
+    target_compile_definitions(cslib PRIVATE -DZMQ_NO)
+    target_include_directories(cslib PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src/STUBS_ZMQ)
+  endif()
+
+  list(APPEND LAMMPS_LINK_LIBS cslib)
+  include_directories(${LAMMPS_LIB_SOURCE_DIR}/message/cslib/src)
+endif()

cmake/Modules/Packages/MSCG.cmake

@@ -0,0 +1,45 @@
+if(PKG_MSCG)
+  find_package(GSL REQUIRED)
+  find_package(MSCG QUIET)
+  if(MSGC_FOUND)
+    set(DOWNLOAD_MSCG_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_MSCG_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+  if(DOWNLOAD_MSCG)
+    if (CMAKE_VERSION VERSION_LESS "3.7") # due to SOURCE_SUBDIR
+      message(FATAL_ERROR "For downlading MSCG you need at least cmake-3.7")
+    endif()
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded MSCG library with Ninja build tool")
+    endif()
+    include(ExternalProject)
+    if(NOT LAPACK_FOUND)
+      set(EXTRA_MSCG_OPTS "-DLAPACK_LIBRARIES=${CMAKE_CURRENT_BINARY_DIR}/liblinalg.a")
+    endif()
+    ExternalProject_Add(mscg_build
+      URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
+      URL_MD5 8c45e269ee13f60b303edd7823866a91
+      SOURCE_SUBDIR src/CMake
+      CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
+      BUILD_COMMAND make mscg INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(mscg_build BINARY_DIR)
+    set(MSCG_LIBRARIES ${BINARY_DIR}/libmscg.a)
+    ExternalProject_get_property(mscg_build SOURCE_DIR)
+    set(MSCG_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS mscg_build)
+    if(NOT LAPACK_FOUND)
+      file(MAKE_DIRECTORY ${MSCG_INCLUDE_DIRS})
+      add_dependencies(mscg_build linalg)
+    endif()
+  else()
+    find_package(MSCG)
+    if(NOT MSCG_FOUND)
+      message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIRS, or set DOWNLOAD_MSCG=ON to download it")
+    endif()
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS ${MSCG_LIBRARIES} ${GSL_LIBRARIES} ${LAPACK_LIBRARIES})
+  include_directories(${MSCG_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/OPT.cmake

@@ -0,0 +1,13 @@
+if(PKG_OPT)
+    set(OPT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPT)
+    set(OPT_SOURCES)
+    set_property(GLOBAL PROPERTY "OPT_SOURCES" "${OPT_SOURCES}")
+
+    # detects styles which have OPT version
+    RegisterStylesExt(${OPT_SOURCES_DIR} opt OPT_SOURCES)
+
+    get_property(OPT_SOURCES GLOBAL PROPERTY OPT_SOURCES)
+
+    list(APPEND LIB_SOURCES ${OPT_SOURCES})
+    include_directories(${OPT_SOURCES_DIR})
+endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -0,0 +1,6 @@
+if(PKG_PYTHON)
+  find_package(PythonLibs REQUIRED)
+  add_definitions(-DLMP_PYTHON)
+  include_directories(${PYTHON_INCLUDE_DIR})
+  list(APPEND LAMMPS_LINK_LIBS ${PYTHON_LIBRARY})
+endif()

cmake/Modules/Packages/QEQ.cmake

@@ -0,0 +1,20 @@
+# Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
+if(PKG_QEQ)
+  set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
+  file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
+  file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
+
+  if(NOT PKG_MANYBODY)
+    list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+    list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+
+  foreach(MY_HEADER ${QEQ_HEADERS})
+    AddStyleHeader(${MY_HEADER} FIX)
+  endforeach()
+
+  get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
+  list(APPEND LIB_SOURCES ${QEQ_SOURCES})
+  include_directories(${QEQ_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-COLVARS.cmake

@@ -0,0 +1,42 @@
+if(PKG_USER-COLVARS)
+
+  set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+
+  file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+
+  # Build Lepton by default
+  set(COLVARS_LEPTON_DEFAULT ON)
+  # but not if C++11 is disabled per user request
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if(DISABLE_CXX11_REQUIREMENT)
+      set(COLVARS_LEPTON_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(COLVARS_LEPTON "Build and link the Lepton library" ${COLVARS_LEPTON_DEFAULT})
+
+  # Verify that the user's choice is consistent
+  if(DEFINED DISABLE_CXX11_REQUIREMENT)
+    if((DISABLE_CXX11_REQUIREMENT) AND (COLVARS_LEPTON))
+      message(FATAL_ERROR "Building the Lepton library requires C++11 or later.")
+    endif()
+  endif()
+
+  if(COLVARS_LEPTON)
+    set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+    file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+    add_library(lepton STATIC ${LEPTON_SOURCES})
+    target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
+  endif()
+
+  add_library(colvars STATIC ${COLVARS_SOURCES})
+  target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
+  list(APPEND LAMMPS_LINK_LIBS colvars)
+
+  if(COLVARS_LEPTON)
+    list(APPEND LAMMPS_LINK_LIBS lepton)
+    target_compile_options(colvars PRIVATE -DLEPTON)
+    target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
+  endif()
+
+endif()

cmake/Modules/Packages/USER-H5MD.cmake

@@ -0,0 +1,8 @@
+if(PKG_USER-H5MD)
+  enable_language(C)
+
+  find_package(HDF5 REQUIRED)
+  target_link_libraries(h5md ${HDF5_LIBRARIES})
+  target_include_directories(h5md PRIVATE ${HDF5_INCLUDE_DIRS})
+  include_directories(${HDF5_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-INTEL.cmake

@@ -0,0 +1,118 @@
+if(PKG_USER-INTEL)
+  check_include_file_cxx(immintrin.h FOUND_IMMINTRIN)
+  if(NOT FOUND_IMMINTRIN)
+    message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
+  endif()
+
+  add_definitions(-DLMP_USER_INTEL)
+
+  set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+  set(INTEL_ARCH_VALUES cpu knl)
+  set_property(CACHE INTEL_ARCH PROPERTY STRINGS ${INTEL_ARCH_VALUES})
+  validate_option(INTEL_ARCH INTEL_ARCH_VALUES)
+  string(TOUPPER ${INTEL_ARCH} INTEL_ARCH)
+
+  find_package(Threads QUIET)
+  if(Threads_FOUND)
+    set(INTEL_LRT_MODE "threads" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  else()
+    set(INTEL_LRT_MODE "none" CACHE STRING "Long-range threads mode (none, threads, or c++11)")
+  endif()
+  set(INTEL_LRT_VALUES none threads c++11)
+  set_property(CACHE INTEL_LRT_MODE PROPERTY STRINGS ${INTEL_LRT_VALUES})
+  validate_option(INTEL_LRT_MODE INTEL_LRT_VALUES)
+  string(TOUPPER ${INTEL_LRT_MODE} INTEL_LRT_MODE)
+  if(INTEL_LRT_MODE STREQUAL "THREADS")
+    if(Threads_FOUND)
+      add_definitions(-DLMP_INTEL_USELRT)
+      list(APPEND LAMMPS_LINK_LIBS ${CMAKE_THREAD_LIBS_INIT})
+    else()
+      message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+    endif()
+  endif()
+  if(INTEL_LRT_MODE STREQUAL "C++11")
+    add_definitions(-DLMP_INTEL_USERLRT -DLMP_INTEL_LRT11)
+  endif()
+
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
+      message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    endif()
+  else()
+    message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  endif()
+
+  find_package(TBB QUIET)
+  if(TBB_FOUND)
+    list(APPEND LAMMPS_LINK_LIBS ${TBB_MALLOC_LIBRARIES})
+  else()
+    add_definitions(-DLMP_INTEL_NO_TBB)
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    endif()
+  endif()
+
+  find_package(MKL QUIET)
+  if(MKL_FOUND)
+    add_definitions(-DLMP_USE_MKL_RNG)
+    list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
+  else()
+    message(STATUS "Pair style dpd/intel will be faster with MKL libraries")
+  endif()
+
+  if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
+    message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  endif()
+
+  if(INTEL_ARCH STREQUAL "KNL")
+    if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    endif()
+    set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
+    set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
+    add_compile_options(-xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
+    add_definitions(-DLMP_INTEL_OFFLOAD)
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost")
+      endif()
+      include(CheckCXXCompilerFlag)
+      foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+        check_cxx_compiler_flag("${__FLAG}" COMPILER_SUPPORTS${_FLAG})
+        if(COMPILER_SUPPORTS${_FLAG})
+          add_compile_options(${_FLAG})
+        endif()
+      endforeach()
+    else()
+      add_compile_options(-O3 -ffast-math)
+    endif()
+  endif()
+
+  # collect sources
+  set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
+  set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
+                         ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
+                         ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+
+  set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+
+  # detect styles which have a USER-INTEL version
+  RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
+  RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
+  RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
+  RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+
+  get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+  if(PKG_KSPACE)
+    list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+    RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  endif()
+
+  list(APPEND LIB_SOURCES ${USER-INTEL_SOURCES})
+  include_directories(${USER-INTEL_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -0,0 +1,14 @@
+if(PKG_USER-MOLFILE)
+  if (CMAKE_VERSION VERSION_LESS "3.10") # due to INTERFACE without a library
+    message(FATAL_ERROR "For configuring USER-MOLFILE you need CMake 3.10 or later")
+  endif()
+
+  set(MOLFILE_INCLUDE_DIRS "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
+  add_library(molfile INTERFACE)
+  target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+  # no need to link with -ldl on windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+  endif()
+  list(APPEND LAMMPS_LINK_LIBS molfile)
+endif()

cmake/Modules/Packages/USER-NETCDF.cmake

@@ -0,0 +1,24 @@
+if(PKG_USER-NETCDF)
+  # USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+  # NetCDF library enables dump sytle "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
+  find_package(NetCDF)
+  if(NETCDF_FOUND)
+    find_package(PNetCDF)
+  else(NETCDF_FOUND)
+    find_package(PNetCDF REQUIRED)
+  endif(NETCDF_FOUND)
+
+  if(NETCDF_FOUND)
+    include_directories(${NETCDF_INCLUDE_DIRS})
+    list(APPEND LAMMPS_LINK_LIBS ${NETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_NETCDF)
+  endif(NETCDF_FOUND)
+
+  if(PNETCDF_FOUND)
+    include_directories(${PNETCDF_INCLUDES})
+    list(APPEND LAMMPS_LINK_LIBS ${PNETCDF_LIBRARIES})
+    add_definitions(-DLMP_HAS_PNETCDF)
+  endif(PNETCDF_FOUND)
+
+  add_definitions(-DNC_64BIT_DATA=0x0020)
+endif()

cmake/Modules/Packages/USER-OMP.cmake

@@ -0,0 +1,42 @@
+if(PKG_USER-OMP)
+    set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
+    set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
+                         ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                         ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
+    add_definitions(-DLMP_USER_OMP)
+    set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
+
+    # detects styles which have USER-OMP version
+    RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
+    RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
+
+    get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+    # manually add package dependent source files from USER-OMP that do not provide styles
+
+    if(PKG_ASPHERE)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+    endif()
+
+    if(PKG_RIGID)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+    endif()
+
+    if(PKG_USER-REAXC)
+      list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                   ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+    endif()
+
+    list(APPEND LIB_SOURCES ${USER-OMP_SOURCES})
+    include_directories(${USER-OMP_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -0,0 +1,91 @@
+if(PKG_USER-PLUMED)
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  set(PLUMED_LINK_LIBS "")
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${GSL_LIBRARIES})
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ${ZLIB_LIBRARIES})
+    endif()
+  endif()
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Plumed library with Ninja build tool")
+    endif()
+    if(BUILD_MPI)
+      set(PLUMED_CONFIG_MPI "--enable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+    else()
+      set(PLUMED_CONFIG_MPI "--disable-mpi")
+      set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+      set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    endif()
+    if(BUILD_OMP)
+      set(PLUMED_CONFIG_OMP "--enable-openmp")
+    else()
+      set(PLUMED_CONFIG_OMP "--disable-openmp")
+    endif()
+    message(STATUS "PLUMED download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL https://github.com/plumed/plumed2/releases/download/v2.6.0/plumed-src-2.6.0.tgz
+      URL_MD5 204d2edae58d9b10ba3ad460cad64191
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+                                               ${CONFIGURE_REQUEST_PIC}
+                                               --enable-modules=all
+                                               ${PLUMED_CONFIG_MPI}
+                                               ${PLUMED_CONFIG_OMP}
+                                               CXX=${PLUMED_CONFIG_CXX}
+                                               CC=${PLUMED_CONFIG_CC}
+    )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    set(PLUMED_INSTALL_DIR ${INSTALL_DIR})
+    list(APPEND LAMMPS_DEPS plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed.a ${PLUMED_LINK_LIBS} ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} ${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX} ${CMAKE_DL_LIBS})
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
+      list(APPEND LAMMPS_LINK_LIBS ${PLUMED_INSTALL_DIR}/lib/libplumedWrapper.a -rdynamic ${CMAKE_DL_LIBS})
+    endif()
+    set(PLUMED_INCLUDE_DIRS "${PLUMED_INSTALL_DIR}/include")
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      add_definitions(-D__PLUMED_WRAPPER_CXX=1)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      add_definitions(-D__PLUMED_HAS_DLOPEN=1 -D__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX})
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
+    endif()
+    list(APPEND LAMMPS_LINK_LIBS ${PLUMED_LOAD})
+  endif()
+  include_directories(${PLUMED_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-QMMM.cmake

@@ -0,0 +1,13 @@
+if(PKG_USER-QMMM)
+  enable_language(C)
+
+  if(NOT BUILD_LIB)
+    message(FATAL_ERROR "Building a QM/MM executable with USER-QMMM requires BUILD_LIB=yes")
+  endif()
+  if(NOT BUILD_SHARED_LIBS)
+    message(WARNING "It is recommended to use BUILD_SHARED_LIBS=yes with USER-QMMM")
+  endif()
+  add_library(qmmm STATIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm/libqmmm.c)
+  list(APPEND LAMMPS_LINK_LIBS qmmm)
+  target_include_directories(qmmm PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/qmmm)
+endif()

cmake/Modules/Packages/USER-QUIP.cmake

@@ -0,0 +1,5 @@
+if(PKG_USER-QUIP)
+  enable_language(Fortran)
+  find_package(QUIP REQUIRED)
+  list(APPEND LAMMPS_LINK_LIBS ${QUIP_LIBRARIES} ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -0,0 +1,62 @@
+if(PKG_USER-SCAFACOS)
+  enable_language(Fortran)
+  enable_language(C)
+
+  find_package(GSL REQUIRED)
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_SCAFACOS_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(SCAFACOS QUIET scafacos)
+    if(SCAFACOS_FOUND)
+      set(DOWNLOAD_SCAFACOS_DEFAULT OFF)
+    endif()
+  endif()
+  option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
+  if(DOWNLOAD_SCAFACOS)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded ScaFaCoS library with Ninja build tool")
+    endif()
+    message(STATUS "ScaFaCoS download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(scafacos_build
+      URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
+      URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
+                                               --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
+                                               --with-internal-fftw --with-internal-pfft
+                                               --with-internal-pnfft ${CONFIGURE_REQUEST_PIC}
+                                               FC=${CMAKE_MPI_Fortran_COMPILER}
+                                               CXX=${CMAKE_MPI_CXX_COMPILER}
+                                               CC=${CMAKE_MPI_C_COMPILER}
+                                               F77=
+    )
+    ExternalProject_get_property(scafacos_build INSTALL_DIR)
+    set(SCAFACOS_BUILD_DIR ${INSTALL_DIR})
+    set(SCAFACOS_INCLUDE_DIRS ${SCAFACOS_BUILD_DIR}/include)
+    list(APPEND LAMMPS_DEPS scafacos_build)
+    # list and order from pkg_config file of ScaFaCoS build
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_direct.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_ewald.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fmm.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p2nfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_p3m.a)
+    list(APPEND LAMMPS_LINK_LIBS ${GSL_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_near.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_gridsort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_resort.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_redist.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_common.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pnfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_pfft.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3_mpi.a)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_BUILD_DIR}/lib/libfcs_fftw3.a)
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_Fortran_LIBRARIES})
+    list(APPEND LAMMPS_LINK_LIBS ${MPI_C_LIBRARIES})
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(SCAFACOS REQUIRED scafacos)
+    list(APPEND LAMMPS_LINK_LIBS ${SCAFACOS_LDFLAGS})
+  endif()
+  include_directories(${SCAFACOS_INCLUDE_DIRS})
+endif()

cmake/Modules/Packages/USER-SDPD.cmake

@@ -0,0 +1,13 @@
+# Fix rigid/meso requires RIGID to be installed
+if(PKG_USER-SDPD)
+  set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+
+  get_property(hlist GLOBAL PROPERTY FIX)
+  if(NOT PKG_RIGID)
+    list(REMOVE_ITEM hlist ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.h)
+    list(REMOVE_ITEM LIB_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  endif()
+  set_property(GLOBAL PROPERTY FIX "${hlist}")
+
+  include_directories(${USER-SDPD_SOURCES_DIR})
+endif()

cmake/Modules/Packages/USER-SMD.cmake

@@ -0,0 +1,28 @@
+if(PKG_USER-SMD)
+  find_package(Eigen3 NO_MODULE)
+  if(EIGEN3_FOUND)
+    set(DOWNLOAD_EIGEN3_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_EIGEN3_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
+  if(DOWNLOAD_EIGEN3)
+    message(STATUS "Eigen3 download requested - we will build our own")
+    include(ExternalProject)
+    ExternalProject_Add(Eigen3_build
+      URL http://bitbucket.org/eigen/eigen/get/3.3.7.tar.gz
+      URL_MD5 f2a417d083fe8ca4b8ed2bc613d20f07
+      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    )
+    ExternalProject_get_property(Eigen3_build SOURCE_DIR)
+    set(EIGEN3_INCLUDE_DIR ${SOURCE_DIR})
+    list(APPEND LAMMPS_DEPS Eigen3_build)
+  else()
+    find_package(Eigen3 NO_MODULE)
+    mark_as_advanced(Eigen3_DIR)
+    if(NOT EIGEN3_FOUND)
+      message(FATAL_ERROR "Eigen3 not found, help CMake to find it by setting EIGEN3_INCLUDE_DIR, or set DOWNLOAD_EIGEN3=ON to download it")
+    endif()
+  endif()
+  include_directories(${EIGEN3_INCLUDE_DIR})
+endif()

cmake/Modules/Packages/USER-VTK.cmake

@@ -0,0 +1,6 @@
+if(PKG_USER-VTK)
+  find_package(VTK REQUIRED NO_MODULE)
+  include(${VTK_USE_FILE})
+  add_definitions(-DLAMMPS_VTK)
+  list(APPEND LAMMPS_LINK_LIBS ${VTK_LIBRARIES})
+endif()

cmake/Modules/Packages/VORONOI.cmake

@@ -0,0 +1,45 @@
+if(PKG_VORONOI)
+  find_package(VORO)
+  if(VORO_FOUND)
+    set(DOWNLOAD_VORO_DEFAULT OFF)
+  else()
+    set(DOWNLOAD_VORO_DEFAULT ON)
+  endif()
+  option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
+  if(DOWNLOAD_VORO)
+    if(CMAKE_GENERATOR STREQUAL "Ninja")
+      message(FATAL_ERROR "Cannot build downloaded Voro++ library with Ninja build tool")
+    endif()
+    message(STATUS "Voro++ download requested - we will build our own")
+    include(ExternalProject)
+
+    if(BUILD_SHARED_LIBS)
+      set(VORO_BUILD_CFLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    else()
+      set(VORO_BUILD_CFLAGS "${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}")
+    endif()
+    if(APPLE)
+      get_filename_component(VORO_CXX ${CMAKE_CXX_COMPILER} NAME_WE)
+      set(VORO_BUILD_OPTIONS CXX=${VORO_CXX} CFLAGS=${VORO_BUILD_CFLAGS})
+    else()
+      set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
+    endif()
+
+    ExternalProject_Add(voro_build
+      URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
+      URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+      CONFIGURE_COMMAND "" BUILD_COMMAND make ${VORO_BUILD_OPTIONS} BUILD_IN_SOURCE 1 INSTALL_COMMAND ""
+      )
+    ExternalProject_get_property(voro_build SOURCE_DIR)
+    set(VORO_LIBRARIES ${SOURCE_DIR}/src/libvoro++.a)
+    set(VORO_INCLUDE_DIRS ${SOURCE_DIR}/src)
+    list(APPEND LAMMPS_DEPS voro_build)
+  else()
+    find_package(VORO)
+    if(NOT VORO_FOUND)
+      message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+    endif()
+  endif()
+  include_directories(${VORO_INCLUDE_DIRS})
+  list(APPEND LAMMPS_LINK_LIBS ${VORO_LIBRARIES})
+endif()

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

@@ -45,21 +45,24 @@ function(FindStyleHeadersExt path style_class extension headers sources)
 endfunction(FindStyleHeadersExt)
 
 function(CreateStyleHeader path filename)
-    math(EXPR N "${ARGC}-2")
-
     set(temp "")
-    if(N GREATER 0)
-        math(EXPR ARG_END   "${ARGC}-1")
- 
-        foreach(IDX RANGE 2 ${ARG_END})
-            list(GET ARGV ${IDX} FNAME)
+    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)
@@ -84,19 +87,27 @@ function(RegisterNPairStyle path)
     AddStyleHeader(${path} NPAIR)
 endfunction(RegisterNPairStyle)
 
+function(RegisterFixStyle path)
+    AddStyleHeader(${path} FIX)
+endfunction(RegisterFixStyle)
+
+function(RegisterIntegrateStyle path)
+    AddStyleHeader(${path} INTEGRATE)
+endfunction(RegisterIntegrateStyle)
+
 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
@@ -107,35 +118,6 @@ function(RegisterStyles search_path)
     FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
 endfunction(RegisterStyles)
 
-function(RemovePackageHeader headers pkg_header)
-    get_property(hlist GLOBAL PROPERTY ${headers})
-    list(REMOVE_ITEM hlist ${pkg_header})
-    set_property(GLOBAL PROPERTY ${headers} "${hlist}")
-endfunction(RemovePackageHeader)
-
-function(DetectAndRemovePackageHeader fname)
-    RemovePackageHeader(ANGLE     ${fname})
-    RemovePackageHeader(ATOM_VEC  ${fname})
-    RemovePackageHeader(BODY      ${fname})
-    RemovePackageHeader(BOND      ${fname})
-    RemovePackageHeader(COMMAND   ${fname})
-    RemovePackageHeader(COMPUTE   ${fname})
-    RemovePackageHeader(DIHEDRAL  ${fname})
-    RemovePackageHeader(DUMP      ${fname})
-    RemovePackageHeader(FIX       ${fname})
-    RemovePackageHeader(IMPROPER  ${fname})
-    RemovePackageHeader(INTEGRATE ${fname})
-    RemovePackageHeader(KSPACE    ${fname})
-    RemovePackageHeader(MINIMIZE  ${fname})
-    RemovePackageHeader(NBIN      ${fname})
-    RemovePackageHeader(NPAIR     ${fname})
-    RemovePackageHeader(NSTENCIL  ${fname})
-    RemovePackageHeader(NTOPO     ${fname})
-    RemovePackageHeader(PAIR      ${fname})
-    RemovePackageHeader(READER    ${fname})
-    RemovePackageHeader(REGION    ${fname})
-endfunction(DetectAndRemovePackageHeader)
-
 function(RegisterStylesExt search_path extension sources)
     FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
     FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
@@ -181,3 +163,106 @@ function(GenerateStyleHeaders output_path)
     GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
     GenerateStyleHeader(${output_path} REGION     region    ) # domain
 endfunction(GenerateStyleHeaders)
+
+function(DetectBuildSystemConflict lammps_src_dir)
+  if(ARGC GREATER 1)
+    list(REMOVE_AT ARGV 0)
+    foreach(SRC_FILE ${ARGV})
+        get_filename_component(FILENAME ${SRC_FILE} NAME)
+        if(EXISTS ${lammps_src_dir}/${FILENAME})
+            message(FATAL_ERROR "\n########################################################################\n"
+                                  "Found package(s) installed by the make-based build system\n"
+                                  "\n"
+                                  "Please run\n"
+                                  "make -C ${lammps_src_dir} no-all purge\n"
+                                  "to uninstall\n"
+                                  "########################################################################")
+        endif()
+    endforeach()
+  endif()
+endfunction(DetectBuildSystemConflict)
+
+
+function(FindPackagesHeaders path style_class file_pattern headers)
+    file(GLOB files "${path}/${file_pattern}*.h")
+    get_property(plist GLOBAL PROPERTY ${headers})
+
+    foreach(file_name ${files})
+        file(STRINGS ${file_name} is_style LIMIT_COUNT 1 REGEX ${style_class})
+        if(is_style)
+            list(APPEND plist ${file_name})
+        endif()
+    endforeach()
+    set_property(GLOBAL PROPERTY ${headers} "${plist}")
+endfunction(FindPackagesHeaders)
+
+function(RegisterPackages search_path)
+    FindPackagesHeaders(${search_path} ANGLE_CLASS     angle_     PKGANGLE     ) # angle     ) # force
+    FindPackagesHeaders(${search_path} ATOM_CLASS      atom_vec_  PKGATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
+    FindPackagesHeaders(${search_path} BODY_CLASS      body_      PKGBODY      ) # body      ) # atom_vec_body
+    FindPackagesHeaders(${search_path} BOND_CLASS      bond_      PKGBOND      ) # bond      ) # force
+    FindPackagesHeaders(${search_path} COMMAND_CLASS   "[^.]"     PKGCOMMAND   ) # command   ) # input
+    FindPackagesHeaders(${search_path} COMPUTE_CLASS   compute_   PKGCOMPUTE   ) # compute   ) # modify
+    FindPackagesHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  PKGDIHEDRAL  ) # dihedral  ) # force
+    FindPackagesHeaders(${search_path} DUMP_CLASS      dump_      PKGDUMP      ) # dump      ) # output    write_dump
+    FindPackagesHeaders(${search_path} FIX_CLASS       fix_       PKGFIX       ) # fix       ) # modify
+    FindPackagesHeaders(${search_path} IMPROPER_CLASS  improper_  PKGIMPROPER  ) # improper  ) # force
+    FindPackagesHeaders(${search_path} INTEGRATE_CLASS "[^.]"     PKGINTEGRATE ) # integrate ) # update
+    FindPackagesHeaders(${search_path} KSPACE_CLASS    "[^.]"     PKGKSPACE    ) # kspace    ) # force
+    FindPackagesHeaders(${search_path} MINIMIZE_CLASS  min_       PKGMINIMIZE  ) # minimize  ) # update
+    FindPackagesHeaders(${search_path} NBIN_CLASS      nbin_      PKGNBIN      ) # nbin      ) # neighbor
+    FindPackagesHeaders(${search_path} NPAIR_CLASS     npair_     PKGNPAIR     ) # npair     ) # neighbor
+    FindPackagesHeaders(${search_path} NSTENCIL_CLASS  nstencil_  PKGNSTENCIL  ) # nstencil  ) # neighbor
+    FindPackagesHeaders(${search_path} NTOPO_CLASS     ntopo_     PKGNTOPO     ) # ntopo     ) # neighbor
+    FindPackagesHeaders(${search_path} PAIR_CLASS      pair_      PKGPAIR      ) # pair      ) # force
+    FindPackagesHeaders(${search_path} READER_CLASS    reader_    PKGREADER    ) # reader    ) # read_dump
+    FindPackagesHeaders(${search_path} REGION_CLASS    region_    PKGREGION    ) # region    ) # domain
+endfunction(RegisterPackages)
+
+function(CreatePackagesHeader path filename)
+  set(temp "")
+  if(ARGC GREATER 2)
+    list(REMOVE_AT ARGV 0 1)
+    foreach(FNAME ${ARGV})
+      set_property(DIRECTORY APPEND PROPERTY CMAKE_CONFIGURE_DEPENDS "${FNAME}")
+      get_filename_component(DNAME ${FNAME} DIRECTORY)
+      get_filename_component(DNAME ${DNAME} NAME)
+      get_filename_component(FNAME ${FNAME} NAME)
+      set(temp "${temp}#undef PACKAGE\n#define PACKAGE \"${DNAME}\"\n")
+      set(temp "${temp}#include \"${DNAME}/${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(CreatePackagesHeader)
+
+function(GeneratePackagesHeader path property style)
+  get_property(files GLOBAL PROPERTY ${property})
+  CreatePackagesHeader("${path}" "packages_${style}.h" ${files})
+endfunction(GeneratePackagesHeader)
+
+function(GeneratePackagesHeaders output_path)
+    GeneratePackagesHeader(${output_path} PKGANGLE      angle     ) # force
+    GeneratePackagesHeader(${output_path} PKGATOM_VEC   atom      ) # atom      atom_vec_hybrid
+    GeneratePackagesHeader(${output_path} PKGBODY       body      ) # atom_vec_body
+    GeneratePackagesHeader(${output_path} PKGBOND       bond      ) # force
+    GeneratePackagesHeader(${output_path} PKGCOMMAND    command   ) # input
+    GeneratePackagesHeader(${output_path} PKGCOMPUTE    compute   ) # modify
+    GeneratePackagesHeader(${output_path} PKGDIHEDRAL   dihedral  ) # force
+    GeneratePackagesHeader(${output_path} PKGDUMP       dump      ) # output    write_dump
+    GeneratePackagesHeader(${output_path} PKGFIX        fix       ) # modify
+    GeneratePackagesHeader(${output_path} PKGIMPROPER   improper  ) # force
+    GeneratePackagesHeader(${output_path} PKGINTEGRATE  integrate ) # update
+    GeneratePackagesHeader(${output_path} PKGKSPACE     kspace    ) # force
+    GeneratePackagesHeader(${output_path} PKGMINIMIZE   minimize  ) # update
+    GeneratePackagesHeader(${output_path} PKGNBIN       nbin      ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNPAIR      npair     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNSTENCIL   nstencil  ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGNTOPO      ntopo     ) # neighbor
+    GeneratePackagesHeader(${output_path} PKGPAIR       pair      ) # force
+    GeneratePackagesHeader(${output_path} PKGREADER     reader    ) # read_dump
+    GeneratePackagesHeader(${output_path} PKGREGION     region    ) # domain
+endfunction(GeneratePackagesHeaders)
+

cmake/Modules/Testing.cmake

@@ -0,0 +1,52 @@
+###############################################################################
+# Testing
+###############################################################################
+option(ENABLE_TESTING "Enable testing" OFF)
+if(ENABLE_TESTING AND BUILD_EXE)
+  enable_testing()
+  option(LAMMPS_TESTING_SOURCE_DIR "Location of lammps-testing source directory" "")
+  option(LAMMPS_TESTING_GIT_TAG    "Git tag of lammps-testing" "master")
+  mark_as_advanced(LAMMPS_TESTING_SOURCE_DIR LAMMPS_TESTING_GIT_TAG)
+
+  if (CMAKE_VERSION VERSION_GREATER "3.10.3" AND NOT LAMMPS_TESTING_SOURCE_DIR)
+    include(FetchContent)
+
+    FetchContent_Declare(lammps-testing
+      GIT_REPOSITORY https://github.com/lammps/lammps-testing.git
+      GIT_TAG ${LAMMPS_TESTING_GIT_TAG}
+    )
+
+    FetchContent_GetProperties(lammps-testing)
+    if(NOT lammps-testing_POPULATED)
+      message(STATUS "Downloading tests...")
+      FetchContent_Populate(lammps-testing)
+    endif()
+
+    set(LAMMPS_TESTING_SOURCE_DIR ${lammps-testing_SOURCE_DIR})
+  elseif(NOT LAMMPS_TESTING_SOURCE_DIR)
+    message(WARNING "Full test-suite requires CMake >= 3.11 or copy of\n"
+                    "https://github.com/lammps/lammps-testing in LAMMPS_TESTING_SOURCE_DIR")
+  endif()
+
+  add_test(ShowHelp ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -help)
+
+  if(EXISTS ${LAMMPS_TESTING_SOURCE_DIR})
+    message(STATUS "Running test discovery...")
+
+    file(GLOB_RECURSE TEST_SCRIPTS ${LAMMPS_TESTING_SOURCE_DIR}/tests/core/*/in.*)
+    foreach(script_path ${TEST_SCRIPTS})
+      get_filename_component(TEST_NAME ${script_path} EXT)
+      get_filename_component(SCRIPT_NAME ${script_path} NAME)
+      get_filename_component(PARENT_DIR ${script_path} DIRECTORY)
+      string(SUBSTRING ${TEST_NAME} 1 -1 TEST_NAME)
+      string(REPLACE "-" "_" TEST_NAME ${TEST_NAME})
+      string(REPLACE "+" "_" TEST_NAME ${TEST_NAME})
+      set(TEST_NAME "test_core_${TEST_NAME}_serial")
+      add_test(${TEST_NAME} ${CMAKE_BINARY_DIR}/${LAMMPS_BINARY} -in ${SCRIPT_NAME})
+      set_tests_properties(${TEST_NAME} PROPERTIES WORKING_DIRECTORY ${PARENT_DIR})
+    endforeach()
+    list(LENGTH TEST_SCRIPTS NUM_TESTS)
+
+    message(STATUS "Found ${NUM_TESTS} tests.")
+  endif()
+endif()

cmake/Modules/generate_lmpgitversion.cmake

@@ -0,0 +1,30 @@
+set(temp "#ifndef LMP_GIT_VERSION_H\n#define LMP_GIT_VERSION_H\n")
+set(temp_git_commit "(unknown)")
+set(temp_git_branch "(unknown)")
+set(temp_git_describe "(unknown)")
+set(temp_git_info "false")
+if(GIT_FOUND AND EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/../.git)
+  set(temp_git_info "true")
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse HEAD
+    OUTPUT_VARIABLE temp_git_commit
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. rev-parse --abbrev-ref HEAD
+    OUTPUT_VARIABLE temp_git_branch
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${CMAKE_CURRENT_SOURCE_DIR}/.. describe --dirty=-modified
+    OUTPUT_VARIABLE temp_git_describe
+    ERROR_QUIET
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+endif()
+
+set(temp "${temp}const bool LAMMPS_NS::LAMMPS::has_git_info = ${temp_git_info};\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_commit[] = \"${temp_git_commit}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_branch[] = \"${temp_git_branch}\";\n")
+set(temp "${temp}const char LAMMPS_NS::LAMMPS::git_descriptor[] = \"${temp_git_describe}\";\n")
+set(temp "${temp}#endif\n\n")
+
+message(STATUS "Generating lmpgitversion.h...")
+file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")

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

@@ -0,0 +1,4 @@
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
+if ( "$?LAMMPS_POTENTIALS" == 0 ) setenv LAMMPS_POTENTIALS @LAMMPS_INSTALL_DATADIR@/potentials
+if ( "$?MSI2LMP_LIBRARY" == 0 ) setenv MSI2LMP_LIBRARY @LAMMPS_INSTALL_DATADIR@/frc_files

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

@@ -0,0 +1,5 @@
+# set environment for LAMMPS and msi2lmp executables
+# to find potential and force field files
+LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS-@LAMMPS_INSTALL_DATADIR@/potentials}
+MSI2LMP_LIBRARY=${MSI2LMP_LIBRARY-@LAMMPS_INSTALL_DATADIR@/frc_files}
+export LAMMPS_POTENTIALS MSI2LMP_LIBRARY

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${libdir} -llammps@LAMMPS_MACHINE@
+Libs: -L${libdir} -llammps@LAMMPS_LIB_SUFFIX@
 Libs.private: -lm
 Cflags: -I${includedir} @LAMMPS_API_DEFINES@

cmake/presets/all_off.cmake

@@ -0,0 +1,18 @@
+# preset that turns on all existing packages off. can be used to reset
+# an existing package selection without losing any other settings
+
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
+        USER-H5MD 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/all_on.cmake

@@ -0,0 +1,20 @@
+# preset that turns on all existing packages. using the combination
+# this preset followed by the nolib.cmake preset should configure a
+# LAMMPS binary, with as many packages included, that can be compiled
+# with just a working C++ compiler and an MPI library.
+
+set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MOLECULE
+        MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+        SRD VORONOI
+        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
+        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
+        USER-H5MD 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-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
+        USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
+        USER-TALLY USER-UEF USER-VTK USER-YAFF)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/clang.cmake

@@ -0,0 +1,17 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "-Wall -Wextra -g -O2 -DNDEBG" CACHE STRING "" FORCE)
+set(MPI_CXX "clang++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "clang" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "/usr/lib64/libomp.so" CACHE PATH "" FORCE)
+

cmake/presets/mingw-cross.cmake

@@ -0,0 +1,17 @@
+set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
+                 GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI POEMS QEQ
+                 REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI USER-ATC USER-AWPMD
+                 USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
+                 USER-DPD USER-DRUDE USER-EFF USER-FEP USER-INTEL USER-MANIFOLD
+                 USER-MEAMC USER-MESO USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE
+                 USER-OMP USER-PHONON USER-PTM USER-QTB USER-REAXC USER-SDPD
+                 USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF USER-YAFF)
+
+foreach(PKG ${WIN_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()
+
+set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
+set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_BINARY_DIR}/lammps-installer")

cmake/presets/minimal.cmake

@@ -0,0 +1,8 @@
+# preset that turns on just a few, frequently used packages
+# this will be compiled quickly and handle a lot of common inputs.
+
+set(ALL_PACKAGES KSPACE MANYBODY MOLECULE RIGID)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/most.cmake

@@ -0,0 +1,15 @@
+# preset that turns on a wide range of packages, some of which require
+# external libraries. Compared to all_on.cmake some more unusual packages
+# are removed. The resulting binary should be able to run most inputs.
+
+set(ALL_PACKAGES ASPHERE CLASS2 COLLOID CORESHELL DIPOLE
+        GRANULAR KSPACE MANYBODY MC MISC MOLECULE OPT PERI
+        PYTHON QEQ REPLICA RIGID SHOCK SNAP SRD VORONOI
+        USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION USER-DPD
+        USER-DRUDE USER-FEP USER-MEAMC USER-MESO
+        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REAXC
+        USER-SPH USER-SMD USER-UEF USER-YAFF)
+
+foreach(PKG ${ALL_PACKAGES})
+  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
+endforeach()

cmake/presets/nolib.cmake

@@ -0,0 +1,11 @@
+# preset that turns off all packages that require some form of external
+# library or special compiler (fortran or cuda) or equivalent.
+
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
+        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
+        USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
+        USER-SCAFACOS USER-SMD USER-VTK)
+
+foreach(PKG ${PACKAGES_WITH_LIB})
+  set(PKG_${PKG} OFF CACHE BOOL "" FORCE)
+endforeach()

doc/.gitignore

@@ -1,6 +1,12 @@
+/old
 /html
+/html-offline
+/latex
+/mathjax
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi
 /Manual.pdf
 /Developer.pdf
+/doctrees
+/docenv

doc/Makefile

@@ -1,14 +1,15 @@
 # Makefile for LAMMPS documentation
 
-SHELL 	      = /bin/bash
-SHA1          = $(shell echo $USER-$PWD | python utils/sha1sum.py)
-BUILDDIR      = /tmp/lammps-docs-$(SHA1)
-RSTDIR        = $(BUILDDIR)/rst
+SHELL         = /bin/bash
+BUILDDIR      = ${CURDIR}
+RSTDIR        = $(BUILDDIR)/src
 VENV          = $(BUILDDIR)/docenv
+MATHJAX       = $(BUILDDIR)/mathjax
 TXT2RST       = $(VENV)/bin/txt2rst
-ANCHORCHECK   = $(VENV)/bin/doc_anchor_check
+ANCHORCHECK   = $(VENV)/bin/rst_anchor_check
 
 PYTHON        = $(shell which python3)
+VIRTUALENV     = virtualenv
 HAS_PYTHON3    = NO
 HAS_VIRTUALENV = NO
 
@@ -16,82 +17,93 @@ ifeq ($(shell which python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3 = YES
 endif
 
+ifeq ($(shell which virtualenv-3 >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv-3
+HAS_VIRTUALENV = YES
+endif
+
 ifeq ($(shell which virtualenv >/dev/null 2>&1; echo $$?), 0)
+VIRTUALENV     = virtualenv
 HAS_VIRTUALENV = YES
 endif
 
 SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
-SOURCES=$(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 clean-spelling epub mobi rst html pdf spelling anchor_check style_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 "  fetch      fetch HTML and PDF files from LAMMPS web site"
-	@echo "  epub       create ePUB format manual for e-book readers"
-	@echo "  clean      remove all intermediate RST files"
-	@echo "  clean-all  reset the entire build environment"
-	@echo "  txt2html   build txt2html tool"
+	@echo "  html          create HTML doc pages in html dir"
+	@echo "  pdf           create Developer.pdf and Manual.pdf in this 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 "  anchor_check  scan for duplicate anchor labels"
+	@echo "  style_check   check for complete and consistent style lists"
+	@echo "  package_check check for complete and consistent package lists"
+	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
 
-clean-all:
-	rm -rf $(BUILDDIR)/* utils/txt2html/txt2html.exe
+clean-all: clean
+	rm -rf $(BUILDDIR)/docenv $(BUILDDIR)/doctrees $(BUILDDIR)/mathjax
 
-clean:
-	rm -rf $(RSTDIR) html
-	rm -rf spelling
+clean: clean-spelling
+	rm -rf html epub latex
 
 clean-spelling:
 	rm -rf spelling
 
-html: $(OBJECTS) $(ANCHORCHECK)
+html: $(ANCHORCHECK) $(MATHJAX)
 	@(\
 		. $(VENV)/bin/activate ;\
-		cp -r src/* $(RSTDIR)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		echo "############################################" ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		python utils/check-packages.py -s ../src -d src ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
-	-rm html/searchindex.js
 	@rm -rf html/_sources
 	@rm -rf html/PDF
 	@rm -rf html/USER
+	@rm -rf html/JPG
 	@cp -r src/PDF html/PDF
 	@cp -r src/USER html/USER
+	@mkdir -p html/JPG
+	@cp `grep -A2 '\.\. image::' src/*.rst | grep ':target:' | sed -e 's,.*:target: JPG/,src/JPG/,' | sort | uniq` html/JPG/
 	@rm -rf html/PDF/.[sg]*
 	@rm -rf html/USER/.[sg]*
 	@rm -rf html/USER/*/.[sg]*
 	@rm -rf html/USER/*/*.[sg]*
+	@mkdir -p html/_static/mathjax
+	@cp -r $(MATHJAX)/es5 html/_static/mathjax/
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: $(OBJECTS) utils/sphinx-config/false_positives.txt
+spelling: $(VENV) utils/sphinx-config/false_positives.txt
 	@(\
 		. $(VENV)/bin/activate ;\
 		pip install sphinxcontrib-spelling ;\
-		cp -r src/* $(RSTDIR)/ ;\
-        cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
+		cp utils/sphinx-config/false_positives.txt $(RSTDIR)/ ;\
 		sphinx-build -b spelling -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		deactivate ;\
 	)
 	@echo "Spell check finished."
 
-epub: $(OBJECTS)
-	@mkdir -p epub
+epub: $(VENV)
+	@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)/ ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		deactivate ;\
 	)
@@ -99,30 +111,52 @@ 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: $(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; \
+		cd src/Developer; \
 		pdflatex developer; \
 		pdflatex developer; \
 		mv developer.pdf ../../Developer.pdf; \
+		cd ../../; \
 	)
-
-old: utils/txt2html/txt2html.exe
-	@rm -rf old
-	@mkdir old; mkdir old/Eqs; mkdir old/JPG; mkdir old/PDF
-	@cd src; ../utils/txt2html/txt2html.exe -b *.txt; \
-	  mv *.html ../old; \
-	  cp Eqs/*.jpg ../old/Eqs; \
-	  cp JPG/* ../old/JPG; \
-	  cp PDF/* ../old/PDF;
+	@(\
+		. $(VENV)/bin/activate ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c utils/sphinx-config -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		echo "############################################" ;\
+		rst_anchor_check src/*.rst ;\
+		python utils/check-packages.py -s ../src -d src ;\
+		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		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 && \
+		make && \
+		mv LAMMPS.pdf ../Manual.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."
 
 fetch:
 	@rm -rf html_www Manual_www.pdf Developer_www.pdf
@@ -132,39 +166,42 @@ fetch:
 	@tar xzf lammps-doc.tar.gz
 	@rm -f lammps-doc.tar.gz
 
-txt2html: utils/txt2html/txt2html.exe
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
-		doc_anchor_check src/*.txt ;\
+		rst_anchor_check src/*.rst ;\
+		deactivate ;\
+	)
+
+style_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-styles.py -s ../src -d src ;\
+		deactivate ;\
+	)
+
+package_check : $(VENV)
+	@(\
+		. $(VENV)/bin/activate ;\
+		python utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 # ------------------------------------------
 
-utils/txt2html/txt2html.exe: utils/txt2html/txt2html.cpp
-	g++ -O -Wall -o $@ $<
-
-$(RSTDIR)/%.rst : src/%.txt $(TXT2RST)
-	@(\
-		mkdir -p $(RSTDIR) ; \
-		. $(VENV)/bin/activate ;\
-		txt2rst $< > $@ ;\
-		deactivate ;\
-	)
-
 $(VENV):
 	@if [ "$(HAS_PYTHON3)" == "NO" ] ; then echo "Python3 was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@if [ "$(HAS_VIRTUALENV)" == "NO" ] ; then echo "virtualenv was not found! Please check README.md for further instructions" 1>&2; exit 1; fi
 	@( \
-		virtualenv -p $(PYTHON) $(VENV); \
+		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip install Sphinx; \
-		pip install sphinxcontrib-images; \
 		deactivate;\
 	)
 
+$(MATHJAX):
+	@git clone --depth 1 https://github.com/mathjax/MathJax.git mathjax
+
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \

doc/README

@@ -5,7 +5,7 @@ sub-directories and optionally 2 PDF files and an ePUB file:
 
 src             content files for LAMMPS documentation
 html            HTML version of the LAMMPS manual (see html/Manual.html)
-tools           tools and settings for building the documentation
+utils           utilities and settings for building the documentation
 Manual.pdf      large PDF version of entire manual
 Developer.pdf   small PDF with info about how LAMMPS is structured
 LAMMPS.epub     Manual in ePUB format
@@ -25,17 +25,12 @@ the fetched documentation will include those changes (but your source
 code will not, unless you update your local repository).
 
 (b) You can build the HTML and PDF files yourself, by typing "make
-html" followed by "make pdf".  Note that the PDF make requires the
-HTML files already exist.  This requires various tools including
-Sphinx, which the build process will attempt to download and install
-on your system, if not already available.  See more details below.
-
-(c) You can genererate an older, simpler, less-fancy style of HTML
-documentation by typing "make old".  This will create an "old"
-directory.  This can be useful if (b) does not work on your box for
-some reason, or you want to quickly view the HTML version of a doc
-page you have created or edited yourself within the src directory.
-E.g. if you are planning to submit a new feature to LAMMPS.
+html" or by "make pdf", respectively.  This requires various tools
+including the Python documentation processing tool Sphinx, which the
+build process will attempt to download and install on your system into
+a python virtual environment, if not already available.  The PDF file
+will require a working LaTeX installation with several add-on packages
+in addition to the Python/Sphinx setup.  See more details below.
 
 ----------------
 
@@ -46,11 +41,10 @@ Options:
 
 make html         # generate HTML in html dir using Sphinx
 make pdf          # generate 2 PDF files (Manual.pdf,Developer.pdf)
-                  #   in this dir via htmldoc and pdflatex
-make old          # generate old-style HTML pages in old dir via txt2html
+                  #   in this dir via Sphinx and PDFLaTeX
 make fetch        # fetch HTML doc pages and 2 PDF files from web site
                   #   as a tarball and unpack into html dir and 2 PDFs
-make epub         # generate LAMMPS.epub in ePUB format using Sphinx 
+make epub         # generate LAMMPS.epub in ePUB format using Sphinx
 make clean        # remove intermediate RST files created by HTML build
 make clean-all    # remove entire build folder and any cached data
 
@@ -94,8 +88,17 @@ This will install virtualenv from the Python Package Index.
 
 Installing prerequisites for PDF build
 
-[TBA]
-
+Same as for HTML plus a compatible LaTeX installation with
+support for PDFLaTeX. Also the following LaTeX packages need
+to be installed (e.g. from texlive):
+- amsmath
+- babel
+- cmap
+- fncychap
+- geometry
+- hyperref
+- hypcap
+- times
 ----------------
 
 Installing prerequisites for epub build
@@ -103,7 +106,11 @@ Installing prerequisites for epub build
 ## ePUB
 
 Same as for HTML. This uses the same tools and configuration
-files as the HTML tree.
+files as the HTML tree. The ePUB format conversion currently
+does not support processing mathematical expressions via MathJAX,
+so there will be limitations on some pages. For the time being
+until this is resolved, building and using the PDF format file
+is recommended instead.
 
 For converting the generated ePUB file to a mobi format file
 (for e-book readers like Kindle, that cannot read ePUB), you

doc/github-development-workflow.md

@@ -0,0 +1,199 @@
+# 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.rst`)
+  * 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_*.rst`, `doc/src/{fixes,computes,pairs,bonds,...}.rst`
+  * check whether manual cleanly translates with `make html` and `make pdf`
+  * if documentation is (still) provided as a .txt file, convert to .rst
+  and remove the .txt file. For files in doc/txt the conversion is automatic.
+  * remove all .txt files in `doc/txt` that are out of sync with their .rst counterparts in `doc/src`
+  * check spelling of manual with `make spelling` in doc folder
+  * check style tables and command lists with `make style_check`
+  * 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 (review the "checkstyle" test on pull requests)
+  * 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/include-file-conventions.md

@@ -0,0 +1,133 @@
+# Outline of include file conventions in LAMMPS
+
+This purpose of this document is to provide a point of reference
+for LAMMPS developers and contributors as to what include files
+and definitions to put where into LAMMPS source.
+Last change 2019-07-05
+
+## Table of Contents
+
+  * [Motivation](#motivation)
+  * [Rules](#rules)
+  * [Tools](#tools)
+  * [Legacy Code](#legacy-code)
+
+## Motivation
+
+The conventions outlined in this document are supposed to help make
+maintenance of the LAMMPS software easier.  By trying to achieve
+consistency across files contributed by different developers, it will
+become easier for the code maintainers to modify and adjust files and,
+overall, the chance for errors or portability issues will be reduced.
+The rules employed are supposed to minimize naming conflicts and
+simplify dependencies between files and thus speed up compilation. They
+may, as well, make otherwise hidden dependencies visible.
+
+## Rules
+
+Below are the various rules that are applied.  Not all are enforced
+strictly and automatically.  If there are no significant side effects,
+exceptions may be possible for cases where a full compliance to the
+rules may require a large effort compared to the benefit.
+
+### Core Files Versus Package Files
+
+All rules listed below are most strictly observed for core LAMMPS files,
+which are the files that are not part of a package, and the files of the
+packages MOLECULE, MANYBODY, KSPACE, and RIGID.  On the other end of
+the spectrum are USER packages and legacy packages that predate these
+rules and thus may not be fully compliant.  Also, new contributions
+will be checked more closely, while existing code will be incrementally
+adapted to the rules as time and required effort permits.
+
+### System Versus Local Header Files
+
+All system- or library-provided include files are included with angular
+brackets (examples: `#include <cstring>` or `#include <mpi.h>`) while
+include files provided with LAMMPS are included with double quotes
+(examples: `#include "pointers.h"` or `#include "compute_temp.h"`).
+
+For headers declaring functions of the C-library, the corresponding
+C++ versions should be included (examples: `#include <cstdlib>` or
+`#include <cctypes>`).  However, these includes are limited to those defined
+in the C++98 standard.  Some files thus must use the older style until
+the minimum C++ standard requirement of LAMMPS is lifted to C++11 or
+even beyond (examples: `#include <stdint.h>` versus `#include <cstdint>`
+or `#include <inttypes.h>` versus `#include <cinttypes>`).
+
+### C++ Standard Compliance
+
+LAMMPS core files currently correspond to the C++98 standard. Files
+requiring C++11 or later are only permitted in (optional) packages
+and particularly packages that are not part of the list of commonly
+used packages such as MOLECULE, KSPACE, MANYBODY, or RIGID.
+
+Also, LAMMPS uses the C-style stdio library for I/O instead of iostreams.
+Since using both at the same time can cause problems, iostreams should
+be avoided where possible.
+
+### Lean Header Files
+
+Header files will typically contain the definition of a (single) class.
+These header files should have as few include statements as possible.
+This is particularly important for classes that implement a "style" and
+thus use a macro of the kind `SomeStyle(some/name,SomeName)`. These will
+all be included in the auto-generated `"some_style.h"` files which 
+results in a high potential for direct or indirect symbol name clashes.
+
+In the ideal case, the header would only include one file defining the
+parent class. That would typically be either `#include "pointers.h"` for
+the `Pointers` class, or a header of a class derived from it like
+`#include "pair.h"` for the `Pair` class and so on.  References to other
+classes inside the class should be make through pointers, for which forward
+declarations (inside the `LAMMPS_NS` or the new class' namespace) can
+be employed.  The full definition will then be included into the corresponding
+implementation file.  In the given example from above, the header file
+would be called `some_name.h` and the implementation `some_name.cpp` (all
+lower case with underscores, while the class itself would be in camel case
+and no underscores `SomeName`, and the style name with lower case names separated by
+a forward slash).
+
+### Implementation Files
+
+In the implementation files (typically, those would have the same base name
+as the corresponding header with a .cpp extension instead of .h) include
+statements should follow the "include what you use" principle.
+
+### Order of Include Statements
+
+Include files should be included in this order:
+* the header matching the implementation (`some_class.h` for file `some_class.cpp`)
+* mpi.h
+* system and library headers (anything that is using angular brackets; C-library headers first, then C++)
+* LAMMPS local headers (preferably in alphabetical order)
+
+### Special Cases and Exceptions
+
+#### pointers.h
+
+The `pointer.h` header file also includes `cstdio` and `lmptype.h`
+(and through it `stdint.h`, `intttypes.h`, cstdlib, and `climits`).
+This means any header including `pointers.h` can assume that `FILE`,
+`NULL`, `INT_MAX` are defined.
+
+## Tools
+
+The [Include What You Use tool](https://include-what-you-use.org/)
+can be used to provide supporting information about compliance with
+the rules listed here.  There are some limitations and the IWYU tool
+may give incorrect advice.  The tools is activated by setting the
+CMake variable `CMAKE_CXX_INCLUDE_WHAT_YOU_USE` variable to the
+path of the `include-what-you-use` command.  When activated, the
+tool will be run after each compilation and provide suggestions for
+which include files should be added or removed.
+
+## Legacy Code
+
+A lot of code predates the application of the rules in this document
+and the rules themselves are a moving target.  So there are going to be
+significant chunks of code that do not fully comply.  This applies
+for example to the USER-REAXC, or the USER-ATC package.  The LAMMPS
+developers are dedicated to make an effort to improve the compliance
+and welcome volunteers wanting to help with the process.
+

doc/lammps.1

@@ -0,0 +1,269 @@
+.TH LAMMPS "3 March 2020" "2020-03-03"
+.SH NAME
+.B LAMMPS
+\- Molecular Dynamics Simulator.
+
+.SH SYNOPSIS
+.B lmp
+\-in <input file> [OPTIONS] ...
+
+or
+
+mpirun \-np 2
+.B lmp
+\-in <input file> [OPTIONS] ...
+
+or
+
+.B lmp
+\-r2data file.restart file.data
+
+or
+
+.B lmp
+\-h
+
+.SH DESCRIPTION
+.B LAMMPS
+is a classical molecular dynamics code, and an acronym for \fBL\fRarge-scale
+\fBA\fRtomic/\fBM\fRolecular \fBM\fRassively \fBP\fRarallel \fBS\fRimulator.
+.B LAMMPS
+has potentials for soft
+materials (bio-molecules, 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 https://lammps.sandia.gov/ for more information and documentation.
+
+.SH EXECUTABLE NAME
+The
+.B LAMMPS
+executable can have different names depending on how it was configured,
+compiled and installed. It will be either
+.B lmp
+or
+.B lmp_<machine name>.
+The <machine name> suffix corresponds to the (machine specific) makefile
+used to compile
+.B LAMMPS
+when using the conventional build process. When building
+.B LAMMPS
+using
+.B CMake
+this <machine name> parameter can be chosen arbitrarily at configuration
+time, but more common is to just use
+.B lmp
+without a suffix. In this manpage we will use
+.B lmp
+to represent any of those names.
+
+.SH OPTIONS
+
+.TP
+\fB\-h\fR or \fB\-help\fR
+Print a brief help summary and a list of settings and options compiled
+into this executable. It also explicitly lists all LAMMPS styles
+(atom_style, fix, compute, pair_style, bond_style, etc) available in
+the specific executable. This can tell you if the command you want to
+use was included via the appropriate package at compile time.
+LAMMPS will print the info and immediately exit if this switch is used.
+.TP
+\fB\-e\fR or \fB\-echo\fR
+Set the style of command echoing. The style can be
+.B none
+or
+.B screen
+or
+.B log
+or
+.B both.
+Depending on the style, each command read from the input script will
+be echoed to the screen and/or logfile. This can be useful to figure
+out which line of your script is causing an input error.
+The default value is
+.B log.
+.TP
+\fB\-i <input file>\fR or \fB\-in <input file>\fR
+Specify a file to use as an input script. If it is not specified,
+LAMMPS reads its script from standard input. This is a required
+switch when running LAMMPS in multi-partition mode.
+.TP
+\fB\-k on/off [keyword value]\fR or \fB\-kokkos on/off [keyword value]\fR
+Enable or disable general KOKKOS support, as provided by the KOKKOS
+package.  Even if LAMMPS is built with this package, this switch must
+be set to \fBon\fR to enable running with KOKKOS-enabled styles. More
+details on this switch and its optional keyword value pairs are discussed
+at: https://lammps.sandia.gov/doc/Run_options.html
+.TP
+\fB\-l <log file>\fR or \fB\-log <log file>\fR
+Specify a log file for LAMMPS to write status information to.
+The default value is "log.lammps". If the file name "none" is used,
+\fBLAMMPS\fR will not write a log file. In multi-partition mode only
+some high-level all-partition information is written to the "<log file>"
+file, the remainder is written in a per-partition file "<log file>.N"
+with "N" being the respective partition number, unless overridden
+by the \-plog flag (see below).
+.TP
+\fB\-m <number>\fR or \fB\-mpicolor <number>\fR
+If used, this must be the first command-line argument after the
+.B LAMMPS
+executable name. It is only used when
+.B LAMMPS
+is launched by an mpirun command which also launches one or more
+other executable(s) at the same time.
+.B LAMMPS
+and the other executable(s) perform an MPI_Comm_split(), each with
+their own different colors, to split the MPI_COMM_WORLD communicator
+for each executable to the subset of processors they are supposed to
+be actually running on. Currently, this is only used in
+.B LAMMPS
+to perform client/server messaging with another application.
+.B LAMMPS
+can act as either a client or server (or both).
+.TP
+\fB\-nc\fR or \fB\-nocite\fR
+Disable writing the "log.cite" file which is normally written to
+list references for specific cite-able features used during a
+.B LAMMPS
+run.
+.TP
+\fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
+Invoke the \fBpackage\R command with <style> and optional arguments.
+The syntax is the same as if the command appeared in an input script.
+For example "-pk gpu 2" is the same as "package gpu 2" in the input
+script. The possible styles and options are discussed in the
+.B LAMMPS
+manual for the "package" command. This switch can be used multiple
+times, e.g. to set options for the USER-INTEL and USER-OMP packages
+when used together. Along with the "-sf" or "-suffix" switch, this
+is a convenient mechanism for invoking accelerator packages and their
+options without having to edit an input script.
+.TP
+\fB\-p\fR or \fB\-partition\fR
+Invoke
+.B LAMMPS
+in multi-partition mode. Without this,
+.B LAMMPS
+uses all P processors allocated via MPI to run a single simulation.
+If this switch is used, the P processors are split into separate
+partitions and each partition runs its own simulation. The arguments
+to the switch specify the number of processors in each partition.
+Arguments of the form "MxN" mean M partitions, each with N processors.
+Arguments of the form "N" mean a single partition with N processors.
+The sum of processors in all partitions must be equal P. Thus the
+command “-partition 8x2 4 5” has 10 partitions and runs on a total
+of 25 processors.  Running with multiple partitions is required for
+multi-replica simulations, where each replica runs on on one or more
+few processors.
+.TP
+\fB\-pl <basename>\fR or \fB\-plog <basename>\fR
+Specify the base name for the per-partition log files in multi-partition
+runs, where partition N writes log information to <basename>.N.
+If basename is set to "none", then no per-partition log files are created.
+This overrides the name specified in the \-log command-line option.
+.TP
+\fB\-ps <basename>\fR or \fB\-pscreen <basename>\fR
+Specify the base name for the per-partition screen files in multi-partition
+runs, where partition N writes screen output to <basename>.N.
+If basename is set to "none", then no per-partition screen files are created.
+The default value is "screen" or whatever is set by the \-screen flag.
+.TP
+\fB\-r2data <restart file> [remap] <data file>\fR or
+\fB\-restart2data <restart file> [remap] <data file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a data file and immediately exit. This option has replaced the
+external restart2data executable. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <data file> name is identical to the
+arguments of the "write_data" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-r2dump <restart file> [remap] <dump file>\fR or
+\fB\-restart2dump <restart file> [remap] <dump file>\fR
+Convert <restart file> previously written by
+.B LAMMPS
+into a dump file and immediately exit. Following <restart file>
+argument, the optional word "remap" may be used. This has the
+same effect like adding it to a "read_restart" command.
+The syntax following the <dump file> name is identical to the
+arguments of the "dump" command. See the
+.B LAMMPS
+manual for details on either of the two commands.
+.TP
+\fB\-sc <file name>\fR or \fB\-screen <file name>\fR
+Specify a file for
+.B LAMMPS
+to write its screen information to. By default, this will be
+the standard output. If <file name> is "none", (most) screen
+output will be suppressed.  In multi-partition mode only
+some high-level all-partition information is written to the
+screen or "<file name>" file, the remainder is written in a
+per-partition file "screen.N" or "<file name>.N" 
+with "N" being the respective partition number, and unless
+overridden by the \-pscreen flag (see above).
+.TP
+\fB\-sf <suffix>\fR or \fB\-suffix <suffix>\fR
+Use variants of various styles in the input, if they exist. This is
+achieved by transparently trying to convert a style named <my/style>
+into <my/style/suffix> if that latter style exists, but otherwise
+fall back to the former. The most useful suffixes are  "gpu",
+"intel", "kk", "omp", "opt", or "hybrid". These refer to styles from
+optional packages that LAMMPS can be built with. The hybrid suffix is
+special, as it enables, having two suffixes tried (e.g. first "intel"
+and then "omp") and thus requires two arguments. Along with the
+"-package" command-line switch, this is a convenient mechanism for
+invoking styles from accelerator packages and setting their options
+without having to edit an input script.
+
+See https://lammps.sandia.gov/doc/Run_options.html for additional
+details and discussions on command-line options.
+
+.SH LAMMPS BASICS
+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 or change an
+internal, read and parse 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.
+
+The ordering of commands in an input script is usually not very important
+unless a command like "run" is encountered, which starts some calculation
+using the current internal state. Also, if a "pair_style" or "bond_style"
+other similar style command is issued that has a different name from what
+was previously active, it will replace the previous style and wipe out
+all corresponding "pair_coeff" or "bond_coeff" or equivalent settings.
+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 of a given name. Sometimes command B will use values
+that can be set by command A. This means command A must precede command
+B in the input to have the desired effect. Some commands must be issued
+.B before
+the simulation box is defined and others can only be issued
+.B after.
+Many input script errors are detected by
+.B LAMMPS
+and an ERROR or WARNING message is printed.  The documentation for
+each command lists restrictions on how the command can be used, and
+the chapter on errors in the
+.B LAMMPS
+manual gives some additional information about error messages, if possible.
+
+.SH COPYRIGHT
+© 2003--2020 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
+
+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/msi2lmp.1

@@ -0,0 +1,111 @@
+.TH MSI2LMP "v3.9.9" "2018-11-05"
+.SH NAME
+.B MSI2LMP
+\- Converter for Materials Studio files to LAMMPS
+
+.SH SYNOPSIS
+.B msi2lmp
+<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+
+.SH DESCRIPTION
+.PP
+.B MSI2LMP
+is a tool bundled with LAMMPS to aide in the conversion of simulation
+inputs from Biovia's Materials Studio software for use with LAMMPS.
+It is a standalone program that generates a LAMMPS data file based on
+the information in an MS .car file (atom coordinates), an .mdf file
+(molecular topology and atom types) and an .frc (forcefield parameters)
+file.  The .car and .mdf files are specific to a molecular system while
+the .frc file is specific to a forcefield (variant).  The only coherency
+needed between .frc and .car/.mdf files are the atom types.
+.PP
+
+.SH OPTIONS
+.TP
+\fB\<ROOTNAME>\fR
+This has to be the first argument and is a
+.B mandatory
+argument. It defines the root of the file names; i.e. for a
+.B <ROOTNAME>
+of benzene, you have to provide the files 'benzene.car' and 'benzene.mdf'
+in the current working directory.
+.B msi2lmp
+will then read and process those files according to its remaining settings.
+All other settins are optional and have defaults as listed.
+.TP
+\fB\-c <I,1,II,2,O,0>\fR, \fB\-class <I,1,II,2,O,0>\fR
+The \-c or \-class option selects the force field class, i.e which pair
+styles and bond styles and so on are required in the LAMMPS input file.
+Class I or class 1 uses similar combination of functional forms as Amber
+and Charmm force field and support the force fields 
+.B cvff
+and
+.B clayff.
+Class II or class 2 corresponds to the more complex force fields
+.B COMPASS
+and
+.B pcff.
+Class O or class 0 finally is an experimental and incomplete extension
+and supports generating output for
+.B OPLS-AA
+.TP
+\fB\-f <ffname>\fR, \fB\-frc <ffname>\fR
+The \-c or \-frc option allows the selection of the force field parameter
+file
+.B<ffname>.frc.
+Valid names for <ffname> with this distribution are: cvff, clayff, cvff_aug,
+pcff, compass_published, cff91, and oplsaa. If the argument is a pathname,
+i.e. it starts with a '.' or a '/', then this absolute path is used to read
+the force field, otherwise
+.B msi2lmp
+will look in the folder pointed to by the environment variable
+$MSI2LMP_LIBRARY. If the variable is not set, then it will look in the current
+directory. The extension '.frc' is appended, if missing.
+Default is to look for the cvff.frc force field file.
+.TP
+\fB\-p <loglevel>\fR, \fB\-print <loglevel>\fR,
+Selects the amount of information messages about the progress of the
+conversion printed to the screen.
+.B <loglevel>
+can be a number from 0 (silent except for errors) to 3 (very detailed).
+.TP
+\fB\-i\fR, \fB\-ignore\fR,
+Ignore errors about missing parameters and use 0.0 for the respective
+force constants making these no-ops. Is correct to be used for a few
+molecules and settings, but often an indication, that either the atom
+type assignment have errors, or the force field file is missing entries.
+.TP
+\fB\-n\fR, \fB\-nocenter\fR,
+Do not center the box around the (geometrical) center of the atoms,
+but around the origin. Default is to recenter.
+.TP
+\fB\-o\fR, \fB\-oldstyle\fR,
+Write out a data file without style hint comments to be compatible
+with old LAMMPS versions. Default is to write out those comments.
+.TP
+\fB-s <x> <y> <z>\fR, \fB-shift <x> <y> <z>\fR,
+Shift the entire system (box and coordinates) by a vector
+(default: 0.0 0.0 0.0).
+.TP
+
+.SH EXAMPLES
+
+msi2lmp benzene -c 2 -p 1 -f ../frc_files/pcff.frc
+
+msi2lmp benzene-class1 -c I
+
+msi2lmp decane -c 0 -f oplsaa
+
+
+.SH COPYRIGHT
+© 2003--2019 Sandia Corporation
+
+This package is free software; you can redistribute it and/or modify
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
+
+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.
+

doc/src/.gitignore

@@ -0,0 +1,3 @@
+/Eqs
+/JPG
+/false_positives.txt

doc/src/Build.rst

@@ -0,0 +1,23 @@
+Build LAMMPS
+************
+
+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 :doc:`Install <Install>` doc page.
+
+
+.. toctree::
+   :maxdepth: 1
+
+   Build_cmake
+   Build_make
+   Build_link
+   Build_basics
+   Build_settings
+   Build_package
+   Build_extras
+   Build_windows
+   Build_development

doc/src/Build_basics.rst

@@ -0,0 +1,501 @@
+Basic build options
+===================
+
+The following topics are covered on this page, for building both with
+CMake and make:
+
+* :ref:`Serial vs parallel build <serial>`
+* :ref:`Choice of compiler and compile/link options <compile>`
+* :ref:`Build LAMMPS as an executable or a library <exe>`
+* :ref:`Build the LAMMPS documentation <doc>`
+* :ref:`Install LAMMPS after a build <install>`
+
+
+----------
+
+
+.. _serial:
+
+Serial vs parallel build
+-------------------------------------
+
+LAMMPS is written to use the ubiquitous `MPI (Message Passing Interface)
+<https://en.wikipedia.org/wiki/Message_Passing_Interface>`_ library API
+for distributed memory parallel computation.  You need to have such a
+library installed for building and running LAMMPS in parallel using a
+domain decomposition parallelization.  It is compatible with the MPI
+standard version 2.x and later.  LAMMPS can also be built into a
+"serial" executable for use with a single processor using the bundled
+MPI STUBS library.
+
+Independent of the distributed memory MPI parallelization, parts of
+LAMMPS are also written with support for shared memory parallelization
+using the OpenMP threading standard. A more detailed discussion of that
+is below.
+
+**CMake build**\ :
+
+.. code-block:: bash
+
+   -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+   -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
+   -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
+                             # no default value
+
+The executable created by CMake (after running make) is named *lmp* unless
+the LAMMPS\_MACHINE option is set.  When setting `LAMMPS_MACHINE=name`
+the executable will be named *lmp\_name*\.  Using `BUILD\_MPI=no` will
+enforce building a serial executable using the MPI STUBS library.
+
+**Traditional make**\ :
+
+The build with traditional makefiles has to be done inside the source folder `src`.
+
+.. code-block:: bash
+
+   make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+   make serial             # serial build, produces lmp_serial using Makefile/serial
+   make mybox              # uses Makefile.mybox to produce lmp_mybox
+
+
+Any "make machine" command will look up the make settings from a file
+Makefile.machine, create a folder Obj\_machine with all objects and
+generated files and an executable called *lmp\_machine*\ .  The standard
+parallel build with `make mpi` assumes a standard MPI installation with
+MPI compiler wrappers where all necessary compiler and linker flags to
+get access and link with the suitable MPI headers and libraries are set
+by the wrapper programs.  For other cases or the serial build, you have
+to adjust the make file variables MPI\_INC, MPI\_PATH, MPI\_LIB as well
+as CC and LINK.  To enable OpenMP threading usually a compiler specific
+flag needs to be added to the compile and link commands.  For the GNU
+compilers, this is *-fopenmp*\ , which can be added to the CC and LINK
+makefile variables.
+
+For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
+
+.. code-block:: make
+
+   CC =            g++
+   LINK =          g++
+   MPI_INC =       -I../STUBS
+   MPI_PATH =      -L../STUBS
+   MPI_LIB =       -lmpi_stubs
+
+You also need to build the STUBS library for your platform before making
+LAMMPS itself.  A "make serial" build does this for you automatically,
+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 stubs library does not provide
+MPI/IO functions required by some LAMMPS packages, e.g. MPIIO or USER-LB,
+and thus is not compatible with those packages.
+
+.. note::
+
+   The file STUBS/mpi.c provides a CPU timer function called
+   MPI\_Wtime() that calls gettimeofday() .  If your operating system
+   does not support gettimeofday() , you will 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.
+
+**MPI and OpenMP support info**\ :
+
+If you are installing MPI yourself to build a parallel LAMMPS
+executable, we recommend either MPICH or OpenMPI which are regularly
+used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
+downloaded from the `MPICH home page <https://www.mpich.org>`_ and
+OpenMPI can be downloaded correspondingly from the `OpenMPI home page
+<https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
+specific vendor provided and standard compliant MPI library is currently
+known to be incompatible with LAMMPS.  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 you should study the provided
+documentation to 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 :doc:`Speed omp <Speed_omp>` doc page for
+details. The USER-INTEL package also includes OpenMP threading (it is
+compatible with USER-OMP) and adds vectorization support when compiled
+with compatible compilers, in particular the Intel compilers on top of
+OpenMP. Also, the KOKKOS package can be compiled to include OpenMP
+threading.
+
+In addition, there are a few commands in LAMMPS that have native OpenMP
+support included as well.  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 :doc:`Packages details
+<Packages_details>` 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.
+
+.. _default-none-issues:
+
+**OpenMP Compiler compatibility info**\ : 
+
+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.
+
+
+----------
+
+
+.. _compile:
+
+Choice of compiler and compile/link options
+---------------------------------------------------------
+
+The choice of compiler and compiler flags can be important for
+performance.  Vendor provided compilers for a specific hardware can
+produce faster code than open-source compilers like the GNU compilers.
+On x86 hardware most popular compilers are quite similar in performance
+of C/C++ code at high optimization levels.  When using the USER-INTEL
+package, there is a distinct advantage in using the `Intel C++ compiler
+<intel_>`_ due to much improved vectorization through SSE and AVX
+instructions on compatible hardware as the source code includes changes
+and compiler directives to enable high degrees of vectorization.
+
+.. _intel: https://software.intel.com/en-us/intel-compilers
+
+On parallel clusters or supercomputers which use "environment modules"
+for their compile/link environments, you can often access different
+compilers by simply loading the appropriate module before building
+LAMMPS.
+
+**CMake build**\ :
+
+By default CMake will use a compiler it finds and it will add
+optimization flags appropriate to that compiler and any
+:doc:`accelerator packages <Speed_packages>` 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:
+
+.. code-block:: bash
+
+   -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
+
+   -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
+
+
+A few example command lines are:
+
+.. code-block:: bash
+
+   # 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
+
+For compiling with the Clang/LLVM compilers a special CMake preset is
+included that can be loaded with `-C ../cmake/presets/clang.cmake`.
+
+.. note::
+
+   When the cmake command completes, it prints a summary to the screen
+   which compilers it is using and what flags and settings will be used
+   for 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 CMake will try to determine and report.  You should check
+   to confirm you are using the compiler and optimization flags you want.
+
+**Makefile.machine settings for traditional make**\ :
+
+The "compiler/linker settings" section of a Makefile.machine lists
+compiler and linker settings for your C++ compiler, including
+optimization flags.  For a parallel build it is recommended to use
+mpicxx or mpiCC, since these compiler wrappers will include a variety of
+settings appropriate for your MPI installation and thus avoiding the
+guesswork of finding the right flags.
+
+Parallel build (see src/MAKE/Makefile.mpi):
+
+.. code-block:: bash
+
+   CC =            mpicxx
+   CCFLAGS =       -g -O3
+   LINK =          mpicxx
+   LINKFLAGS =     -g -O
+
+Serial build (see src/MAKE/Makefile.serial):
+
+.. code-block:: make
+
+   CC =            g++
+   CCFLAGS =       -g -O3
+   LINK =          g++
+   LINKFLAGS =     -g -O
+
+.. note::
+
+   If you build LAMMPS with any :doc:`accelerator packages <Speed_packages>`
+   included, there may be specific optimization flags that are either
+   required or recommended to enable required features and to achieve
+   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 :doc:`Speed packages <Speed_packages>` 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:
+
+.. code-block:: bash
+
+   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)
+
+----------
+
+.. _exe:
+
+Build LAMMPS as an executable or a library
+----------------------------------------------------
+
+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 :doc:`Howto couple <Howto_couple>` doc
+page for more info on coupling LAMMPS to other codes.  See the
+:doc:`Python <Python_head>` doc page for more info on wrapping and
+running LAMMPS from Python via its library interface.
+
+**CMake build**\ :
+
+For CMake builds, you can select through setting CMake variables which
+files the compilation produces during the configuration step.  If none
+are set, defaults are applied.
+
+.. code-block:: bash
+
+   -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)
+   -D LAMMPS_LIB_SUFFIX=name    # name = mpi, serial, mybox, titan, laptop, etc
+                                # no default value
+
+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* instead. If LAMMPS\_LIB\_SUFFIX is
+set to *name* in addition, the name of the generated libraries will be
+changed to either *liblammps\_name.a* or *liblammps\_name.so*\ ,
+respectively.
+
+**Traditional make**\ :
+
+With the traditional makefile based build process, the choice of
+the generated executable or library depends on the "mode" setting.
+Several options are available and "mode=exe" is the default.
+
+.. code-block:: bash
+
+   make machine               # build LAMMPS executable lmp_machine
+   mkae mode=exe machine      # same as "make machine"
+   make mode=lib machine      # build LAMMPS static lib liblammps_machine.a
+   make mode=shlib machine    # build LAMMPS shared lib liblammps_machine.so
+   make mode=shexe machine    # same as "mode=exe" but uses objects from "mode=shlib"
+
+The two "exe" builds will generate and executable *lmp\_machine*\ ,
+while the two library builds will create a file *liblammps\_machine.a*
+or *liblammps\_machine.so*\ . They will also create generic soft links,
+named *liblammps.a* and *liblammps.so*\ , which point to the specific
+*liblammps\_machine.a/so* 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 in a shared
+library compatible way using the -fPIC switch.  However, if a library
+like MPI or FFTW does not exist as a shared library, the shared library
+build may 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, as a shared library
+in the default /usr/local/lib location:
+
+.. _mpich: https://www.mpich.org
+
+.. code-block:: bash
+
+   ./configure --enable-shared
+   make
+   make install
+
+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.  On many Linux installations the
+folder "${HOME}/.local" is an alternative to using /usr/local and does
+not require superuser or sudo access.  In that case the configuration
+step becomes:
+
+.. code-block:: bash
+
+  ./configure --enable-shared --prefix=${HOME}/.local
+
+Avoiding using "sudo" for custom software installation (i.e. from source
+and not through a package manager tool provided by the OS) is generally
+recommended to ensure the integrity of the system software installation.
+
+----------
+
+
+.. _doc:
+
+Build the LAMMPS documentation
+----------------------------------------
+
+The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
+can be translated to different output format using the `Sphinx <sphinx_>`_
+document generator tool.  Currently the translation to HTML and PDF (via
+LaTeX) are supported.  For that to work a Python 3 interpreter and
+internet access is required.  For the documentation build a python
+based virtual environment is set up in the folder doc/docenv and various
+python packages are installed into that virtual environment via the pip
+tool.  The actual translation is then done via make commands.
+
+.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _sphinx: https://sphinx-doc.org
+
+**Documentation make option**\ :
+
+The following make commands can be issued in the doc folder of the
+LAMMPS source distribution.
+
+.. code-block:: bash
+
+  make html          # create HTML doc pages in html directory
+  make pdf           # create Developer.pdf and Manual.pdf in this directory
+  make fetch         # fetch HTML and PDF files from LAMMPS web site
+  make clean         # remove all intermediate files
+  make clean-all     # reset the entire doc build environment
+  make anchor_check  # scan for duplicate anchor labels
+  make style_check   # check for complete and consistent style lists
+  make package_check # check for complete and consistent package lists
+  make spelling      # spell-check the manual
+
+
+Thus "make html" will create a "doc/html" directory with the HTML format
+manual pages so that you can browse them with a web browser locally on
+your system.
+
+.. 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>`_.
+
+
+**CMake build option**\ :
+
+It is also possible to create the HTML version of the manual within
+the :doc:`CMake build directory <Build_cmake>`.  The reason for this
+option is to include the installation of the HTML manual pages into
+the "install" step when installing LAMMPS after the CMake build via
+"make install".
+
+.. code-block:: bash
+
+   -D BUILD_DOC=value       # yes or no (default)
+
+
+----------
+
+
+.. _tools:
+
+Build LAMMPS tools
+------------------------------
+
+Some tools described in :doc:`Auxiliary tools <Tools>` can be built directly
+using CMake or Make.
+
+**CMake build3**\ :
+
+
+.. code-block:: bash
+
+   -D BUILD_TOOLS=value       # yes or no (default)
+
+The generated binaries will also become part of the LAMMPS installation
+(see below).
+
+**Traditional make**\ :
+
+
+.. code-block:: bash
+
+   cd lammps/tools
+   make all              # build all binaries of tools
+   make binary2txt       # build only binary2txt tool
+   make chain            # build only chain tool
+   make micelle2d        # build only micelle2d tool
+   make thermo_extract   # build only thermo_extract tool
+
+
+----------
+
+
+.. _install:
+
+Install LAMMPS after a build
+------------------------------------------
+
+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 build**\ :
+
+
+.. code-block:: bash
+
+   cmake -D CMAKE_INSTALL_PREFIX=path [options ...] ../cmake
+   make                        # perform make after CMake command
+   make install                # perform the installation into prefix
+
+**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.rst

@@ -0,0 +1,240 @@
+Build LAMMPS with CMake
+=======================
+
+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 :doc:`Build <Build>` 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.
+
+
+----------
+
+
+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:
+
+
+.. code-block:: bash
+
+   cd lammps                        # change to the LAMMPS distribution directory
+   mkdir build; cd build            # create a new directory (folder) for build
+   cmake [options ...] ../cmake     # configuration with (command-line) cmake
+   make                             # compilation
+
+The cmake command will detect available features, enable selected
+packages and options, and will generate the build environment.  By default
+this build environment will be created for "Unix Makefiles" on most
+platforms and particularly on Linux.  However, alternate build tools
+(e.g. Ninja) and support files for Integrated Development Environments
+(IDE) like Eclipse, CodeBlocks, or Kate can be generated, too. This is
+selected via the "-G" command line flag. For the rest of the documentation
+we will assume that the build environment is generated for makefiles
+and thus the make command will be used to compile and link LAMMPS as
+indicated above, producing (by default) an executable called "lmp" and
+a library called "liblammps.a" in the "build" folder.  When generating
+a build environment for the "Ninja" build tool, the build command would
+be "ninja" instead of "make".
+
+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 repeated compilation
+even more.
+
+After compilation, you may optionally install the LAMMPS executable into
+your system with:
+
+
+.. code-block:: bash
+
+   make install    # optional, copy LAMMPS executable & library elsewhere
+
+This will install the lammps executable and library (if requested), some
+tools (if configured) and additional files like library API headers,
+manpages, potential and force field files. The location of the installation
+tree is set by the CMake variable "CMAKE\_INSTALL\_PREFIX" which defaults
+to ${HOME}/.local
+
+
+----------
+
+
+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 :doc:`Build <Build>` 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 :doc:`perform a conventional LAMMPS build <Build_make>`.  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.
+
+
+----------
+
+
+**Command-line version of CMake**\ :
+
+
+.. code-block:: bash
+
+   cmake [options ...] /path/to/lammps/cmake  # build from any dir
+   cmake [options ...] ../cmake               # build from lammps/build
+
+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:
+
+
+.. code-block:: bash
+
+   -D CMAKE_INSTALL_PREFIX=path  # where to install LAMMPS executable/lib if desired
+   -D CMAKE_BUILD_TYPE=type      # type = RelWithDebInfo (default), Release, MinSizeRel, 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
+   -C path/to/preset/file        # load some CMake settings before configuring
+
+All the LAMMPS-specific -D variables that a LAMMPS build supports are
+described on the pages linked to from the :doc:`Build <Build>` 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.
+
+
+----------
+
+
+**Curses version (terminal-style menu) of CMake**\ :
+
+
+.. code-block:: bash
+
+   ccmake ../cmake
+
+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.
+
+
+----------
+
+
+**GUI version of CMake**\ :
+
+
+.. code-block:: bash
+
+   cmake-gui ../cmake
+
+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.
+
+
+----------
+
+
+**Installing CMake**
+
+Check if your machine already has CMake installed:
+
+
+.. code-block:: bash
+
+   which cmake             # do you have it?
+   which cmake3            # version 3 may have this name
+   cmake --version         # what specific version you have
+
+On clusters or supercomputers which use environment modules to manage
+software packages, do this:
+
+
+.. code-block:: bash
+
+   module list            # is a module for cmake already loaded?
+   module avail           # is a module for cmake available?
+   module load cmake3     # load cmake module with appropriate name
+
+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_development.rst

@@ -0,0 +1,114 @@
+Development build options (CMake only)
+======================================
+
+The CMake build of LAMMPS has a few extra options which are useful during
+development,  testing or debugging.
+
+
+----------
+
+
+.. _compilation:
+
+Verify compilation flags
+------------------------------------------
+
+Sometimes it is necessary to verify the complete sequence of compilation flags
+generated by the CMake build. To enable a more verbose output during
+compilation you can use the following option.
+
+
+.. code-block:: bash
+
+   -D CMAKE_VERBOSE_MAKEFILE=value    # value = no (default) or yes
+
+Another way of doing this without reconfiguration is calling make with variable VERBOSE set to 1:
+
+
+.. code-block:: bash
+
+   make VERBOSE=1
+
+
+----------
+
+
+.. _sanitizer:
+
+Address, Undefined Behavior, and Thread Sanitizer Support
+-------------------------------------------------------------------------
+
+Compilers such as GCC and Clang support generating binaries which use different
+sanitizers to detect problems in code during run-time. They can detect `memory leaks <https://clang.llvm.org/docs/AddressSanitizer.html>`_,
+code that runs into `undefined behavior <https://clang.llvm.org/docs/UndefinedBehaviorSanitizer.html>`_ of the
+language and `data races <https://clang.llvm.org/docs/ThreadSanitizer.html>`_ in threaded code.
+
+The following settings allow you enable these features if your compiler supports
+it. Please note that they come with a performance hit. However, they are
+usually faster than using tools like Valgrind.
+
+
+.. code-block:: bash
+
+   -D ENABLE_SANITIZE_ADDRESS=value    # enable Address Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_UNDEFINED=value  # enable Undefined Behaviour Sanitizer, value = no (default) or yes
+   -D ENABLE_SANITIZE_THREAD=value     # enable Thread Sanitizer, value = no (default) or yes
+
+
+----------
+
+
+.. _testing:
+
+Code Coverage and Testing
+---------------------------------------
+
+We do extensive regression testing of the LAMMPS code base on a continuous
+basis. Some of the logic to do this has been added to the CMake build so
+developers can run the tests directly on their workstation.
+
+.. note::
+
+   this is incomplete and only represents a small subset of tests that we run
+
+
+.. code-block:: bash
+
+   -D ENABLE_TESTING=value               # enable simple run tests of LAMMPS, value = no (default) or yes
+   -D LAMMPS_TESTING_SOURCE_DIR=path     # path to lammps-testing repository (option if in custom location)
+   -D LAMMPS_TESTING_GIT_TAG=value       # version of lammps-testing repository that should be used, value = master (default) or custom git commit or tag
+
+If you enable testing in the CMake build it will create an additional target called "test". You can run them with:
+
+
+.. code-block:: bash
+
+   make test
+
+The test cases used come from the lammps-testing repository. They are
+derivatives of the examples folder with some modifications to make the run
+faster.
+
+You can also collect code coverage metrics while running the tests by enabling
+coverage support during building.
+
+
+.. code-block:: bash
+
+   -D ENABLE_COVERAGE=value  # enable coverage measurements, value = no (default) or yes
+
+This will also add the following targets to generate coverage reports after running the LAMMPS executable:
+
+
+.. code-block:: bash
+
+   make test               # run tests first!
+   make gen_coverage_html  # generate coverage report in HTML format
+   make gen_coverage_xml   # generate coverage report in XML format
+
+These reports require GCOVR to be installed. The easiest way to do this to install it via pip:
+
+
+.. code-block:: bash
+
+   pip install git+https://github.com/gcovr/gcovr.git

doc/src/Build_link.rst

@@ -0,0 +1,254 @@
+Link LAMMPS as a library to another code
+========================================
+
+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 :doc:`Howto
+library <Howto_library>` doc page for a description of the interface
+and how to extend it for your needs.
+
+The :doc:`Build basics <Build_basics>` doc page explains how to build
+LAMMPS as either a shared or static library.  This results in one of
+these 2 files:
+
+.. parsed-literal::
+
+   liblammps.so      # shared library
+   liblammps.a       # static library
+
+.. note::
+
+   Care should be taken to use the same MPI library for the calling
+   code and the LAMMPS library.  The library.h file includes mpi.h and
+   uses definitions from it so those need to be available and
+   consistent.  When LAMMPS is compiled with the MPI STUBS library,
+   then its mpi.h file needs to be included.  While it is technically
+   possible to use a full MPI library in the calling code and link to
+   a serial LAMMPS library compiled with MPI STUBS, it is recommended
+   to use the *same* MPI library for both, and then use MPI\_Comm\_split()
+   in the calling code to pass a suitable communicator with a subset
+   of MPI ranks to the function creating the LAMMPS instance.
+
+----------
+
+
+**Link with LAMMPS as a static library**\ :
+
+The calling application can link to LAMMPS as a static library with
+compilation and link commands as in the examples shown below.  These
+are examples for a code written in C in the file *caller.c*.
+The benefit of linking to a static library is, that the resulting
+executable is independent of that library since all required
+executable code from the library is copied into the calling executable.
+
+*CMake build*\ :
+
+This assumes that LAMMPS has been configured with "-D BUILD_LIB=yes"
+and installed with "make install" and the PKG\_CONFIG\_PATH environment
+variable updated to include the *liblammps.pc* file installed into the
+configured destination folder, if needed.  The commands to compile and
+link the coupled executable are then:
+
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
+
+
+*Traditional make*\ :
+
+This assumes that LAMMPS has been compiled in the folder
+"${HOME}/lammps/src" with "make mode=lib mpi". The commands to compile
+and link the coupled executable are then:
+
+.. code-block:: bash
+
+   mpicc -c -O -I${HOME}/lammps/src caller.c
+   mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps
+
+The *-I* argument is the path to the location of the *library.h*
+header file containing the interface to the LAMMPS C-style library
+interface.  The *-L* argument is the path to where the *liblammps.a*
+file is located.  The *-llammps* argument is shorthand for telling the
+compiler to link the file *liblammps.a*\ .
+
+However, it is only as simple as shown above for the case of a plain
+LAMMPS library without any optional packages that depend on libraries
+(bundled or external).  Otherwise, you need to include all flags,
+libraries, and paths for the coupled executable, that are also
+required to link the LAMMPS executable.
+
+*CMake build*\ :
+
+When using CMake, additional libraries with sources in the lib folder
+are built, but not included in liblammps.a and (currently) not
+installed with "make install" and not included in the *pkgconfig*
+configuration file.  They can be found in the top level build folder,
+but you have to determine the necessary link flags manually.  It is
+therefore recommended to either use the traditional make procedure to
+build and link with a static library or build and link with a shared
+library instead.
+
+*Traditional make*\ :
+
+After you have compiled a static LAMMPS library using the conventional
+build system for example with "make mode=lib serial". And you also
+have installed the POEMS package after building its bundled library in
+lib/poems. Then the commands to build and link the coupled executable
+change to:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
+     -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src -llammps -lpoems -lmpi_stubs 
+
+Note, that you need to link with "g++" instead of "gcc", since LAMMPS
+is C++ code.  You can display the currently applied settings for building
+LAMMPS for the "serial" machine target by using the command:
+
+.. code-block:: bash
+
+   make mode=print serial
+
+Which should output something like:
+
+.. code-block:: bash
+
+   # Compiler: 
+   CXX=g++
+   # Linker: 
+   LD=g++
+   # Compilation: 
+   CXXFLAGS=-g -O3 -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64 -I${HOME}/lammps/lib/poems -I${HOME}/lammps/src/STUBS
+   # Linking: 
+   LDFLAGS=-g -O
+   # Libraries: 
+   LDLIBS=-L${HOME}/lammps/lib/poems -L${HOME}/lammps/src/STUBS -lpoems -lmpi_stubs
+
+From this you can gather the necessary paths and flags.  With
+makefiles for other *machine* configurations you need to do the
+equivalent and replace "serial" with the corresponding *machine* name
+of the makefile.
+
+----------
+
+**Link with LAMMPS as a shared library**\ :
+
+When linking to LAMMPS built as a shared library, the situation
+becomes much simpler, as all dependent libraries and objects are
+included in the shared library, which is - technically speaking -
+effectively a regular LAMMPS executable that is missing the `main()`
+function.  Thus those libraries need not to be specified when linking
+the calling executable.  Only the *-I* flags are needed.  So the
+example case from above of the serial version static LAMMPS library
+with the POEMS package installed becomes:
+
+*CMake build*\ :
+
+The commands with a shared LAMMPS library compiled with the CMake
+build process are the same as for the static library.
+
+.. code-block:: bash
+
+   mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+   mpicxx -o caller caller.o -$(pkgconf --libs)
+
+*Traditional make*\ :
+
+The commands with a shared LAMMPS library compiled with the
+traditional make build using "make mode=shlib serial" becomes:
+
+.. code-block:: bash
+
+   gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+   g++ -o caller caller.o -L${HOME}/lammps/src -llammps
+
+*Locating liblammps.so at runtime*\ :
+   
+However, now the `liblammps.so` file is required at runtime and needs
+to be in a folder, where the shared linker program of the operating
+system can find it.  This would be either a folder like "/usr/local/lib64"
+or "${HOME}/.local/lib64" or a folder pointed to by the LD\_LIBRARY\_PATH
+environment variable. You can type
+
+.. code-block:: bash
+
+   printenv LD_LIBRARY_PATH
+
+to see what directories are in that list.
+
+Or you can add the LAMMPS src directory (or the directory you performed
+a CMake style 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 Bourne or Korn shells (/bin/sh, /bin/ksh, /bin/bash etc.), you
+would add something like this to your ~/.profile file:
+
+.. code-block:: bash
+
+   LD_LIBRARY_PATH ${LD_LIBRARY_PATH-/usr/lib64}:${HOME}/lammps/src
+   export LD_LIBRARY_PATH
+
+For the csh or tcsh shells, you would equivalently add something like this
+to your ~/.cshrc file:
+
+
+.. code-block:: csh
+
+   setenv LD_LIBRARY_PATH ${LD_LIBRARY_PATH}:${HOME}/lammps/src
+
+You can verify whether all required shared libraries are found with the
+`ldd` tool.  Example:
+
+.. code-block:: bash
+
+   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller 
+        linux-vdso.so.1 (0x00007ffe729e0000)
+        liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
+        libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
+        libm.so.6 => /lib64/libm.so.6 (0x00007fc91b83e000)
+        libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fc91b824000)
+        libc.so.6 => /lib64/libc.so.6 (0x00007fc91b65b000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fc91c094000)
+
+
+If a required library is missing, you would get a 'not found' entry:
+
+.. code-block:: bash
+
+   $  ldd caller 
+        linux-vdso.so.1 (0x00007ffd672fe000)
+        liblammps.so => not found
+        libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)
+        libm.so.6 => /usr/lib64/libm.so.6 (0x00007fb7c7d40000)
+        libgcc_s.so.1 => /usr/lib64/libgcc_s.so.1 (0x00007fb7c7d26000)
+        libc.so.6 => /usr/lib64/libc.so.6 (0x00007fb7c7b5d000)
+        /lib64/ld-linux-x86-64.so.2 (0x00007fb7c80a2000)
+
+
+----------
+
+
+**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, most of the symbols and functions in LAMMPS are wrapped
+in a LAMMPS\_NS namespace; you can safely use any of its classes and
+methods from within the calling code, as needed, and you will not incur
+conflicts with functions and variables in your code that share the name.
+This, however, does not extend to all additional libraries bundled with
+LAMMPS in the lib folder and some of the low-level code of some packages.
+
+To be compatible with C, Fortran, Python programs, the library has a simple
+C-style interface, provided in src/library.cpp and src/library.h.
+
+See the :doc:`Python library <Python_library>` doc page for a
+description of the Python interface to LAMMPS, which wraps the C-style
+interface from a shared library through the ctypes python module.
+
+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 :doc:`Howto couple <Howto_couple>` doc page.

doc/src/Build_make.rst

@@ -0,0 +1,107 @@
+Build LAMMPS with make
+======================
+
+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.
+
+Those makefiles are written for and tested with GNU make and may not
+be compatible with other make programs.  In most cases, if the "make"
+program is not GNU make, then there will be a GNU make program
+available under the name "gmake".  If GNU make or a compatible make is
+not available, you may have to first install it or switch to building
+with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
+make based build process and the scripts they are calling expect a few
+additional tools to be available and functioning.
+
+  * a Bourne shell compatible "Unix" shell program (often this is bash)
+  * a few shell utilities: ls, mv, ln, rm, grep, sed, tr, cat, touch, diff, dirname
+  * python (optional, required for "make lib-XXX" in the src folder)
+
+To include LAMMPS packages (i.e. optional commands and styles) you
+must enable them first, as discussed on the :doc:`Build package
+<Build_package>` doc page.  If a packages requires (provided or
+external) libraries, you must configure and build those libraries
+**before** building LAMMPS itself and especially **before** enabling
+such a package with "make yes-<package>".  Building :doc:`LAMMPS
+with CMake <Build_cmake>` can automate much of this for many types of
+machines, especially workstations, desktops, and laptops, so we suggest
+you try it first when building LAMMPS in those cases.
+
+The commands below perform a default LAMMPS build, producing the LAMMPS
+executable lmp\_serial and lmp\_mpi in lammps/src:
+
+.. code-block:: bash
+
+   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
+
+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::
+
+   Before the actual compilation starts, LAMMPS will perform several
+   steps to collect information from the configuration and setup that
+   is then embedded into the executable.  When you build LAMMPS for
+   the first time, it will also compile a tool to quickly assemble
+   a list of dependencies, that are required for the make program to
+   correctly detect which parts need to be recompiled after changes
+   were made to the sources.
+
+----------
+
+The lammps/src/MAKE tree contains 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, respectively.  Other makefiles
+are in these directories:
+
+
+.. parsed-literal::
+
+   OPTIONS      # Makefiles which enable specific options
+   MACHINES     # Makefiles for specific machines
+   MINE         # customized Makefiles you create (you may need to create this folder)
+
+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 directories 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:
+
+
+.. code-block:: bash
+
+   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

doc/src/Build_package.rst

@@ -0,0 +1,251 @@
+Include packages in build
+=========================
+
+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 :doc:`Packages <Packages>` doc
+page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` 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.  If the command or style
+*is* available in a package included in the LAMMPS distribution,
+the error message will indicate which package would be needed.
+Running LAMMPS with the :doc:`-h command-line switch <Run_options>`
+will print *all* optional commands and packages that were enabled
+when building 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 :doc:`Build extras <Build_extras>` doc page.
+
+These links take you to the extra instructions for those select
+packages:
+
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
++----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+
+The mechanism for including packages is simple but different for CMake
+versus make.
+
+**CMake build**\ :
+
+
+.. code-block:: bash
+
+   -D PKG_NAME=value          # yes or no (default)
+
+Examples:
+
+
+.. code-block:: bash
+
+   -D PKG_MANYBODY=yes
+   -D PKG_USER-INTEL=yes
+
+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**\ :
+
+
+.. code-block:: bash
+
+   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
+
+Examples:
+
+
+.. code-block:: bash
+
+   make no-rigid
+   make yes-user-intel
+
+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 repository, 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.
+
+
+----------
+
+
+**CMake shortcuts for installing many packages**\ :
+
+Instead of specifying all the CMake options via the command-line,
+CMake allows initializing its settings cache using script files.
+These are regular CMake files which can manipulate and set CMake
+variables (which represent selected options), and can also contain
+control flow constructs for more complex operations.
+
+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.
+
+.. code-block:: bash
+
+    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/minimal.cmake [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/most.cmake    [OPTIONS] ../cmake  # enable most common packages
+    cmake -C ../cmake/presets/nolib.cmake   [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/clang.cmake   [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/mingw.cmake   [OPTIONS] ../cmake  # enable all packages compatible with MinGW compilers
+
+.. note::
+
+   Running cmake this way manipulates the CMake settings cache in your
+   current build directory. You can combine multiple presets and options
+   in a single cmake run, or change settings incrementally by running
+   cmake with new flags.
+
+**Example:**
+
+
+.. code-block:: bash
+
+   # build LAMMPS with most commonly used packages, but then remove
+   # those requiring additional library or tools, but still enable
+   # GPU package and configure it for using CUDA. You can run.
+   mkdir build
+   cd build
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
+
+   # to add another package, say BODY to the previous configuration you can run:
+   cmake -D PKG_BODY=on .
+
+   # to reset the package selection from above to the default of no packages
+   # but leaving all other settings untouched. You can run:
+   cmake -C ../cmake/presets/no_all.cmake .
+
+
+----------
+
+
+**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:
+
+.. code-block:: bash
+
+    make yes-all                        # install all packages
+    make no-all                         # uninstall all packages
+    make yes-standard or make yes-std   # install standard packages
+    make no-standard or make no-std     # uninstall standard packages
+    make yes-user                       # install user packages
+    make no-user                        # uninstall user packages
+    make yes-lib                        # install packages that require extra libraries
+    make no-lib                         # uninstall packages that require extra libraries
+    make yes-ext                        # install packages that require external libraries
+    make no-ext                         # uninstall packages that require external libraries
+
+which install/un-install various sets of packages.  Typing "make
+package" will list all the these commands.
+
+.. note::
+
+   Installing or un-installing a package for the make based build process
+   works by simply copying files back and forth between the main source
+   directory src and the 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.  Only source files in the src folder will be
+   compiled. 
+
+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
+:doc:`installing a patch <Install_patch>` 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 :doc:`patch has been applied <Install_patch>`,
+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 source directory and the package directory.

doc/src/Build_settings.rst

@@ -0,0 +1,466 @@
+Optional build settings
+=======================
+
+LAMMPS can be built with several optional settings.  Each sub-section
+explain how to do this for building both with CMake and make.
+
+* :ref:`C++11 standard compliance <cxx11>` when building all of LAMMPS
+* :ref:`FFT library <fft>` for use with the :doc:`kspace_style pppm <kspace_style>` command
+* :ref:`Size of LAMMPS data types <size>`
+* :ref:`Read or write compressed files <gzip>`
+* :ref:`Output of JPG and PNG files <graphics>` via the :doc:`dump image <dump_image>` command
+* :ref:`Output of movie files <graphics>` via the :doc:`dump_movie <dump_image>` command
+* :ref:`Memory allocation alignment <align>`
+* :ref:`Workaround for long long integers <longlong>`
+* :ref:`Error handling exceptions <exceptions>` when using LAMMPS as a library  
+
+
+----------
+
+
+.. _cxx11:
+
+C++11 standard compliance
+------------------------------------------
+
+The LAMMPS developers plan to transition to make the C++11 standard the
+minimum requirement for compiling LAMMPS.  Currently this only applies to
+some packages like KOKKOS while the rest aims to be compatible with the C++98
+standard.  Most currently used compilers are compatible with C++11; some need
+to set extra flags to enable C++11 compliance.  Example for GNU c++:
+
+.. code-block:: make
+
+   CCFLAGS = -g -O3 -std=c++11
+
+----------
+
+
+.. _fft:
+
+FFT library
+---------------------
+
+When the KSPACE package is included in a LAMMPS build, the
+:doc:`kspace_style pppm <kspace_style>` 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**\ :
+
+
+.. code-block:: bash
+
+   -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
+
+.. 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 FFTW3 is selected,
+then CMake will try to detect, if threaded FFTW libraries are available
+and enable them by default.  This setting is independent of whether
+OpenMP threads are enabled and a packages like KOKKOS or USER-OMP is
+used.  If CMake cannot detect the FFT library, you can set these variables
+to assist:
+
+
+.. code-block:: bash
+
+   -D FFTW3_INCLUDE_DIRS=path  # path to FFTW3 include files
+   -D FFTW3_LIBRARIES=path     # path to FFTW3 libraries
+   -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
+   -D MKL_INCLUDE_DIRS=path    # ditto for Intel MKL library
+   -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
+   -D MKL_LIBRARIES=path
+
+**Makefile.machine settings**\ :
+
+
+.. code-block:: make
+
+   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_FFTW_THREADS  # enable using threaded FFTW3 libraries
+   FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
+   FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+
+# default is FFT\_PACK\_ARRAY if not specified
+
+
+.. code-block:: make
+
+   FFT_INC =       -I/usr/local/include
+   FFT_PATH =      -L/usr/local/lib
+   FFT_LIB =       -lfftw3             # FFTW3 double precision
+   FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
+   FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compier, serial interface
+   FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+   FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+   FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
+
+As with CMake, you do not need to set paths in FFT\_INC or FFT\_PATH, if
+the compiler can find the FFT header and library files in its default search path.
+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 when using the
+:doc:`kspace_style pppm <kspace_style>` command. The :doc:`Run output <Run_output>`
+doc page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
+:doc:`kspace_modify fftbench yes <kspace_modify>` command.
+
+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 or libfftw3f.so.
+
+
+.. code-block:: bash
+
+   make clean
+   ./configure --enable-single; make; make install
+
+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.
+
+
+----------
+
+
+.. _size:
+
+Size of LAMMPS data types
+------------------------------------
+
+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**\ :
+
+
+.. code-block:: bash
+
+   -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
+
+**Makefile.machine setting**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+
+# 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
+
+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)
+
+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)
+
+Atom IDs are not required for atomic systems which do not store bond
+topology information, though IDs are enabled by default.  The
+:doc:`atom_modify id no <atom_modify>` 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
+:doc:`dump <dump>` 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 :doc:`compute msd <compute_msd>` command, to be faulty.
+
+Note that the USER-ATC package and the USER-INTEL package are currently
+not compatible with the "bigbig" setting. Also, there are limitations
+when using the library interface. Some functions with known issues
+have been replaced by dummy calls printing a corresponding error rather
+than crashing randomly or corrupting data.
+
+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.
+
+
+----------
+
+
+.. _graphics:
+
+Output of JPG, PNG, and movie files
+--------------------------------------------------
+
+The :doc:`dump image <dump_image>` command has options to output JPEG or
+PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
+outputs movie files in MPEG format.  Using these options requires the
+following settings:
+
+**CMake variables**\ :
+
+
+.. code-block:: bash
+
+   -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
+
+Usually these settings are all that is needed.  If CMake cannot find
+the graphics header, library, executable files, you can set these
+variables:
+
+
+.. code-block:: bash
+
+   -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
+
+**Makefile.machine settings**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_JPEG
+   LMP_INC = -DLAMMPS_PNG
+   LMP_INC = -DLAMMPS_FFMPEG
+
+   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
+
+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,
+that is a directory 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 call (required by popen()) can interfere with the fast
+   communication library and lead to simulations using ffmpeg to hang or
+   crash.
+
+
+----------
+
+
+.. _gzip:
+
+Read or write compressed files
+-----------------------------------------
+
+If this option is enabled, large files can be read or written with
+gzip compression by several LAMMPS commands, including
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
+
+**CMake variables**\ :
+
+
+.. code-block:: bash
+
+   -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
+
+**Makefile.machine setting**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_GZIP
+
+**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 call (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 :ref:`COMPRESS package <PKG-COMPRESS>` enables.
+
+
+----------
+
+
+.. _align:
+
+Memory allocation alignment
+---------------------------------------
+
+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**\ :
+
+
+.. code-block:: bash
+
+   -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
+
+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**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
+
+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.
+
+
+----------
+
+
+.. _longlong:
+
+Workaround for long long integers
+------------------------------------------------
+
+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**\ :
+
+
+.. code-block:: bash
+
+   -D LAMMPS_LONGLONG_TO_LONG=value     # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
+
+
+----------
+
+
+.. _exceptions:
+
+Exception handling when using LAMMPS as a library
+------------------------------------------------------------------
+
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled, LAMMPS errors do not kill the calling code.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python. Of course the calling code has to be set up to
+*catch* exceptions from within LAMMPS.
+
+**CMake variable**\ :
+
+
+.. code-block:: bash
+
+   -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
+
+**Makefile.machine setting**\ :
+
+
+.. code-block:: make
+
+   LMP_INC = -DLAMMPS_EXCEPTIONS

doc/src/Build_windows.rst

@@ -0,0 +1,108 @@
+Notes for building LAMMPS on Windows
+====================================
+
+* :ref:`General remarks <generic>`
+* :ref:`Running Linux on Windows <linux>`
+* :ref:`Using GNU GCC ported to Windows <gnu>`
+* :ref:`Using a cross-compiler <cross>`
+
+
+----------
+
+
+.. _generic:
+
+General remarks
+-----------------------------
+
+LAMMPS is developed and tested primarily on Linux machines.  The vast
+majority of HPC clusters and supercomputers today runs on Linux as well.
+While portability to other platforms is desired, it is not always achieved.
+The LAMMPS developers strongly rely on LAMMPS users giving feedback and
+providing assistance in resolving portability issues. This is particularly
+true for compiling LAMMPS on Windows, since this platform has significant
+differences with some low-level functionality.
+
+.. _linux:
+
+Running Linux on Windows
+------------------------------------
+
+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 you to compile LAMMPS
+on a Windows machine (e.g. because it is your main desktop), please also
+consider using a virtual machine software and compile and run LAMMPS in
+a Linux virtual machine, or - if you have a recently updated Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows 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 and more). For more details on that, please
+see :doc:`this tutorial <Howto_bash>`
+
+.. _gnu:
+
+Using a GNU GCC ported to Windows
+-----------------------------------------
+
+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. Using CMake for this mode of compilation
+is untested and not likely to work.
+
+When compiling for Windows do **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.
+
+.. _cross:
+
+Using a cross-compiler
+----------------------------------
+
+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. A CMake preset
+selecting all packages compatible with this cross-compilation build
+is provided. You will likely need to disable the GPU package unless you
+download and install the contents of the pre-compiled `OpenCL ICD loader library <https://download.lammps.org/thirdparty/opencl-win-devel.tar.gz>`_
+into your MinGW64 cross-compiler environment. The cross-compilation
+currently will only produce non-MPI serial binaries.
+
+Please keep in mind, though, that this only applies to **compiling** LAMMPS.
+Whether the resulting binaries do work correctly is not 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:
+
+Native Visual C++ support
+--------------------------------------
+
+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.