Merge pull request #2957 from akohlmey/next_release_version

Step version strings for stable release

.gitattributes

@@ -2,3 +2,4 @@
 .gitignore export-ignore
 .github export-ignore
 .lgtm.yml export-ignore
+SECURITY.md export-ignore

.github/CODEOWNERS

@@ -13,43 +13,51 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
-src/COMPRESS/*        @akohlmey
+src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
 src/MESSAGE/*         @sjplimp
+src/MLIAP/*           @athomps
+src/SNAP/*            @athomps
 src/SPIN/*            @julient31
-src/USER-CGDNA/*      @ohenrich
-src/USER-CGSDK/*      @akohlmey
-src/USER-COLVARS/*    @giacomofiorin
-src/USER-INTEL/*      @wmbrownintel
-src/USER-MANIFOLD/*   @Pakketeretet2
-src/USER-MEAMC/*      @martok
-src/USER-MESONT/*     @iafoss
-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
-
+src/BROWNIAN/*        @samueljmcameron
+src/CG-DNA/*          @ohenrich
+src/CG-SDK/*          @akohlmey
+src/COLVARS/*         @giacomofiorin
+src/DIELECTRIC/*      @ndtrung81
+src/FEP/*             @agiliopadua
+src/ML-HDNNP/*        @singraber
+src/INTEL/*           @wmbrownintel
+src/MANIFOLD/*        @Pakketeretet2
+src/MDI/*             @taylor-a-barnes
+src/MEAM/*            @martok
+src/MESONT/*          @iafoss
+src/MOFFF/*           @hheenen
+src/MOLFILE/*         @akohlmey
+src/NETCDF/*          @pastewka
+src/ML-PACE/*         @yury-lysogorskiy
+src/PLUMED/*          @gtribello
+src/PHONON/*          @lingtikong
+src/PTM/*             @pmla
+src/OPENMP/*          @akohlmey
+src/QMMM/*            @akohlmey
+src/REAXFF/*          @hasanmetin @stanmoore1
+src/REACTION/*        @jrgissing
+src/SCAFACOS/*        @rhalver
+src/TALLY/*           @akohlmey
+src/UEF/*             @danicholson
+src/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-REACTION/fix_bond_react.*  @jrgissing
-src/USER-MISC/*_grem.*              @dstelter92
-src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+src/REPLICA/*_grem.*                @dstelter92
+src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/MISC/*_tracker.*                @jtclemm
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -73,6 +81,7 @@ src/kspace.*              @sjplimp
 src/lmptyp.h              @sjplimp
 src/library.*             @sjplimp
 src/main.cpp              @sjplimp
+src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
 src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
@@ -101,7 +110,6 @@ 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
@@ -114,23 +122,26 @@ src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
+src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
 tools/msi2lmp/*       @akohlmey
 tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
-tools/code_standard/* @rbberger
+tools/coding_standard/* @rbberger
 tools/valgrind/*      @akohlmey
+tools/swig/*          @akohlmey
+tools/offline/*       @rbberger
 
 # tests
 unittest/*            @akohlmey @rbberger
 
 # cmake
 cmake/*               @junghans @rbberger
-cmake/Modules/Packages/USER-COLVARS.cmake @junghans @rbberger @giacomofiorin
+cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
-cmake/presets/*.cmake @junghans @rbberger @akohlmey
+cmake/presets/*.cmake @akohlmey
 
 # python
 python/*              @rbberger
@@ -142,6 +153,7 @@ fortran/*             @akohlmey
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+examples/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/CONTRIBUTING.md

@@ -5,8 +5,9 @@ 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 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](https://lammps.sandia.gov/doc/Modify_contribute.html)
-* [The LAMMPS GitHub Tutorial in the Manual](http://lammps.sandia.gov/doc/Howto_github.html)
+* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 ## Table of Contents
 
@@ -26,11 +27,11 @@ __
 
 ## 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 either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). 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. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
+> **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 either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). 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. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
 
 ## 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 or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
+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 or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
 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
@@ -62,37 +63,12 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 ### Contributing Code
 
-We encourage users to submit new features or modifications for LAMMPS to the core developers so they can be added to the LAMMPS distribution. The preferred way to manage and coordinate this is by submitting a pull request at the LAMMPS project on GitHub. For any larger modifications or programming project, you are encouraged to contact the LAMMPS developers ahead of time, in order to discuss implementation strategies and coding guidelines, that will make it easier to integrate your contribution and result in less work for everybody involved. You are also encouraged to search through the list of open issues on GitHub and submit a new issue for a planned feature, so you would not duplicate the work of others (and possibly get scooped by them) or have your work duplicated by others.
+We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
+and recommendations are in the following sections of the LAMMPS manual:
+* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
-How quickly your contribution will be integrated depends largely on how much effort it will cause to integrate and test it, how much it requires changes to the core code base, and of how much interest it is to the larger LAMMPS community. Please see below for a checklist of typical requirements. Once you have prepared everything, see [this tutorial](https://lammps.sandia.gov/doc/Howto_github.html)
- for instructions on how to submit your changes or new files through a GitHub pull request
-
-Here is a checklist of steps you need to follow to submit a single file or user package for our consideration. Following these steps will save both you and us time. See existing files in packages in the source directory for examples. If you are uncertain, please ask on the lammps-users mailing list.
-
-* C++ source code must be compatible with the C++-11 standard. Packages may require a later standard, if justified.
-* 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 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 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). The text files can include mathematical expressions and symbol in ".. math::" sections or ":math:" expressions 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`, `make pdf` 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
-* For new utility functions or class (i.e. anything that does not depend on a LAMMPS object), new unit tests should be added to the unittest tree.
-* When adding a new LAMMPS style, a .yaml file with a test configuration and reference data should be added for the styles where a suitable tester program already exists (e.g. pair styles, bond styles, etc.).
-* 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 <name>.cpp source file. See src/USER-EFF/atom_vec_electron.cpp for an example. A LaTeX citation is stored in a variable at the top of the file and a single line of code that references the variable is added to the constructor of the class. Whenever a user invokes your feature from their input script, this will cause LAMMPS to output the citation to a log.cite file and prompt the user to examine the file. Note that you should only use this for a paper you or your group authored. E.g. adding a cite in the code for a paper by Nose and Hoover if you write a fix that implements their integrator is not the intended usage. That kind of citation should just be in the doc page you provide.
-
-Finally, as a general rule-of-thumb, the more clear and self-explanatory you make your documentation and README files, and the easier you make it for people to get started, e.g. by providing example scripts, the more likely it is that users will try out your new feature.
-
-If the new features/files are broadly useful we may add them as core files to LAMMPS or as part of a standard package. Else we will add them as a user-contributed file or package. Examples of user packages are in src sub-directories that start with USER. The USER-MISC package is simply a collection of (mostly) unrelated single files, which is the simplest way to have your contribution quickly added to the LAMMPS distribution. You can see a list of the both standard and user packages by typing "make package" in the LAMMPS src directory.
-
-Note that by providing us files to release, you are agreeing to make them open-source, i.e. we can release them under the terms of the GPL, used as a license for the rest of LAMMPS. See Section 1.4 for details.
-
-With user packages and files, all we are really providing (aside from the fame and fortune that accompanies having your name in the source code and on the Authors page of the LAMMPS WWW site), is a means for you to distribute your work to the LAMMPS user community, and a mechanism for others to easily try out your new feature. This may help you find bugs or make contact with new collaborators. Note that you are also implicitly agreeing to support your code which means answer questions, fix bugs, and maintain it if LAMMPS changes in some way that breaks it (an unusual event).
-
-To be able to submit an issue on GitHub, you have to register for an account (for GitHub in general). If you do not want to do that, or have other reservations or difficulties to submit a pull request, you can - as an alternative - contact one or more of the core LAMMPS developers and ask if one of them would be interested in manually merging your code into LAMMPS and send them your source code. Since the effort to merge a pull request is a small fraction of the effort of integrating source code manually (which would usually be done by converting the contribution into a pull request), your chances to have your new code included quickly are the best with a pull request.
-
-If you prefer to submit patches or full files, you should first make certain, that your code works correctly with the latest patch-level version of LAMMPS and contains all bug fixes from it. Then create a gzipped tar file of all changed or added files or a corresponding patch file using 'diff -u' or 'diff -c' and compress it with gzip. Please only use gzip compression, as this works well on all platforms.
 
 ## GitHub Workflows
 
@@ -102,17 +78,17 @@ This section briefly summarizes the steps that will happen **after** you have su
 
 After submitting an issue, one or more of the LAMMPS developers will review it and categorize it by assigning labels. Confirmed bug reports will be labeled `bug`; if the bug report also contains a suggestion for how to fix it, it will be labeled `bugfix`; if the issue is a feature request, it will be labeled `enhancement`. Other labels may be attached as well, depending on which parts of the LAMMPS code are affected. If the assessment is, that the issue does not warrant any changes, the `wontfix` label will be applied and if the submission is incorrect or something that should not be submitted as an issue, the `invalid` label will be applied. In both of the last two cases, the issue will then be closed without further action.
 
-For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will usually be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below.
+For feature requests, what happens next is that developers may comment on the viability or relevance of the request, discuss and make suggestions for how to implement it. If a LAMMPS developer or user is planning to implement the feature, the issue will be assigned to that developer. For developers, that are not yet listed as LAMMPS project collaborators, they will receive an invitation to be added to the LAMMPS project as a collaborator so they can get assigned. If the requested feature or enhancement is implemented, it will be submitted as a pull request, which will contain a reference to the issue number. And once the pull request is reviewed and accepted for inclusion into LAMMPS, the issue will be closed. For details on how pull requests are processed, please see below. Feature requests may be labeled with `volunteer_needed` if none of the LAMMPS developers has the time and the required knowledge implement the feature.
 
-For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix is likely to be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
+For bug reports, the next step is that one of the core LAMMPS developers will self-assign to the issue and try to confirm the bug. If confirmed, the `bug` label and potentially other labels are added to classify the issue and its impact to LAMMPS. Otherwise the `unconfirmed` label will be applied and some comment about what was tried to confirm the bug added. Before confirming, further questions may be asked or requests for providing additional input files or details about the steps required to reproduce the issue. Any bugfix will be submitted as a pull request (more about that below) and since most bugs require only local changes, the bugfix may be included in a pull request specifically set up to collect such local bugfixes or small enhancements. Once the bugfix is included in the master branch, the issue will be closed.
 
 ### Pull Requests
 
-For submitting pull requests, there is a [detailed tutorial](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. As part of the assessment, 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). 
+Pull requests are the **only** way that changes get made to the LAMMPS distribution.  So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub.  Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request.  That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
+Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. 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 time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission.  If you submitted a draft pull request, this will not happen unless you mark it "ready for review".  If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository.  As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
-If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.
-Since the learning curve for git is quite steep for efficiently managing remote repositories, local and remote branches, pull requests and more, do not hesitate to ask questions, if you are not sure about how to do certain steps that are asked of you. Even if the changes asked of you do not make sense to you, they may be important for the LAMMPS developers. Please also note, that these all are guidelines and nothing set in stone. So depending on the nature of the contribution, the workflow may be adjusted.
+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.  The minimum requirement to merge a pull request is that all automated tests have to pass and at least one LAMMPS developer has approved integrating the submitted code. Since the approver will not be the person merging a pull request, you will have at least two LAMMPS developers that looked at your contribution.
+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 work flow may be adjusted.
 

.gitignore

@@ -12,6 +12,7 @@
 *.sif
 *.dll
 *.pyc
+a.out
 __pycache__
 
 Obj_*
@@ -43,6 +44,8 @@ Thumbs.db
 /build*
 /CMakeCache.txt
 /CMakeFiles/
+/Testing
 /Makefile
+/Testing
 /cmake_install.cmake
 /lmp

.lgtm.yml

@@ -4,7 +4,7 @@ extraction:
       command:
       - "mkdir build"
       - "cd build"
-      - "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
+      - "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake"
     index:
       build_command:
       - "cd build"

README

@@ -14,10 +14,10 @@ LAMMPS is a classical molecular dynamics simulation code designed to
 run efficiently on parallel computers.  It was developed at Sandia
 National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
-under the terms of the GNU Public License (GPL).
+under the terms of the GNU Public License (GPL) version 2.
 
 The primary author of the code is Steve Plimpton, who can be emailed
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:
@@ -37,14 +37,14 @@ tools                      pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://lammps.sandia.gov/doc/Manual.html         LAMMPS manual
-https://lammps.sandia.gov/doc/Intro.html          hi-level introduction
-https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
-https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
-https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
-https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
+https://docs.lammps.org/Manual.html         LAMMPS manual
+https://docs.lammps.org/Intro.html          hi-level introduction
+https://docs.lammps.org/Build.html          how to build LAMMPS
+https://docs.lammps.org/Run_head.html       how to run LAMMPS
+https://docs.lammps.org/Commands_all.html   Table of available commands
+https://docs.lammps.org/Library.html        LAMMPS library interfaces
+https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
+https://docs.lammps.org/Developer.html      LAMMPS developer info
 
 You can also create these doc pages locally:
 

bench/POTENTIALS/README

@@ -1,7 +1,7 @@
 These are input scripts used to run benchmark tests for many of the
 interatomic potentials in LAMMPS.  The results of running these
 scripts on different machines are shown on the Potentials section of
-the Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+the Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 Examples are shown below of how to run these scripts.  Log files for
 running them on 1 and 4 processors of a Linux box are included in the

bench/POTENTIALS/in.meam

@@ -8,7 +8,7 @@ region		box block 0 20 0 20 0 20
 create_box	1 box
 create_atoms	1 box
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 
 velocity	all create 1600.0 376847 loop geom

bench/POTENTIALS/log.9Oct20.meam.1

@@ -15,7 +15,7 @@ create_atoms	1 box
 Created 32000 atoms
   create_atoms CPU = 0.002 seconds
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 Reading potential file library.meam with DATE: 2012-06-29
 Reading potential file Ni.meam with DATE: 2007-06-11
@@ -38,12 +38,12 @@ Neighbor list info ...
   ghost atom cutoff = 5
   binsize = 2.5, bins = 29 29 29
   2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam/c, perpetual
+  (1) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-  (2) pair meam/c, perpetual, half/full from (1)
+  (2) pair meam, perpetual, half/full from (1)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none

bench/POTENTIALS/log.9Oct20.meam.4

@@ -15,7 +15,7 @@ create_atoms	1 box
 Created 32000 atoms
   create_atoms CPU = 0.001 seconds
 
-pair_style	meam/c
+pair_style	meam
 pair_coeff	* * library.meam Ni4 Ni.meam Ni4
 Reading potential file library.meam with DATE: 2012-06-29
 Reading potential file Ni.meam with DATE: 2007-06-11
@@ -38,12 +38,12 @@ Neighbor list info ...
   ghost atom cutoff = 5
   binsize = 2.5, bins = 29 29 29
   2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair meam/c, perpetual
+  (1) pair meam, perpetual
       attributes: full, newton on
       pair build: full/bin/atomonly
       stencil: full/bin/3d
       bin: standard
-  (2) pair meam/c, perpetual, half/full from (1)
+  (2) pair meam, perpetual, half/full from (1)
       attributes: half, newton on
       pair build: halffull/newton
       stencil: none

bench/POTENTIALS/log.9Oct20.reaxc.1

@@ -24,7 +24,7 @@ velocity	all create 300.0 9999
 
 pair_style	reax/c NULL
 pair_coeff      * * ffield.reax C H O N
-WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
+WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
 
 timestep	0.1
 fix		1 all nve

bench/POTENTIALS/log.9Oct20.reaxc.4

@@ -24,7 +24,7 @@ velocity	all create 300.0 9999
 
 pair_style	reax/c NULL
 pair_coeff      * * ffield.reax C H O N
-WARNING: Changed valency_val to valency_boc for X (src/USER-REAXC/reaxc_ffield.cpp:315)
+WARNING: Changed valency_val to valency_boc for X (src/REAXFF/reaxc_ffield.cpp:315)
 
 timestep	0.1
 fix		1 all nve

bench/README

@@ -2,7 +2,7 @@ LAMMPS benchmark problems
 
 This directory contains 5 benchmark problems which are discussed in
 the Benchmark section of the LAMMPS documentation, and on the
-Benchmark page of the LAMMPS WWW site (lammps.sandia.gov/bench).
+Benchmark page of the LAMMPS WWW site (https://www.lammps.org/bench.html).
 
 This directory also has several sub-directories:
 
@@ -11,7 +11,7 @@ KEPLER          benchmark scripts for GPU cluster with Kepler GPUs
 POTENTIALS      benchmarks scripts for various potentials in LAMMPS
 
 The results for all of these benchmarks are displayed and discussed on
-the Benchmark page of the LAMMPS WWW site: lammps.sandia.gov/bench.
+the Benchmark page of the LAMMPS WWW site: https://www.lammps.org/bench.html
 
 The remainder of this file refers to the 5 problems in the top-level
 of this directory and how to run them on CPUs, either in serial or

cmake/.coveragerc.in

@@ -0,0 +1,10 @@
+[run]
+source = @LAMMPS_PYTHON_DIR@
+parallel=True
+branch=True
+omit=*/install.py
+     */setup.py
+
+[paths]
+sources = python
+          @LAMMPS_PYTHON_DIR@

cmake/CMakeLists.txt

@@ -7,6 +7,11 @@ cmake_minimum_required(VERSION 3.10)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+# set policy to silence warnings about missing executable permissions in
+# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
+if(POLICY CMP0109)
+  cmake_policy(SET CMP0109 OLD)
+endif()
 ########################################
 
 project(lammps CXX)
@@ -31,7 +36,11 @@ find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (NOT CMAKE_CROSSCOMPILING))
+    set(CMAKE_INSTALL_PREFIX "$ENV{USERPROFILE}/LAMMPS" CACHE PATH "Default install path" FORCE)
+  else()
+    set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+  endif()
 endif()
 
 # If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
@@ -72,7 +81,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
     set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@@ -85,6 +94,15 @@ endif()
 set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
+# ugly hack for MSVC which by default always reports an old C++ standard in the __cplusplus macro
+if(MSVC)
+  add_compile_options(/Zc:__cplusplus)
+endif()
+
+# export all symbols when building a .dll file on windows
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
+  set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
+endif()
 
 ########################################################################
 # User input options                                                   #
@@ -104,11 +122,23 @@ endif()
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
+# allow enabling clang-tidy for C++ files
+set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
+if(ENABLE_CLANG_TIDY)
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
+endif()
+
 include(GNUInstallDirs)
 file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
 file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
+
+# tell CMake to export all symbols to a .dll on Windows with MinGW cross-compilers
+if(BUILD_SHARED_LIBS AND (CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  set_target_properties(lammps PROPERTIES LINK_FLAGS "-Wl,--export-all-symbols")
+endif()
+
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
@@ -116,17 +146,92 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
-  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
-  USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
-  USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
+set(STANDARD_PACKAGES
+  ADIOS
+  ASPHERE
+  ATC
+  AWPMD
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  H5MD
+  INTERLAYER
+  KIM
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
-set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
+set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
 
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
@@ -137,7 +242,7 @@ endforeach()
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
 
-if(PKG_USER-ADIOS)
+if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
@@ -147,7 +252,6 @@ if(PKG_USER-ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
@@ -155,8 +259,11 @@ else()
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
-  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
     target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
   else()
@@ -190,7 +297,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
 target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
 else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@@ -206,12 +313,16 @@ endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
-pkg_depends(MLIAP SNAP)
+pkg_depends(ML-IAP ML-SNAP)
 pkg_depends(MPIIO MPI)
-pkg_depends(USER-ATC MANYBODY)
-pkg_depends(USER-LB MPI)
-pkg_depends(USER-PHONON KSPACE)
-pkg_depends(USER-SCAFACOS MPI)
+pkg_depends(ATC MANYBODY)
+pkg_depends(LATBOLTZ MPI)
+pkg_depends(PHONON KSPACE)
+pkg_depends(SCAFACOS MPI)
+pkg_depends(DIELECTRIC KSPACE)
+pkg_depends(DIELECTRIC EXTRA-PAIR)
+pkg_depends(CG-DNA MOLECULE)
+pkg_depends(CG-DNA ASPHERE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -232,8 +343,10 @@ if(BUILD_OMP)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
 
-  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
-      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+  if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@@ -245,7 +358,7 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
   find_package(BLAS)
@@ -265,6 +378,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   endif()
 endif()
 
+# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
+set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
@@ -296,7 +411,7 @@ find_program(GZIP_EXECUTABLE gzip)
 find_package_handle_standard_args(GZIP REQUIRED_VARS GZIP_EXECUTABLE)
 option(WITH_GZIP "Enable GZIP support" ${GZIP_FOUND})
 if(WITH_GZIP)
-  if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
+  if(GZIP_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
     target_compile_definitions(lammps PRIVATE -DLAMMPS_GZIP)
   else()
     message(FATAL_ERROR "gzip executable not found")
@@ -307,7 +422,7 @@ find_program(FFMPEG_EXECUTABLE ffmpeg)
 find_package_handle_standard_args(FFMPEG REQUIRED_VARS FFMPEG_EXECUTABLE)
 option(WITH_FFMPEG "Enable FFMPEG support" ${FFMPEG_FOUND})
 if(WITH_FFMPEG)
-  if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING))
+  if(FFMPEG_FOUND OR ((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
     target_compile_definitions(lammps PRIVATE -DLAMMPS_FFMPEG)
   else()
     message(FATAL_ERROR "ffmpeg executable not found")
@@ -324,10 +439,10 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
-        USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
+foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MESSAGE MSCG COMPRESS ML-PACE)
   if(PKG_${PKG_WITH_INCL})
-    include(Packages/${PKG_WITH_INCL}) 
+    include(Packages/${PKG_WITH_INCL})
   endif()
 endforeach()
 
@@ -418,11 +533,10 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
-  if(PKG_${SIMPLE_LIB})
-    string(REGEX REPLACE "^USER-" "" PKG_LIB "${SIMPLE_LIB}")
+foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
+  if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    if(PKG_LIB STREQUAL mesont)
+    if(PKG_LIB STREQUAL "mesont")
       enable_language(Fortran)
       file(GLOB_RECURSE ${PKG_LIB}_SOURCES
         ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
@@ -434,9 +548,9 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
-    if(PKG_LIB STREQUAL awpmd)
+    if(PKG_LIB STREQUAL "awpmd")
       target_include_directories(awpmd PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/awpmd/systems/interact ${LAMMPS_LIB_SOURCE_DIR}/awpmd/ivutils/include)
-    elseif(PKG_LIB STREQUAL h5md)
+    elseif(PKG_LIB STREQUAL "h5md")
       target_include_directories(h5md PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/h5md/include ${HDF5_INCLUDE_DIRS})
     else()
       target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})
@@ -444,13 +558,13 @@ foreach(SIMPLE_LIB POEMS USER-ATC USER-AWPMD USER-H5MD USER-MESONT)
   endif()
 endforeach()
 
-if(PKG_USER-AWPMD)
+if(PKG_AWPMD)
   target_link_libraries(awpmd PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
-if(PKG_USER-ATC)
-  if(LAMMPS_SIZES STREQUAL BIGBIG)
-    message(FATAL_ERROR "The USER-ATC Package is not compatible with -DLAMMPS_BIGBIG")
+if(PKG_ATC)
+  if(LAMMPS_SIZES STREQUAL "BIGBIG")
+    message(FATAL_ERROR "The ATC Package is not compatible with -DLAMMPS_BIGBIG")
   endif()
   target_link_libraries(atc PRIVATE ${LAPACK_LIBRARIES})
   if(BUILD_MPI)
@@ -462,15 +576,15 @@ if(PKG_USER-ATC)
   target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 endif()
 
-if(PKG_USER-H5MD)
-  include(Packages/USER-H5MD)
+if(PKG_H5MD)
+  include(Packages/H5MD)
 endif()
 
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -493,7 +607,7 @@ endif()
 # and the MPI library - if use - has to be linked right before those
 # and after everything else that is compiled locally
 ######################################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
@@ -542,8 +656,8 @@ add_dependencies(lammps gitversion)
 # Actually add executable and lib to build
 ############################################
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-list (FIND LANGUAGES "Fortran" _index)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "Fortran" _index)
+if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
@@ -621,7 +735,7 @@ if(BUILD_SHARED_LIBS)
   else()
     find_package(Python COMPONENTS Interpreter)
   endif()
-  if (Python_EXECUTABLE)
+  if(Python_EXECUTABLE)
     add_custom_target(
       install-python ${CMAKE_COMMAND} -E remove_directory build
       COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
@@ -654,7 +768,7 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
   else()
     find_package(Python COMPONENTS Interpreter)
   endif()
-  if (Python_EXECUTABLE)
+  if(Python_EXECUTABLE)
     file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
     install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
   endif()
@@ -663,6 +777,13 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
+find_package(ClangFormat 8.0)
+
+if(ClangFormat_FOUND)
+  add_custom_target(format-src
+    COMMAND ${ClangFormat_EXECUTABLE} --verbose -i -style=file *.cpp *.h */*.cpp */*.h
+    WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
+endif()
 
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
@@ -699,15 +820,15 @@ if(OPTIONS)
   message("      Options:       ${OPTIONS}")
 endif()
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
-list (FIND LANGUAGES "Fortran" _index)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "Fortran" _index)
+if(_index GREATER -1)
   message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
       Type:          ${CMAKE_Fortran_COMPILER_ID}
       Version:       ${CMAKE_Fortran_COMPILER_VERSION}
       Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
-list (FIND LANGUAGES "C" _index)
-if(${_index} GREATER -1)
+list(FIND LANGUAGES "C" _index)
+if(_index GREATER -1)
   message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
@@ -772,7 +893,7 @@ if(PKG_KSPACE)
   endif()
   if(PKG_KOKKOS)
     if(Kokkos_ENABLE_CUDA)
-      if (${FFT} STREQUAL "KISS")
+      if(FFT STREQUAL "KISS")
         message(STATUS "Kokkos FFT: KISS")
       else()
         message(STATUS "Kokkos FFT: cuFFT")

cmake/Modules/CodeCoverage.cmake

@@ -54,6 +54,8 @@ if(ENABLE_COVERAGE)
 
     if(COVERAGE_FOUND)
         set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
+        configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
+
         add_custom_command(
             OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
             COMMAND ${COVERAGE_BINARY} combine
@@ -63,16 +65,16 @@ if(ENABLE_COVERAGE)
 
         add_custom_target(
             gen_python_coverage_html
-            COMMAND ${COVERAGE_BINARY} html -d ${PYTHON_COVERAGE_HTML_DIR}
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
             COMMENT "Generating HTML Python coverage report..."
         )
 
         add_custom_target(
             gen_python_coverage_xml
-            COMMAND ${COVERAGE_BINARY} xml -o ${CMAKE_BINARY_DIR}/python_coverage.xml
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+            COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
+            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
             WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
             COMMENT "Generating XML Python coverage report..."
         )

cmake/Modules/CodingStandard.cmake

@@ -15,6 +15,11 @@ if(Python3_EXECUTABLE)
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
           WORKING_DIRECTORY  ${LAMMPS_DIR}
           COMMENT "Check for whitespace errors")
+        add_custom_target(
+          check-homepage
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Check for homepage URL errors")
         add_custom_target(
           check-permissions
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
@@ -25,6 +30,11 @@ if(Python3_EXECUTABLE)
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
           WORKING_DIRECTORY  ${LAMMPS_DIR}
           COMMENT "Fix whitespace errors")
+        add_custom_target(
+          fix-homepage
+          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
+          WORKING_DIRECTORY  ${LAMMPS_DIR}
+          COMMENT "Fix homepage URL errors")
         add_custom_target(
           fix-permissions
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .

cmake/Modules/FindFFTW3.cmake

@@ -38,7 +38,7 @@ if(FFTW3_FOUND)
       add_library(FFTW3::FFTW3_OMP UNKNOWN IMPORTED)
       set_target_properties(FFTW3::FFTW3_OMP PROPERTIES
         IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-	IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
+        IMPORTED_LOCATION "${FFTW3_OMP_LIBRARY}"
         INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIRS}")
     endif()
   endif()

cmake/Modules/FindFFTW3F.cmake

@@ -37,7 +37,7 @@ if(FFTW3F_FOUND)
       add_library(FFTW3F::FFTW3F_OMP UNKNOWN IMPORTED)
       set_target_properties(FFTW3F::FFTW3F_OMP PROPERTIES
         IMPORTED_LINK_INTERFACE_LANGUAGES "C"
-	IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
+        IMPORTED_LOCATION "${FFTW3F_OMP_LIBRARY}"
         INTERFACE_INCLUDE_DIRECTORIES "${FFTW3F_INCLUDE_DIRS}")
     endif()
   endif()

cmake/Modules/FindN2P2.cmake

@@ -0,0 +1,61 @@
+include(FindPackageHandleStandardArgs)
+
+# Check if N2P2_DIR is set manually.
+if (DEFINED ENV{N2P2_DIR})
+  set(N2P2_DIR "${N2P2_DIR}")
+# If not, try if directory "lib/hdnnp/n2p2" exists.
+else()
+  get_filename_component(_fullpath "${LAMMPS_LIB_SOURCE_DIR}/hdnnp/n2p2" REALPATH)
+  if (EXISTS ${_fullpath})
+    set(N2P2_DIR "${_fullpath}")
+  endif()
+endif()
+
+# Set path to include directory.
+find_path(N2P2_INCLUDE_DIR InterfaceLammps.h HINTS "${N2P2_DIR}/include")
+# Two libraries need to be linked: libnnp and libnnpif.
+find_library(N2P2_LIBNNP NAMES nnp HINTS "${N2P2_DIR}/lib")
+find_library(N2P2_LIBNNPIF NAMES nnpif HINTS "${N2P2_DIR}/lib")
+# Users could compile n2p2 with extra flags which are then also required for
+# pair_hdnnp.cpp compilation. To forward them to the LAMMPS build process n2p2
+# writes a file with cmake commands, e.g.
+#
+# target_compile_definitions(lammps PRIVATE -DN2P2_NO_SF_GROUPS)
+#
+# to "lib/lammps-extra.cmake" which is then included by ML-HDNNP.cmake.
+find_file(N2P2_CMAKE_EXTRA NAMES lammps-extra.cmake HINTS "${N2P2_DIR}/lib")
+
+find_package_handle_standard_args(N2P2 DEFAULT_MSG
+  N2P2_DIR
+  N2P2_INCLUDE_DIR
+  N2P2_LIBNNP
+  N2P2_LIBNNPIF
+  N2P2_CMAKE_EXTRA)
+
+if(N2P2_FOUND)
+  if (NOT TARGET N2P2::N2P2)
+    # n2p2 core library "libnnp"
+    add_library(N2P2::LIBNNP UNKNOWN IMPORTED)
+    set_target_properties(N2P2::LIBNNP PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
+      IMPORTED_LOCATION ${N2P2_LIBNNP})
+    # n2p2 interface library "libnnpif"
+    add_library(N2P2::LIBNNPIF UNKNOWN IMPORTED)
+    set_target_properties(N2P2::LIBNNPIF PROPERTIES
+      INTERFACE_INCLUDE_DIRECTORIES ${N2P2_INCLUDE_DIR}
+      IMPORTED_LOCATION ${N2P2_LIBNNPIF})
+    # Put libnnp, libnnpif and include directory together.
+    add_library(N2P2::N2P2 INTERFACE IMPORTED)
+    set_property(TARGET N2P2::N2P2 PROPERTY
+      INTERFACE_LINK_LIBRARIES N2P2::LIBNNPIF N2P2::LIBNNP)
+    set(N2P2_CMAKE_EXTRAS ${N2P2_CMAKE_EXTRA})
+  endif()
+endif()
+
+mark_as_advanced(
+  N2P2_DIR
+  N2P2_INCLUDE_DIR
+  N2P2_LIBNNP
+  N2P2_LIBNNPIF
+  N2P2_CMAKE_EXTRA
+)

cmake/Modules/GTest.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building Google Test library")
 
-if(CMAKE_BUILD_TYPE STREQUAL Debug)
+if(CMAKE_BUILD_TYPE STREQUAL "Debug")
   set(GTEST_LIB_POSTFIX d)
 else()
   set(GTEST_LIB_POSTFIX)

cmake/Modules/LAMMPSUtils.cmake

@@ -67,7 +67,7 @@ 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}")
+    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
   endif()
 endmacro()
 
@@ -106,7 +106,7 @@ function(FetchPotentials pkgfolder potfolder)
 endfunction(FetchPotentials)
 
 # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
-if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
+if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   file(STRINGS /etc/os-release distro REGEX "^NAME=")
   string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
   file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.09.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "3b3882627964bd02e5c3b02065daac3c" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

cmake/Modules/Packages/DPD-SMOOTH.cmake

@@ -1,13 +1,13 @@
 # Fix rigid/meso requires RIGID to be installed
-set(USER-SDPD_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-SDPD)
+set(DPD-SMOOTH_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/DPD-SMOOTH)
 
 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 hlist ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.h)
   get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${USER-SDPD_SOURCES_DIR}/fix_rigid_meso.cpp)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${DPD-SMOOTH_SOURCES_DIR}/fix_rigid_meso.cpp)
   set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
 set_property(GLOBAL PROPERTY FIX "${hlist}")
 
-target_include_directories(lammps PRIVATE ${USER-SDPD_SOURCES_DIR})
+target_include_directories(lammps PRIVATE ${DPD-SMOOTH_SOURCES_DIR})

cmake/Modules/Packages/GPU.cmake

@@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
   file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
-  if (GPU_LIB_OLD_CUBIN_HEADERS)
+  if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
       "Please run\n"
@@ -71,44 +71,47 @@ if(GPU_API STREQUAL "CUDA")
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
-  # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
-  if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") 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 3.0) is supported by CUDA 5 to CUDA 10.2
-  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
-  endif()
-  # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
-  if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
-    string(APPEND GPU_CUDA_GENCODE " -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_EQUAL "6.0")
-    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_EQUAL "8.0")
-    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_EQUAL "9.0")
-    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_EQUAL "10.0")
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
-  endif()
-  # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
-  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
-  endif()
-  # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
-  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
-    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
-  endif()
+
+  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    message(WARNING "Unsupported CUDA version. Use at your own risk.")
+    message(WARNING "Untested CUDA Toolkit version. Use at your own risk")
+  else()
+    # Fermi (GPU Arch 2.x) is supported by CUDA 3.2 to CUDA 8.0
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "3.2") 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 3.0) is supported by CUDA 5 to CUDA 10.2
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+    endif()
+    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+      string(APPEND GPU_CUDA_GENCODE " -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_EQUAL "6.0")
+      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_EQUAL "8.0")
+      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_EQUAL "9.0")
+      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_EQUAL "10.0")
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+    endif()
+    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+    endif()
+    # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+    endif()
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -154,7 +157,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   endif()
   option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
   mark_as_advanced(USE_STATIC_OPENCL_LOADER)
-  if (USE_STATIC_OPENCL_LOADER)
+  if(USE_STATIC_OPENCL_LOADER)
     include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)
@@ -214,13 +217,20 @@ elseif(GPU_API STREQUAL "OPENCL")
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
-          set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to which HIP has been installed")
+          set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
       else()
-          set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to which HIP has been installed")
+          set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
       endif()
   endif()
-  set(CMAKE_MODULE_PATH "${HIP_PATH}/cmake" ${CMAKE_MODULE_PATH})
-  find_package(HIP REQUIRED)
+  if(NOT DEFINED ROCM_PATH)
+      if(NOT DEFINED ENV{ROCM_PATH})
+          set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
+      else()
+          set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
+      endif()
+  endif()
+  list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+  find_package(hip REQUIRED)
   option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
 
   if(NOT DEFINED HIP_PLATFORM)
@@ -322,10 +332,11 @@ elseif(GPU_API STREQUAL "HIP")
 
   set_directory_properties(PROPERTIES ADDITIONAL_MAKE_CLEAN_FILES "${LAMMPS_LIB_BINARY_DIR}/gpu/*_cubin.h ${LAMMPS_LIB_BINARY_DIR}/gpu/*.cu.cpp")
 
-  hip_add_library(gpu STATIC ${GPU_LIB_SOURCES})
+  add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
   target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
   target_compile_definitions(gpu PRIVATE -DUSE_HIP)
+  target_link_libraries(gpu PRIVATE hip::host)
 
   if(HIP_USE_DEVICE_SORT)
     # add hipCUB
@@ -374,8 +385,9 @@ elseif(GPU_API STREQUAL "HIP")
     endif()
   endif()
 
-  hip_add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
+  add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
+  target_link_libraries(hip_get_devices hip::host)
 
   if(HIP_PLATFORM STREQUAL "nvcc")
     target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)

cmake/Modules/Packages/INTEL.cmake

@@ -3,9 +3,9 @@ if(NOT FOUND_IMMINTRIN)
   message(FATAL_ERROR "immintrin.h header not found, Intel package won't work without it")
 endif()
 
-target_compile_definitions(lammps PRIVATE -DLMP_USER_INTEL)
+target_compile_definitions(lammps PRIVATE -DLMP_INTEL)
 
-set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by USER-INTEL (cpu or knl)")
+set(INTEL_ARCH "cpu" CACHE STRING "Architectures used by 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)
@@ -40,10 +40,10 @@ 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}")
+    message(FATAL_ERROR "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")
+  message(WARNING "INTEL gives best performance with Intel compilers")
 endif()
 
 find_package(TBB_MALLOC QUIET)
@@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND)
 else()
   target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
   endif()
 endif()
 
@@ -65,12 +65,12 @@ else()
 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")
+  message(FATAL_ERROR "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")
+    message(FATAL_ERROR "Must use Intel compiler with 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\\\"\"")
@@ -91,26 +91,26 @@ else()
 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(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL)
+set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp
+                       ${INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                       ${INTEL_SOURCES_DIR}/intel_buffers.cpp
+                       ${INTEL_SOURCES_DIR}/nbin_intel.cpp
+                       ${INTEL_SOURCES_DIR}/npair_intel.cpp)
 
-set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${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)
+# detect styles which have a INTEL version
+RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES)
+RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h)
+RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h)
+RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h)
 
-get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+get_property(INTEL_SOURCES GLOBAL PROPERTY 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)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+  RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
-target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
-target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})
+target_sources(lammps PRIVATE ${INTEL_SOURCES})
+target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,6 +1,8 @@
 ########################################################################
 # As of version 3.3.0 Kokkos requires C++14
-set(CMAKE_CXX_STANDARD 14)
+if(CMAKE_CXX_STANDARD LESS 14)
+  set(CMAKE_CXX_STANDARD 14)
+endif()
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
@@ -37,8 +39,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -58,7 +60,7 @@ if(DOWNLOAD_KOKKOS)
   target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.4.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.4.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -74,11 +76,12 @@ else()
   target_link_libraries(lammps PRIVATE kokkos)
   target_link_libraries(lmp PRIVATE kokkos)
 endif()
-target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
+target_compile_definitions(lammps PUBLIC $<BUILD_INTERFACE:LMP_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_map_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
@@ -99,7 +102,7 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
-    if(NOT ${FFT} STREQUAL "KISS")
+    if(NOT (FFT STREQUAL "KISS"))
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()
@@ -116,7 +119,7 @@ RegisterNBinStyle(${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)
+if(PKG_DPD-REACT)
   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)
@@ -126,4 +129,4 @@ endif()
 get_property(KOKKOS_PKG_SOURCES GLOBAL PROPERTY KOKKOS_PKG_SOURCES)
 
 target_sources(lammps PRIVATE ${KOKKOS_PKG_SOURCES})
-target_include_directories(lammps PRIVATE ${KOKKOS_PKG_SOURCES_DIR})
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${KOKKOS_PKG_SOURCES_DIR}>)

cmake/Modules/Packages/LATTE.cmake

@@ -19,6 +19,14 @@ if(DOWNLOAD_LATTE)
   set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
   mark_as_advanced(LATTE_URL)
   mark_as_advanced(LATTE_MD5)
+
+  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
+  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
+  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
+  endif()
+
   include(ExternalProject)
   ExternalProject_Add(latte_build
     URL     ${LATTE_URL}

cmake/Modules/Packages/MACHDYN.cmake

@@ -7,8 +7,8 @@ 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")
-  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
-  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "609286804b0f79be622ccf7f9ff2b660" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
@@ -30,3 +30,8 @@ else()
   endif()
   target_link_libraries(lammps PRIVATE Eigen3::Eigen)
 endif()
+
+# PGI/Nvidia compiler internals collide with vector intrinsics support in Eigen3
+if((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+  target_compile_definitions(lammps PRIVATE -DEIGEN_DONT_VECTORIZE)
+endif()

cmake/Modules/Packages/MDI.cmake

@@ -0,0 +1,118 @@
+find_package(mdi QUIET)
+if(${mdi_FOUND})
+  set(DOWNLOAD_MDI_DEFAULT OFF)
+else()
+  set(DOWNLOAD_MDI_DEFAULT ON)
+endif()
+option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
+
+if(DOWNLOAD_MDI)
+  message(STATUS "MDI download requested - we will build our own")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
+  mark_as_advanced(MDI_URL)
+  mark_as_advanced(MDI_MD5)
+  enable_language(C)
+
+  # only ON/OFF are allowed for "mpi" flag when building MDI library
+  # so translate boolean value of BUILD_MPI
+  # always disable MPI when cross-compiling to Windows.
+  if((BUILD_MPI) AND NOT((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING))
+    set(MDI_USE_MPI ON)
+  else()
+    set(MDI_USE_MPI OFF)
+  endif()
+
+  # detect if we have python development support and thus can enable python plugins
+  set(MDI_USE_PYTHON_PLUGINS OFF)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonLibs QUIET) # Deprecated since version 3.12
+    if(PYTHONLIBS_FOUND)
+      set(MDI_USE_PYTHON_PLUGINS ON)
+    endif()
+  else()
+    find_package(Python QUIET COMPONENTS Development)
+    if(Python_Development_FOUND)
+      set(MDI_USE_PYTHON_PLUGINS ON)
+    endif()
+  endif()
+
+  # download/ build MDI library
+  # always build static library with -fpic
+  # support cross-compilation and ninja-build
+  include(ExternalProject)
+  ExternalProject_Add(mdi_build
+    URL     ${MDI_URL}
+    URL_MD5 ${MDI_MD5}
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
+    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    -Dlanguage=C
+    -Dlibtype=STATIC
+    -Dmpi=${MDI_USE_MPI}
+    -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
+    UPDATE_COMMAND ""
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    )
+
+  # where is the compiled library?
+  ExternalProject_get_property(mdi_build BINARY_DIR)
+  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
+  # workaround for older CMake versions
+  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
+
+  # create imported target for the MDI library
+  add_library(LAMMPS::MDI UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::MDI mdi_build)
+  set_target_properties(LAMMPS::MDI PROPERTIES
+    IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
+    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
+    )
+
+  set(MDI_DEP_LIBS "")
+  # if compiling with python plugins we need
+  # to add python libraries as dependency.
+  if(MDI_USE_PYTHON_PLUGINS)
+    if(CMAKE_VERSION VERSION_LESS 3.12)
+      list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
+    else()
+      list(APPEND MDI_DEP_LIBS Python::Python)
+    endif()
+
+  endif()
+  # need to add support for dlopen/dlsym, except when compiling for Windows.
+  if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+    list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")
+  endif()
+  if(MDI_DEP_LIBS)
+    set_target_properties(LAMMPS::MDI PROPERTIES
+      IMPORTED_LINK_INTERFACE_LIBRARIES "${MDI_DEP_LIBS}")
+  endif()
+
+  target_link_libraries(lammps PRIVATE LAMMPS::MDI)
+  target_link_libraries(lmp PRIVATE LAMMPS::MDI)
+
+else()
+
+  find_package(mdi)
+  if(NOT mdi_FOUND)
+    message(FATAL_ERROR "MDI library not found. Help CMake to find it "
+      "by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
+      "to download and compile it")
+  endif()
+
+  # Link the lammps library against MDI
+  target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
+
+  # Link the lammps executable against MDI
+  target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
+endif()
+
+target_compile_definitions(lammps PRIVATE -DLMP_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_MDI)

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,4 +1,4 @@
-if(LAMMPS_SIZES STREQUAL BIGBIG)
+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)

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -0,0 +1,133 @@
+find_package(N2P2 QUIET)
+if(N2P2_FOUND)
+  set(DOWNLOAD_N2P2_DEFAULT OFF)
+else()
+  set(DOWNLOAD_N2P2_DEFAULT ON)
+endif()
+option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
+if(DOWNLOAD_N2P2)
+  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
+  set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
+  mark_as_advanced(N2P2_URL)
+  mark_as_advanced(N2P2_MD5)
+
+  # adjust settings from detected compiler to compiler platform in n2p2 library
+  # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang"))
+    set(N2P2_COMP llvm)
+    set(N2P2_CXX_STD "-std=c++11")
+  elseif((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
+    set(N2P2_COMP intel)
+    set(N2P2_CXX_STD "-std=c++11")
+  elseif(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+    set(N2P2_COMP gnu)
+    set(N2P2_CXX_STD "-std=gnu++11")
+  elseif((CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+    set(N2P2_COMP gnu)
+    set(N2P2_CXX_STD "--c++11")
+  else() # default
+    set(N2P2_COMP "")
+  endif()
+
+  # pass on archive creator command. prefer compiler specific version, if set.
+  # important when using cross compiler.
+  if(CMAKE_CXX_COMPILER_AR)
+    set(N2P2_AR ${CMAKE_CXX_COMPILER_AR})
+  else()
+    set(N2P2_AR ${CMAKE_AR})
+  endif()
+
+  # adjust compilation of n2p2 library to whether MPI is requested in LAMMPS or not
+  # need special care for compiling for MPICH2 with Linux-to-Windows cross compiler.
+  if(NOT BUILD_MPI)
+    set(N2P2_PROJECT_OPTIONS "-DN2P2_NO_MPI")
+  else()
+    # get path to MPI include directory when cross-compiling to windows
+    if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+      get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
+      set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
+    endif()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+      get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
+      set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
+      set(MPI_CXX_COMPILER ${CMAKE_CXX_COMPILER})
+    endif()
+  endif()
+
+  # prefer GNU make, if available. N2P2 lib seems to need it.
+  find_program(N2P2_MAKE NAMES gmake make)
+
+  # override compiler (optimization) flags in n2p2 library to flags used for LAMMPS
+  # specifically -march=native can result in problems when compiling on HPC clusters or with a cross compiler
+  # this convoluted way gets correct quoting/escaping when configuring the external project
+  string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+  set(N2P2_BUILD_FLAGS "${CMAKE_SHARED_LIBRARY_CXX_FLAGS} ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}} ${N2P2_CXX_STD}")
+  set(N2P2_BUILD_OPTIONS INTERFACES=LAMMPS COMP=${N2P2_COMP} "PROJECT_OPTIONS=${N2P2_PROJECT_OPTIONS}" "PROJECT_DEBUG="
+    "PROJECT_CC=${CMAKE_CXX_COMPILER}" "PROJECT_MPICC=${MPI_CXX_COMPILER}" "PROJECT_CFLAGS=${N2P2_BUILD_FLAGS}"
+    "PROJECT_AR=${N2P2_AR}")
+  # echo final flag for debugging
+  message(STATUS "N2P2 BUILD OPTIONS: ${N2P2_BUILD_OPTIONS}")
+
+  # must have "sed" command to compile n2p2 library (for now)
+  find_program(HAVE_SED sed)
+  if(NOT HAVE_SED)
+    message(FATAL_ERROR "Must have 'sed' program installed to compile 'n2p2' library for ML-HDNNP package")
+  endif()
+
+  # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
+  include(ExternalProject)
+  ExternalProject_Add(n2p2_build
+    URL     ${N2P2_URL}
+    URL_MD5 ${N2P2_MD5}
+    UPDATE_COMMAND ""
+    CONFIGURE_COMMAND ""
+    PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
+    BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
+    BUILD_ALWAYS YES
+    INSTALL_COMMAND ""
+    BUILD_IN_SOURCE 1
+    LOG_BUILD ON
+    SOURCE_SUBDIR src/
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libnnp.a <SOURCE_DIR>/lib/libnnpif.a
+    )
+
+  # create imported target LAMMPS::N2P2 from two libraries nnp and nnpif
+  ExternalProject_get_property(n2p2_build SOURCE_DIR)
+  # n2p2 core library "libnnp"
+  add_library(LAMMPS::N2P2::LIBNNP UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::N2P2::LIBNNP PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnp.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
+  # n2p2 interface library "libnnpif"
+  add_library(LAMMPS::N2P2::LIBNNPIF UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libnnpif.a"
+    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include")
+  # nnpif library has MPI calls if MPI is enabled, so we must link with MPI libs
+  if(BUILD_MPI)
+    set_target_properties(LAMMPS::N2P2::LIBNNPIF PROPERTIES
+      INTERFACE_LINK_LIBRARIES MPI::MPI_CXX)
+    if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+      add_dependencies(LAMMPS::N2P2::LIBNNPIF MPI::MPI_CXX)
+    endif()
+  endif()
+
+  # final step to define imported target
+  add_library(LAMMPS::N2P2 INTERFACE IMPORTED)
+  set_property(TARGET LAMMPS::N2P2 PROPERTY
+    INTERFACE_LINK_LIBRARIES LAMMPS::N2P2::LIBNNPIF LAMMPS::N2P2::LIBNNP)
+  target_link_libraries(lammps PRIVATE LAMMPS::N2P2)
+
+  add_dependencies(LAMMPS::N2P2 n2p2_build)
+  # work around issues with older CMake versions
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+  file(MAKE_DIRECTORY "${SOURCE_DIR}/lib")
+else()
+  find_package(N2P2)
+  if(NOT N2P2_FOUND)
+    message(FATAL_ERROR "n2p2 not found, help CMake to find it by setting N2P2_DIR, or set DOWNLOAD_N2P2=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE N2P2::N2P2)
+  include(${N2P2_CMAKE_EXTRAS})
+endif()

cmake/Modules/Packages/ML-IAP.cmake

@@ -1,4 +1,4 @@
-# if PYTHON package is included we may also include Python support in MLIAP
+# if PYTHON package is included we may also include Python support in ML-IAP
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
@@ -7,25 +7,25 @@ if(PKG_PYTHON)
   endif()
 endif()
 
-option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
+option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
   if(NOT PKG_PYTHON)
-    message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
+    message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
   if(CMAKE_VERSION VERSION_LESS 3.12)
     if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   else()
     if(Python_VERSION VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+      message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
     endif()
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)
+  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
   get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

cmake/Modules/Packages/ML-PACE.cmake

@@ -14,13 +14,12 @@ execute_process(
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
 
-
 file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
 file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
 list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
 
 add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
-set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
 target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
 target_link_libraries(lammps PRIVATE pace)
 

cmake/Modules/Packages/ML-QUIP.cmake

@@ -0,0 +1,70 @@
+enable_language(Fortran)
+find_package(QUIP QUIET)
+
+if(QUIP_FOUND)
+  set(DOWNLOAD_QUIP_DEFAULT OFF)
+else()
+  set(DOWNLOAD_QUIP_DEFAULT ON)
+endif()
+option(DOWNLOAD_QUIP "Download the QUIP library instead of using an already installed one" ${DOWNLOAD_QUIP_DEFAULT})
+if(DOWNLOAD_QUIP)
+  string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
+  set(temp "F77 = ${CMAKE_Fortran_COMPILER}\nF90 = ${CMAKE_Fortran_COMPILER}\nF95 = ${CMAKE_Fortran_COMPILER}\n")
+  set(temp "${temp}CC=${CMAKE_C_COMPILER}\nCPLUSPLUS=${CMAKE_CXX_COMPILER}\nLINKER=${CMAKE_Fortran_COMPILER}\n")
+  if(CMAKE_Fortran_COMPILER_ID STREQUAL Intel)
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
+    set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
+  elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
+    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
+    set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
+    set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
+  else()
+    message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
+  endif()
+  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}MATH_LINKOPTS=")
+  foreach(flag ${BLAS_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  foreach(flag ${LAPACK_LIBRARIES})
+    set(temp "${temp} ${flag}")
+  endforeach()
+  set(temp "${temp}\n")
+  set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
+  set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
+  set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
+  set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
+  set(temp "${temp}HAVE_MBD=0\nHAVE_TTM_NF=0\nHAVE_CH4=0\nHAVE_NETCDF4=0\nHAVE_MDCORE=0\nHAVE_ASAP=0\n")
+  set(temp "${temp}HAVE_CGAL=0\nHAVE_METIS=0\nHAVE_LMTO_TBE=0\nHAVE_SCALAPACK=0\n")
+  file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
+
+  message(STATUS "QUIP download via git requested - we will build our own")
+  # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
+  # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
+  include(ExternalProject)
+  ExternalProject_Add(quip_build
+    GIT_REPOSITORY "https://github.com/libAtoms/QUIP/"
+    GIT_TAG origin/public
+    GIT_SHALLOW YES
+    GIT_PROGRESS YES
+    PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
+    CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
+    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    INSTALL_COMMAND ""
+    BUILD_IN_SOURCE YES
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
+  )
+  ExternalProject_get_property(quip_build SOURCE_DIR)
+  add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
+  set_target_properties(LAMMPS::QUIP PROPERTIES
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
+    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
+  target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
+  add_dependencies(LAMMPS::QUIP quip_build)
+else()
+  find_package(QUIP REQUIRED)
+  target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})
+endif()

cmake/Modules/Packages/MOLFILE.cmake

@@ -1,5 +1,7 @@
 set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to VMD molfile plugin headers")
-set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
 add_library(molfile INTERFACE)
-target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
+target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIR})
+if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
+endif()
 target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/MSCG.cmake

@@ -12,6 +12,13 @@ if(DOWNLOAD_MSCG)
   mark_as_advanced(MSCG_URL)
   mark_as_advanced(MSCG_MD5)
 
+  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
+  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
+  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+    message(FATAL_ERROR "Cannot compile downloaded MSCG library due to a technical limitation")
+  endif()
+
   include(ExternalProject)
   ExternalProject_Add(mscg_build
     URL     ${MSCG_URL}

cmake/Modules/Packages/NETCDF.cmake

@@ -1,4 +1,4 @@
-# USER-NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
+# NETCDF can use NetCDF, Parallel NetCDF (PNetCDF), or both. At least one necessary.
 # NetCDF library enables dump style "netcdf", while PNetCDF enables dump style "netcdf/mpiio"
 
 # may use NetCDF or PNetCDF with MPI, but must have NetCDF without

cmake/Modules/Packages/OPENMP.cmake

@@ -0,0 +1,40 @@
+  set(OPENMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/OPENMP)
+  set(OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/thr_data.cpp
+                       ${OPENMP_SOURCES_DIR}/thr_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_nh_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
+                       ${OPENMP_SOURCES_DIR}/domain_omp.cpp)
+  target_compile_definitions(lammps PRIVATE -DLMP_OPENMP)
+  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${OPENMP_SOURCES}")
+
+  # detects styles which have OPENMP version
+  RegisterStylesExt(${OPENMP_SOURCES_DIR} omp OMP_SOURCES)
+  RegisterFixStyle(${OPENMP_SOURCES_DIR}/fix_omp.h)
+
+  get_property(OPENMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
+
+  # manually add package dependent source files from OPENMP that do not provide styles
+
+  if(PKG_ASPHERE)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
+  endif()
+
+  if(PKG_RIGID)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
+  endif()
+
+  if(PKG_REAXFF)
+    list(APPEND OPENMP_SOURCES ${OPENMP_SOURCES_DIR}/reaxff_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
+  endif()
+
+  target_sources(lammps PRIVATE ${OPENMP_SOURCES})
+  target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR})

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)

cmake/Modules/Packages/QEQ.cmake

@@ -1,18 +1,13 @@
 # Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
 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)
 
+get_property(hlist GLOBAL PROPERTY FIX)
 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)
+  list(REMOVE_ITEM hlist ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
-set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+set_property(GLOBAL PROPERTY FIX "${hlist}")
 
-foreach(MY_HEADER ${QEQ_HEADERS})
-  AddStyleHeader(${MY_HEADER} FIX)
-endforeach()
-
-get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
-target_sources(lammps PRIVATE ${QEQ_SOURCES})
 target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

cmake/Modules/Packages/SCAFACOS.cmake

@@ -23,6 +23,11 @@ if(DOWNLOAD_SCAFACOS)
   file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
           EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
 
+  find_program(HAVE_PATCH patch)
+  if(NOT HAVE_PATCH)
+    message(FATAL_ERROR "The 'patch' program is required to build the ScaFaCoS library")
+  endif()
+
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
     URL     ${SCAFACOS_URL}

cmake/Modules/Packages/USER-MDI.cmake

@@ -1,66 +0,0 @@
-find_package(mdi QUIET)
-if(${mdi_FOUND})
-  set(DOWNLOAD_MDI_DEFAULT OFF)
-else()
-  set(DOWNLOAD_MDI_DEFAULT ON)
-endif()
-option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
-
-if(DOWNLOAD_MDI)
-  message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
-  mark_as_advanced(MDI_URL)
-  mark_as_advanced(MDI_MD5)
-
-  set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
-
-  include(ExternalProject)
-  message(STATUS "Building mdi.")
-  ExternalProject_Add(mdi_external
-      URL     ${MDI_URL}
-      URL_MD5 ${MDI_MD5}
-      UPDATE_COMMAND ""
-      CMAKE_ARGS ${CMAKE_REQUEST_PIC}
-                 -DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
-                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-                 -DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
-                 -DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
-                 -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
-                 -Dlanguage=C
-      CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
-                       -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
-                       -DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
-
-  # Link the lammps library against MDI
-  target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
-  target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
-  target_link_libraries(lammps PRIVATE mdi)
-  add_dependencies(lammps mdi_external)
-
-  # Link the lammps executable against MDI
-  target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
-  target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
-  target_link_libraries(lmp PRIVATE mdi)
-  add_dependencies(lmp mdi_external)
-
-else()
-
-  find_package(mdi)
-  if(NOT mdi_FOUND)
-    message(FATAL_ERROR "MDI library not found. Help CMake to find it "
-      "by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
-      "to download and compile it")
-  endif()
-
-  # Link the lammps library against MDI
-  target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
-  target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
-
-  # Link the lammps executable against MDI
-  target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
-  target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
-endif()
-
-target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
-target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

cmake/Modules/Packages/USER-OMP.cmake

@@ -1,40 +0,0 @@
-  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
-                       ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
-  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
-  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${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()
-
-  target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
-  target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

cmake/Modules/Packages/USER-QUIP.cmake

@@ -1,3 +0,0 @@
-enable_language(Fortran)
-find_package(QUIP REQUIRED)
-target_link_libraries(lammps PRIVATE QUIP::QUIP ${LAPACK_LIBRARIES})

cmake/Modules/Packages/VORONOI.cmake

@@ -26,6 +26,11 @@ if(DOWNLOAD_VORO)
     set(VORO_BUILD_OPTIONS CXX=${CMAKE_CXX_COMPILER} CFLAGS=${VORO_BUILD_CFLAGS})
   endif()
 
+  find_program(HAVE_PATCH patch)
+  if(NOT HAVE_PATCH)
+    message(FATAL_ERROR "The 'patch' program is required to build the voro++ library")
+  endif()
+
   ExternalProject_Add(voro_build
     URL     ${VORO_URL}
     URL_MD5 ${VORO_MD5}

cmake/Modules/PreventInSourceBuilds.cmake

@@ -9,7 +9,7 @@ function(prevent_in_source_builds)
   get_filename_component(bindir "${CMAKE_BINARY_DIR}" REALPATH)
 
   # disallow in-source builds
-  if("${srcdir}" STREQUAL "${bindir}" OR "${srcdir2}" STREQUAL "${bindir}" OR "${srcdir3}" STREQUAL "${bindir}")
+  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. \

cmake/Modules/Testing.cmake

@@ -19,11 +19,11 @@ if(ENABLE_TESTING)
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
   # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
-  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-      AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
-    if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
-        OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
+  if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+        OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+        OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@@ -58,7 +58,7 @@ if(ENABLE_TESTING)
 endif()
 
 # Compiler specific features for testing
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
   mark_as_advanced(ENABLE_COVERAGE)
   if(ENABLE_COVERAGE)
@@ -83,7 +83,7 @@ mark_as_advanced(ENABLE_IWYU)
 if(ENABLE_IWYU)
   # enforce these settings
   set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
-  if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
+  if(NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
     message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
   endif()
   # detect the "native" header folder so we can include them first
@@ -91,7 +91,7 @@ if(ENABLE_IWYU)
   string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
   find_program(IWYU_EXE NAMES include-what-you-use iwyu)
   find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
-  if (IWYU_EXE AND IWYU_TOOL)
+  if(IWYU_EXE AND IWYU_TOOL)
     add_custom_target(
       iwyu
       ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp

cmake/Modules/Tools.cmake

@@ -9,14 +9,16 @@ if(BUILD_TOOLS)
     check_language(Fortran)
     if(CMAKE_Fortran_COMPILER)
       enable_language(Fortran)
-      add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
+      add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f90)
       target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
-      install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
+      add_executable(micelle2d.x ${LAMMPS_TOOLS_DIR}/micelle2d.f90)
+      target_link_libraries(micelle2d.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
+      install(TARGETS chain.x micelle2d.x DESTINATION ${CMAKE_INSTALL_BINDIR})
     else()
-      message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
+      message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x' and 'micelle2d.x'")
     endif()
   else()
-    message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
+    message(WARNING "CMake build doesn't support Fortran, skipping build of 'chain.x' and 'micelle2d.x'")
   endif()
 
   enable_language(C)
@@ -45,7 +47,7 @@ if(BUILD_LAMMPS_SHELL)
   target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
 
   # workaround for broken readline pkg-config file on FreeBSD
-  if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
+  if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
     target_include_directories(lammps-shell PRIVATE /usr/local/include)
   endif()
   target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)

cmake/Modules/YAML.cmake

@@ -6,15 +6,27 @@ set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of li
 mark_as_advanced(YAML_URL)
 mark_as_advanced(YAML_MD5)
 
+# support cross-compilation to windows
+if(CMAKE_CROSSCOMPILING AND (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(YAML_CROSS_HOST --host=i686-mingw64)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(YAML_CROSS_HOST --host=x86_64-mingw64)
+  else()
+    message(FATAL_ERROR "Unsupported cross-compilation "
+      " for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}"
+      " on ${CMAKE_HOST_SYSTEM}/${CMAKE_HOST_SYSTEM_PROCESSOR}")
+  endif()
+endif()
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
                     URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
-                                      CXX=${CMAKE_CXX_COMPILER}
-                                      CC=${CMAKE_C_COMPILER}
-                                      --prefix=<INSTALL_DIR> --disable-shared
+                                      CXX=${CMAKE_CXX_COMPILER} CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared ${YAML_CROSS_HOST}
                     BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 

cmake/iwyu/iwyu-extra-map.imp

@@ -1,7 +1,28 @@
 [
-  { include: [ "<bits/types/struct_rusage.h>", private, "<sys/resource.h>", public ] },
-  { include: [ "<bits/exception.h>", public, "<exception>", public ] },
   { include: [ "@<Eigen/.*>", private, "<Eigen/Eigen>", public ] },
   { include: [ "@<gtest/.*>", private, "\"gtest/gtest.h\"", public ] },
   { include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
+  { include: [ "@<gmock/.*>", private, "\"gmock/gmock.h\"", public ] },
+  { include: [ "@<(cell|c_loops|container).hh>", private, "<voro++.hh>", public ] },
+  { include: [ "@\"atom_vec_.*.h\"", public, "\"style_atom.h\"", public ] },
+  { include: [ "@\"body_.*.h\"", public, "\"style_body.h\"", public ] },
+  { include: [ "@\"compute_.*.h\"", public, "\"style_compute.h\"", public ] },
+  { include: [ "@\"fix_.*.h\"", public, "\"style_fix.h\"", public ] },
+  { include: [ "@\"dump_.*.h\"", public, "\"style_dump.h\"", public ] },
+  { include: [ "@\"min_.*.h\"", public, "\"style_minimize.h\"", public ] },
+  { include: [ "@\"reader_.*.h\"", public, "\"style_reader.h\"", public ] },
+  { include: [ "@\"region_.*.h\"", public, "\"style_region.h\"", public ] },
+  { include: [ "@\"pair_.*.h\"", public, "\"style_pair.h\"", public ] },
+  { include: [ "@\"angle_.*.h\"", public, "\"style_angle.h\"", public ] },
+  { include: [ "@\"bond_.*.h\"", public, "\"style_bond.h\"", public ] },
+  { include: [ "@\"dihedral_.*.h\"", public, "\"style_dihedral.h\"", public ] },
+  { include: [ "@\"improper_.*.h\"", public, "\"style_improper.h\"", public ] },
+  { include: [ "@\"kspace_.*.h\"", public, "\"style_kspace.h\"", public ] },
+  { include: [ "@\"nbin_.*.h\"", public, "\"style_nbin.h\"", public ] },
+  { include: [ "@\"npair_.*.h\"", public, "\"style_npair.h\"", public ] },
+  { include: [ "@\"nstenci_.*.h\"", public, "\"style_nstencil.h\"", public ] },
+  { include: [ "@\"ntopo_.*.h\"", public, "\"style_ntopo.h\"", public ] },
+  { include: [ "<float.h>",   public, "<cfloat>", public ] },
+  { include: [ "<limits.h>",  public, "<climits>", public ] },
+  { include: [ "<bits/types/struct_tm.h>", private, "<ctime>", public ] },
 ]

cmake/pkgconfig/liblammps.pc.in

@@ -24,7 +24,7 @@ includedir=@CMAKE_INSTALL_FULL_INCLUDEDIR@
 
 Name: liblammps@LAMMPS_MACHINE@
 Description: Large-scale Atomic/Molecular Massively Parallel Simulator Library
-URL: http://lammps.sandia.gov
+URL: https://www.lammps.org
 Version: @PROJECT_VERSION@
 Requires:
 Libs: -L${libdir} -llammps@LAMMPS_MACHINE@

cmake/presets/all_off.cmake

@@ -1,17 +1,96 @@
-# preset that turns on all existing packages off. can be used to reset
+# 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 MESSAGE MISC MLIAP MOLECULE
-  MPIIO MSCG OPT PERI PLUGIN 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-MESODPD USER-MESONT USER-MGPT
-  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
-  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-  USER-VTK USER-YAFF)
+set(ALL_PACKAGES
+  ADIOS
+  ASPHERE
+  ATC
+  AWPMD
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,19 +1,98 @@
-# 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
+# Preset that turns on all existing packages. Using the combination
+# of 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 MESSAGE MISC MLIAP MOLECULE
-  MPIIO MSCG OPT PERI PLUGIN 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-MESODPD USER-MESONT USER-MGPT
-  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
-  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
-  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-  USER-VTK USER-YAFF)
+set(ALL_PACKAGES
+  ADIOS
+  ASPHERE
+  ATC
+  AWPMD
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -1,13 +1,26 @@
 # preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
 
+# prefer flang over gfortran, if available
+find_program(CLANG_FORTRAN NAMES flang gfortran f95)
+set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+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)

cmake/presets/download.cmake

@@ -1,7 +1,7 @@
-# preset that turns on packages with automatic downloads of sources of potentials
-# compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
+# Preset that turns on packages with automatic downloads of sources or potentials.
+# Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
 
-set(ALL_PACKAGES KIM LATTE MSCG VORONOI USER-PLUMED USER-SCAFACOS USER-SMD USER-MESONT)
+set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -9,9 +9,11 @@ endforeach()
 
 set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
+set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_PLUMED ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_SCAFACOS ON CACHE BOOL "" FORCE)
 

cmake/presets/gcc.cmake

@@ -1,11 +1,23 @@
-# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
+# preset that will explicitly request gcc/g++ compilers with support for MPI and OpenMP
 
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(MPI_CXX "g++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(MPI_C "gcc" CACHE STRING "" FORCE)
+set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
+set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
 set(OpenMP_C "gcc" CACHE STRING "" FORCE)

cmake/presets/hip.cmake

@@ -1,12 +1,26 @@
-# preset that will enable hipcc plus gcc with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable hipcc plus gcc/gfortran with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER gfortran CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
-set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
+set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/hip_amd.cmake

@@ -0,0 +1,30 @@
+# preset that will enable hip (clang/clang++) with support for MPI and OpenMP (on Linux boxes)
+
+# prefer flang over gfortran, if available
+find_program(CLANG_FORTRAN NAMES flang gfortran f95)
+set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+
+set(CMAKE_CXX_COMPILER "hipcc" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "hipcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
+set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/intel.cmake

@@ -3,10 +3,20 @@
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icc" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -1,13 +1,76 @@
-set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP 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-MESODPD
-                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
-                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-                 USER-YAFF)
+set(WIN_PACKAGES
+  ASPHERE
+  ATC
+  AWPMD
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  INTEL
+  INTERLAYER
+  KSPACE
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-SNAP
+  ML-RANN
+  MOFFF
+  MOLECULE
+  MOLFILE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  POEMS
+  PTM
+  QEQ
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -16,7 +79,7 @@ endforeach()
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
   set(PKG_MPIIO ON CACHE BOOL "" FORCE)
-  set(PKG_USER-LB ON CACHE BOOL "" FORCE)
+  set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)

cmake/presets/most.cmake

@@ -2,13 +2,66 @@
 # 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 BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
-        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
-        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
-        USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
-        USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
-        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
+set(ALL_PACKAGES
+  ASPHERE
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  INTERLAYER
+  KSPACE
+  MACHDYN
+  MANYBODY
+  MC
+  MEAM
+  MISC
+  ML-IAP
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  POEMS
+  PYTHON
+  QEQ
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -1,11 +1,34 @@
 # 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 MESSAGE MPIIO MSCG
-  PYTHON VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
-  USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
-  USER-SMD USER-VTK)
+set(PACKAGES_WITH_LIB
+  ADIOS
+  ATC
+  AWPMD
+  COMPRESS
+  GPU
+  H5MD
+  KIM
+  KOKKOS
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MDI
+  MESONT
+  MESSAGE
+  ML-HDNNP
+  ML-PACE
+  ML-QUIP
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  PLUMED
+  PYTHON
+  QMMM
+  SCAFACOS
+  VORONOI
+  VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/oneapi.cmake

@@ -1,12 +1,22 @@
-# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP and Fortran (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
 
+unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
 set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)

cmake/presets/pedantic.cmake

@@ -0,0 +1,26 @@
+# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Werror=vla -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_CXX "g++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(MPI_C "gcc" CACHE STRING "" FORCE)
+set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -Wno-maybe-uninitialized -g" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -Wno-maybe-uninitialized -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_C_FLAGS_RELEASE "-Wall -O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
+set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

doc/Makefile

@@ -10,7 +10,6 @@ endif
 BUILDDIR       = ${CURDIR}
 RSTDIR         = $(BUILDDIR)/src
 VENV           = $(BUILDDIR)/docenv
-TXT2RST        = $(VENV)/bin/txt2rst
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
@@ -59,7 +58,7 @@ SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiproc
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check xmlgen
+.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen
 
 # ------------------------------------------
 
@@ -68,7 +67,6 @@ help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html          create HTML pages in html dir"
 	@echo "  pdf           create 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)"
@@ -185,13 +183,6 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -rf latex/PDF/.[sg]*
 	@echo "Build finished. Manual.pdf is in this directory."
 
-fetch:
-	@rm -rf html_www Manual_www.pdf
-	@curl -s -o Manual_www.pdf http://lammps.sandia.gov/doc/Manual.pdf
-	@curl -s -o lammps-doc.tar.gz http://lammps.sandia.gov/tars/lammps-doc.tar.gz
-	@tar xzf lammps-doc.tar.gz
-	@rm -f lammps-doc.tar.gz
-
 anchor_check : $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ;\
@@ -213,6 +204,9 @@ package_check : $(VENV)
 		deactivate ;\
 	)
 
+char_check :
+	@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in
@@ -236,9 +230,9 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
 
-$(TXT2RST) $(ANCHORCHECK): $(VENV)
+$(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
 		(cd utils/converters;\

doc/README

@@ -25,16 +25,11 @@ github-development-workflow.md   notes on the LAMMPS development workflow
 include-file-conventions.md      notes on LAMMPS' include file conventions
 documentation_conventions.md     notes on writing documentation for LAMMPS
 
-If you downloaded a LAMMPS tarball from lammps.sandia.gov, then the html
+If you downloaded a LAMMPS tarball from www.lammps.org, then the html
 folder and the PDF manual should be included. If you downloaded LAMMPS
-from GitHub then you either need to download them or build them.
+from GitHub then you either need to build them.
 
-(a) You can "fetch" the current HTML and PDF files from the LAMMPS web
-site.  Just type "make fetch".  This should create a html_www directory
-and Manual_www.pdf file.  These will always represent the latest published
-patch/development version of LAMMPS.
-
-(b) You can build the HTML and PDF files yourself, by typing "make html"
+You can build the HTML and PDF files yourself, by typing "make html"
 or by "make pdf", respectively.  This requires various tools and files.
 Some of them have to be installed (more on that below).  For the rest the
 build process will attempt to download and install into a python virtual
@@ -78,4 +73,4 @@ the tool 'ebook-convert' from the 'calibre' e-book management software
 ----------------
 
 More details this can be found in the manual itself. The online
-version is at: https://lammps.sandia.gov/doc/Manual_build.html
+version is at: https://docs.lammps.org/Build_manual.html

doc/github-development-workflow.md

@@ -6,7 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2018-12-19.
+adapt accordingly. Last change 2021-09-02.
 
 ## Table of Contents
 
@@ -23,10 +23,10 @@ adapt accordingly. Last change 2018-12-19.
 
 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,
+[@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.
 
@@ -55,13 +55,14 @@ 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
+period the `work_in_progress` label may 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.
+merged. In addition, a `ready_for_merge` label may also be assigned
+to signal urgency to merge this pull request quickly.
 
 ### Pull Request Reviews
 
@@ -97,108 +98,50 @@ 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 must follow the C++-11 standard. C++98-only is no longer accepted
-  * Code should use `nullptr` instead of `NULL` where applicable.
-  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.
-  exception is <string>, but it won't need to be explicitly included
-  since pointers.h already includes it. so std::string can be used directly.
-  * 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.
-  * see https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md
-  for general include file conventions and best practices
-  * 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.
+the LAMMPS code or request new features to be added. Bug reports have
+a `[Bug]` marker in the subject line; suggestions for changes or
+adding new functionality are indicated by a `[Feature Request]`
+marker in the subject. This is automatically done when using the
+corresponding template for submitting an issue.  Issues may be assigned
+to one or more developers, if they are working on this feature or
+working to resolve an issue.  Issues that have nobody working
+on them at the moment or in the near future, 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.
+the pull request is merged.  The template for pull requests includes
+a header where connections between pull requests and issues can be listed
+and thus were this comment should be placed.
 
 ## 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.
+testing - that the code in the branch "master" does not get easily
+broken.  These tests are run after every update to a pull request.  More
+extensive and time consuming tests (including regression testing) are
+performed after code is merged to the "master" branch. There are patch
+releases of LAMMPS every 3-5 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
+About 1-2 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.
-
+Also, the last 1-3 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

@@ -1,128 +0,0 @@
-# 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 2020-08-31
-
-## 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>` instead of `#include <stdlib.h>` or
-`#include<ctypes.h>` ).
-
-### C++ Standard Compliance
-
-LAMMPS core files use standard conforming C++ compatible with the
-C++11 standard, unless explicitly noted.  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  (only if needed)
-* LAMMPS local headers (preferably in alphabetical order)
-* system and library headers (anything that is using angular brackets; preferably in alphabetical order)
-* conditional include statements (i.e. anything bracketed with ifdefs)
-
-### Special Cases and Exceptions
-
-#### pointers.h
-
-The `pointer.h` header file also includes (in this order) `lmptype.h`,
-`mpi.h`, `cstddef`, `cstdio`, `string`, `utils.h`, and `fmt/format.h`
-and through `lmptype.h` indirectly also `climits`, `cstdlib`, `cinttypes`.
-This means any header including `pointers.h` can assume that `FILE`,
-`NULL`, `INT_MAX` are defined, and the may freely use the std::string
-for arguments. Corresponding implementation files do not need to include
-those headers.
-
-## 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.  Through setting `-DENABLE_IWYU=on` when running
-CMake, a custom build target is added that will enable recording
-the compilation commands and then run the `iwyu_tool` using the
-recorded compilation commands information when typing `make iwyu`.
-
-## 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

@@ -1,4 +1,4 @@
-.TH LAMMPS "14 May 2021" "2021-05-14"
+.TH LAMMPS "29 September 2021" "2021-09-29"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.
@@ -34,7 +34,7 @@ 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.
+See https://www.lammps.org/ for more information and documentation.
 
 .SH EXECUTABLE NAME
 The
@@ -54,7 +54,7 @@ using
 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
+without a suffix. In this man page we will use
 .B lmp
 to represent any of those names.
 
@@ -94,7 +94,7 @@ 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
+at: https://docs.lammps.org/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.
@@ -122,6 +122,38 @@ to perform client/server messaging with another application.
 .B LAMMPS
 can act as either a client or server (or both).
 .TP
+\fB\-mdi '<mdi_flags>'\fR
+This flag is only recognized and used when
+.B LAMMPS
+has support for the MolSSI
+Driver Interface (MDI) included as part of the MDI package.  This flag is
+specific to the MDI library and controls how
+.B LAMMPS
+interacts with MDI.  There are usually multiple flags that have to follow it
+and those have to be placed in quotation marks.  For more information about
+how to launch LAMMPS in MDI client/server mode please refer to the
+MDI How-to at  https://docs.lammps.org/Howto_mdi.html
+.TP
+\fB\-c\fR or \fB\-cite <style or filename>\fR
+Select how and where to output a reminder about citing contributions
+to the
+.B LAMMPS
+code that were used during the run. Available keywords
+for styles are "both", "none", "screen", or "log".  Any other keyword
+will be considered a file name to write the detailed citation info to
+instead of logfile or screen.  Default is the "log" style where there
+is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See https://docs.lammps.org/Intro_citing.html for more details on
+how to correctly reference and cite
+.B LAMMPS
+.
+.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
@@ -135,7 +167,7 @@ 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
+times, e.g. to set options for the INTEL and OPENMP 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.
@@ -202,7 +234,7 @@ 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" 
+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
@@ -218,8 +250,19 @@ 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.
+.TP
+\fB\-sr\fR or \fB\-skiprun\fR
+Insert the command "timer timeout 0 every 1" at the
+beginning of an input file or after a "clear" command.
+This has the effect that the entire
+.B LAMMPS
+input script is processed without executing actual
+"run" or "minimize" or similar commands (their main loops are skipped).
+This can be helpful and convenient to test input scripts of long running
+calculations for correctness to avoid having them crash after a
+long time due to a typo or syntax error in the middle or at the end.
 
-See https://lammps.sandia.gov/doc/Run_options.html for additional
+See https://docs.lammps.org/Run_options.html for additional
 details and discussions on command-line options.
 
 .SH LAMMPS BASICS
@@ -254,7 +297,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2020 Sandia Corporation
+© 2003--2021 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

doc/msi2lmp.1

@@ -98,7 +98,7 @@ msi2lmp decane -c 0 -f oplsaa
 
 
 .SH COPYRIGHT
-© 2003--2019 Sandia Corporation
+© 2003--2021 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

doc/src/Bibliography.rst

@@ -191,7 +191,7 @@ Bibliography
    A.\  Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
 
 **(Campana)**
-   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*\ , `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
+   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
 
 **(Cao1)**
    J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@@ -767,7 +767,7 @@ Bibliography
    Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
 
 **(Moustafa)**
-   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*\ , `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
 
 **(Muller-Plathe1)**
    Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@@ -1129,6 +1129,9 @@ Bibliography
 **(Sutmann)**
    Sutmann, Arnold, Fahrenberger, et. al., Physical review / E 88(6), 063308 (2013)
 
+**(Sutmann)** G. Sutmann. ScaFaCoS - a Scalable library of Fast Coulomb Solvers for particle Systems.
+  In Bajaj, Zavattieri, Koslowski, Siegmund, Proceedings of the Society of Engineering Science 51st Annual Technical Meeting. 2014.
+
 **(Swinburne)**
    Swinburne and Marinica, Physical Review Letters, 120, 1 (2018)
 
@@ -1285,9 +1288,6 @@ Bibliography
 **(Wennberg)**
    Wennberg, Murtola, Hess, Lindahl, J Chem Theory Comput, 9, 3527 (2013).
 
-**(Who)**
-   Who, Author2, Author3, J of Long Range Solvers, 35, 164-177 (2012).
-
 **(Wicaksono1)**
    Wicaksono, Sinclair, Militzer, Computational Materials Science, 117, 397-405 (2016).
 

doc/src/Build.rst

@@ -22,4 +22,5 @@ page.
    Build_extras
    Build_manual
    Build_windows
+   Build_diskspace
    Build_development

doc/src/Build_basics.rst

@@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
       directory, or ``make`` from the ``src/STUBS`` dir.  If the build
       fails, you may 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``,
+      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -120,19 +120,19 @@ 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`
-page for details. The ``USER-INTEL`` package also includes OpenMP
-threading (it is compatible with ``USER-OMP`` and will usually fall
-back on styles from that package, if a ``USER-INTEL`` does not exist)
+``OPENMP`` package; see the :doc:`Speed_omp`
+page for details. The ``INTEL`` package also includes OpenMP
+threading (it is compatible with ``OPENMP`` and will usually fall
+back on styles from that package, if a ``INTEL`` does not exist)
 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
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  In addition
 some packages support OpenMP threading indirectly through the libraries
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
 See the :doc:`Packages details <Packages_details>` page for more
 info on these packages and the pages for their respective commands
 for OpenMP threading info.
@@ -176,7 +176,7 @@ performance.  Vendor provided compilers for a specific hardware can
 produce faster code than open-source compilers like the GNU compilers.
 On the most common x86 hardware most popular C++ 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
+using the ``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 Intel compiler specific directives to enable
@@ -325,9 +325,9 @@ LAMMPS.
          .. 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.omp                   # OPENMP package
+            Makefile.intel_cpu             # INTEL package for CPUs
+            Makefile.intel_coprocessor     # INTEL package for KNLs
             Makefile.gpu                   # GPU package
             Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
             Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)

doc/src/Build_cmake.rst

@@ -140,7 +140,7 @@ can be used several times in one command.
 For your convenience we provide :ref:`CMake presets <cmake_presets>`
 that combine multiple settings to enable optional LAMMPS packages or use
 a different compiler tool chain.  Those are loaded with the *-C* flag
-(``-C ../cmake/presets/minimal.cmake``).  This step would only be needed
+(``-C ../cmake/presets/basic.cmake``).  This step would only be needed
 once, as the settings from the preset files are stored in the
 ``CMakeCache.txt`` file. It is also possible to customize the build
 by adding one or more *-D* flags to the CMake command line.

doc/src/Build_development.rst

@@ -1,15 +1,15 @@
-Development build options (CMake only)
-======================================
+Development build options
+=========================
 
-The CMake build procedure of LAMMPS offers a few extra options which are
+The build procedures in LAMMPS offers a few extra options which are
 useful during development, testing or debugging.
 
 ----------
 
 .. _compilation:
 
-Monitor compilation flags
--------------------------
+Monitor compilation flags (CMake only)
+--------------------------------------
 
 Sometimes it is necessary to verify the complete sequence of compilation flags
 generated by the CMake build. To enable a more verbose output during
@@ -28,22 +28,46 @@ variable VERBOSE set to 1:
 
 ----------
 
+.. _clang-tidy:
+
+Enable static code analysis with clang-tidy (CMake only)
+--------------------------------------------------------
+
+The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
+static code analysis tool to diagnose (and potentially fix) typical
+programming errors or coding style violations.  It has a modular framework
+of tests that can be adjusted to help identifying problems before they
+become bugs and also assist in modernizing large code bases (like LAMMPS).
+It can be enabled for all C++ code with the following CMake flag
+
+.. code-block:: bash
+
+   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
+
+With this flag enabled all source files will be processed twice, first to
+be compiled and then to be analyzed. Please note that the analysis can be
+significantly more time consuming than the compilation itself.
+
+----------
+
 .. _iwyu_processing:
 
-Report missing and unneeded '#include' statements
--------------------------------------------------
+Report missing and unneeded '#include' statements (CMake only)
+--------------------------------------------------------------
 
 The conventions for how and when to use and order include statements in
-LAMMPS are `documented in a separate file <https://github.com/lammps/lammps/blob/master/doc/include-file-conventions.md>`_
-(also included in the source code distribution).  To assist with following
+LAMMPS are documented in :doc:`Modify_style`.  To assist with following
 these conventions one can use the `Include What You Use tool <https://include-what-you-use.org/>`_.
-This is still under development and for large and complex projects like LAMMPS
+This tool is still under development and for large and complex projects like LAMMPS
 there are some false positives, so suggested changes need to be verified manually.
-It is recommended to use at least version 0.14, which has much fewer incorrect
-reports than earlier versions.
+It is recommended to use at least version 0.16, which has much fewer incorrect
+reports than earlier versions.  To install the IWYU toolkit, you need to have
+the clang compiler **and** its development package installed.  Download the IWYU
+version that matches the version of the clang compiler, configure, build, and
+install it.
 
-The necessary steps to generate the report can be enabled via a
-CMake variable:
+The necessary steps to generate the report can be enabled via a CMake variable
+during CMake configuration.
 
 .. code-block:: bash
 
@@ -64,8 +88,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support
----------------------------------------------------------
+Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
+----------------------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
 which use different sanitizer libraries to detect problems in the code
@@ -94,8 +118,8 @@ compilation and linking stages.  This is done through setting the
 
 .. _testing:
 
-Code Coverage and Unit Testing
-------------------------------
+Code Coverage and Unit Testing (CMake only)
+-------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
 during development: integration testing (i.e. whether the code compiles
@@ -288,7 +312,7 @@ and working.
      parameter needs to be adjusted. Typically a value around 1.0e-13
      can be used, but it may need to be as large as 1.0e-8 in some
      cases.
-   - The tests for pair styles from OPT, USER-OMP and USER-INTEL are
+   - The tests for pair styles from OPT, OPENMP and INTEL are
      performed with automatically rescaled epsilon to account for
      additional loss of precision from code optimizations and different
      summation orders.
@@ -323,7 +347,7 @@ and compared.  If the fix is a thermostat and thus the internal property
 ``t_target`` can be extracted, then this is compared to the reference
 data.  The tests are repeated with the respa run style.
 
-If the fix has a multi-threaded version in the USER-OMP package, then
+If the fix has a multi-threaded version in the OPENMP package, then
 the entire set of tests is repeated for that version as well.
 
 For this to work, some additional conditions have to be met by the
@@ -442,17 +466,56 @@ Coding style utilities
 
 To aid with enforcing some of the coding style conventions in LAMMPS
 some additional build targets have been added. These require Python 3.5
-or later and will only work on Unix-like operating and file systems.
+or later and will only work properly on Unix-like operating and file systems.
+
 The following options are available.
 
 .. code-block:: bash
 
-   make check-whitespace    # generate coverage report in HTML format
-   make fix-whitespace      # generate coverage report in XML format
-   make check-permissions   # delete folder with HTML format coverage report
-   make fix-permissions     # delete all collected coverage data and HTML output
+   make check-whitespace    # search for files with whitespace issues
+   make fix-whitespace      # correct whitespace issues in files
+   make check-homepage      # search for files with old LAMMPS homepage URLs
+   make fix-homepage        # correct LAMMPS homepage URLs in files
+   make check-permissions   # search for files with permissions issues
+   make fix-permissions     # correct permissions issues in files
 
-For the code in the ``unittest`` tree we are using the `clang-format`
-tool (Clang version 8.0 or later is required). If available, the source
-code files in the ``unittest`` tree can be updated to conform to the
-formatting settings using ``make format-tests``.
+These should help to replace all TAB characters with blanks and remove
+any trailing whitespace.  Also all LAMMPS homepage URL references can be
+updated to the location change from Sandia to the lammps.org domain.
+And the permission check can remove executable permissions from non-executable
+files (like source code).
+
+Clang-format support
+--------------------
+
+For the code in the ``unittest`` and ``src`` trees we are transitioning
+to use the `clang-format` tool to assist with having a consistent source
+code formatting style.  The `clang-format` command bundled with Clang
+version 8.0 or later is required.  The configuration is in files called
+``.clang-format`` in the respective folders.  Since the modifications
+from `clang-format` can be significant and - especially for "legacy
+style code" - they are not always improving readability, a large number
+of files currently have a ``// clang-format off`` at the top, which will
+disable the processing.  As of fall 2021 all files have been either
+"protected" this way or are enabled for full or partial `clang-format`
+processing.  Over time, the "protected" files will be refactored and
+updated so that `clang-format` may be applied to them as well.
+
+It is recommended for all newly contributed files to use the clang-format
+processing while writing the code or do the coding style processing
+(including the scripts mentioned in the previous paragraph)
+
+If `clang-format` is available, files can be updated individually with
+commands like the following:
+
+.. code-block:: bash
+
+   $ clang-format -i some_file.cpp
+
+
+The following target are available for both, GNU make and CMake:
+
+.. code-block:: bash
+
+   make format-src       # apply clang-format to all files in src and the package folders
+   make format-tests     # apply clang-format to all files in the unittest tree

doc/src/Build_diskspace.rst

@@ -0,0 +1,45 @@
+Notes for saving disk space when building LAMMPS from source
+------------------------------------------------------------
+
+LAMMPS is a large software project with a large number of source files,
+extensive documentation, and a large collection of example files.
+When downloading LAMMPS by cloning the
+`git repository from GitHub <https://github.com/lammps/lammps>`_ this
+will by default also download the entire commit history since September 2006.
+Compiling LAMMPS will add the storage requirements of the compiled object
+files and libraries to the tally.
+
+In a user account on an HPC cluster with filesystem quotas or in other
+environments with restricted disk space capacity it may be needed to
+reduce the storage requirements. Here are some suggestions:
+
+- Create a so-called shallow repository by cloning only the last commit
+  instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
+  This reduces the downloaded size to about half.  With ``--depth=1`` it is not possible to check out different
+  versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
+  extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).
+
+- Download a tar archive from either the `download section on the LAMMPS homepage <https://www.lammps.org/download.html>`_
+  or from the `LAMMPS releases page on GitHub <https://github.com/lammps/lammps/releases>`_ these will not
+  contain the git history at all.
+
+- Build LAMMPS without the debug flag (remove ``-g`` from the machine makefile or use ``-DCMAKE_BUILD_TYPE=Release``)
+  or use the ``strip`` command on the LAMMPS executable when no more debugging would be needed.  The strip command
+  may also be applied to the LAMMPS shared library. The static library may be deleted entirely.
+
+- Delete compiled object files and libraries after copying the LAMMPS executable to a permanent location.
+  When using the traditional build process, one may use ``make clean-<machine>`` or ``make clean-all``
+  to delete object files in the src folder.  For CMake based builds, one may use ``make clean`` or just
+  delete the entire build folder.
+
+- The folders containing the documentation tree (doc), the examples (examples) are not needed to build and
+  run LAMMPS and can be safely deleted.  Some files in the potentials folder are large and may be deleted,
+  if not needed.  The largest of those files (occupying about 120 MBytes combined) will only be downloaded on
+  demand, when the corresponding package is installed.
+
+- When using the CMake build procedure, the compilation can be done on a (local) scratch storage that will not
+  count toward the quota.  A local scratch file system may offer the additional benefit of speeding up creating
+  object files and linking with libraries compared to a networked file system.  Also with CMake (and unlike with
+  the traditional make) it is possible to compile LAMMPS executables with different settings and packages included
+  from the same source tree since all the configuration information is stored in the build folder.  So it is
+  not necessary to have multiple copies of LAMMPS.

doc/src/Build_extras.rst

@@ -31,36 +31,37 @@ This is the list of packages that may require additional steps.
 .. table_from_list::
    :columns: 6
 
+   * :ref:`ADIOS <adios>`
+   * :ref:`ATC <atc>`
+   * :ref:`AWPMD <awpmd>`
+   * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
    * :ref:`GPU <gpu>`
+   * :ref:`H5MD <h5md>`
+   * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`MDI <mdi>`
+   * :ref:`MESONT <mesont>`
    * :ref:`MESSAGE <message>`
-   * :ref:`MLIAP <mliap>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`SCAFACOS <scafacos>`
    * :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-MDI <user-mdi>`
-   * :ref:`USER-MESONT <user-mesont>`
-   * :ref:`USER-MOLFILE <user-molfile>`
-   * :ref:`USER-NETCDF <user-netcdf>`
-   * :ref:`USER-PACE <user-pace>`
-   * :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>`
+   * :ref:`VTK <vtk>`
 
 ----------
 
@@ -73,7 +74,8 @@ To build with this package you must have the `zlib compression library
 <https://zlib.net>`_ available on your system to build dump styles with
 a '/gz' suffix.  There are also styles using the
 `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
-'/zstd' suffix.
+'/zstd' suffix.  The zstd library version must be at least 1.4.  Older
+versions use an incompatible API and thus LAMMPS will fail to compile.
 
 .. tabs::
 
@@ -456,6 +458,9 @@ They must be specified in uppercase.
    *  - ZEN2
       - HOST
       - AMD Zen2 class CPU (AVX 2)
+   *  - ZEN3
+      - HOST
+      - AMD Zen3 class CPU (AVX 2)
    *  - ARMV80
       - HOST
       - ARMv8.0 Compatible CPU
@@ -559,7 +564,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.4 of the Kokkos library.
+This list was last updated for version 3.4.1 of the Kokkos library.
 
 .. tabs::
 
@@ -618,7 +623,7 @@ This list was last updated for version 3.4 of the Kokkos library.
 
          mkdir build-kokkos-cuda
          cd build-kokkos-cuda
-         cmake -C ../cmake/presets/minimal.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
+         cmake -C ../cmake/presets/basic.cmake -C ../cmake/presets/kokkos-cuda.cmake ../cmake
          cmake --build .
 
    .. tab:: Basic traditional make settings:
@@ -807,16 +812,17 @@ be installed on your system.
 
 .. _mliap:
 
-MLIAP package
+ML-IAP package
 ---------------------------
 
-Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
-package.  There will be an error message if this requirement is not satisfied.
-Using the *mliappy* model also requires enabling Python support, which
-in turn requires the :ref:`PYTHON <PKG-PYTHON>`
-package **and** requires you have the `cython <https://cython.org>`_ software
-installed and with it a working ``cythonize`` command.  This feature requires
-compiling LAMMPS with Python version 3.6 or later.
+Building the ML-IAP package requires including the :ref:`ML-SNAP
+<PKG-ML-SNAP>` package.  There will be an error message if this requirement
+is not satisfied.  Using the *mliappy* model also requires enabling
+Python support, which in turn requires to include the :ref:`PYTHON
+<PKG-PYTHON>` package **and** requires to have the `cython
+<https://cython.org>`_ software installed and with it a working
+``cythonize`` command.  This feature requires compiling LAMMPS with
+Python version 3.6 or later.
 
 .. tabs::
 
@@ -830,9 +836,9 @@ compiling LAMMPS with Python version 3.6 or later.
       suitable Python version and the ``cythonize`` command and choose
       the default accordingly.  During the build procedure the provided
       .pyx file(s) will be automatically translated to C++ code and compiled.
-      Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
+      Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder,
       as that can lead to compilation errors if Python support is not enabled.
-      If you did by accident, please remove the generated .cpp and .h files.
+      If you did it by accident, please remove the generated .cpp and .h files.
 
    .. tab:: Traditional make
 
@@ -841,15 +847,16 @@ compiling LAMMPS with Python version 3.6 or later.
       the ``cythonize`` command in case the corresponding .pyx file(s) were
       modified.  You may need to modify ``lib/python/Makefile.lammps``
       if the LAMMPS build fails.
-      To manually enforce building MLIAP with Python support enabled,
-      you can add
-      ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
-      You may have to manually run the ``cythonize`` command on .pyx file(s)
-      in the ``src`` folder, if this is not automatically done during
-      installing the MLIAP package.  Please do **not** run ``cythonize``
-      in the ``src/MLIAP`` folder, as that can lead to compilation errors
-      if Python support is not enabled.
-      If you did by accident, please remove the generated .cpp and .h files.
+
+      To enable building the ML-IAP package with Python support enabled,
+      you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in
+      your machine makefile.  You may have to manually run the
+      ``cythonize`` command on .pyx file(s) in the ``src`` folder, if
+      this is not automatically done during installing the ML-IAP
+      package.  Please do **not** run ``cythonize`` in the ``src/ML-IAP``
+      folder, as that can lead to compilation errors if Python support
+      is not enabled.  If you did this by accident, please remove the
+      generated .cpp and .h files.
 
 ----------
 
@@ -1050,12 +1057,12 @@ binary package provided by your operating system.
 
 ----------
 
-.. _user-adios:
+.. _adios:
 
-USER-ADIOS package
+ADIOS package
 -----------------------------------
 
-The USER-ADIOS package requires the `ADIOS I/O library
+The ADIOS package requires the `ADIOS I/O library
 <https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
 sure that you have ADIOS built either with or without MPI to match if
 you build LAMMPS with or without MPI.  ADIOS compilation settings for
@@ -1071,38 +1078,38 @@ systems.
       .. code-block:: bash
 
          -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
-         -D PKG_USER-ADIOS=yes
+         -D PKG_ADIOS=yes
 
    .. tab:: Traditional make
 
-      Turn on the USER-ADIOS package before building LAMMPS. If the
+      Turn on the ADIOS package before building LAMMPS. If the
       ADIOS 2.x software is installed in PATH, there is nothing else to
       do:
 
       .. code-block:: bash
 
-         $ make yes-user-adios
+         $ make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         $ ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
+         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
-.. _user-atc:
+.. _atc:
 
-USER-ATC package
+ATC package
 -------------------------------
 
-The USER-ATC package requires the MANYBODY package also be installed.
+The ATC package requires the MANYBODY package also be installed.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-ATC=yes``
+      No additional settings are needed besides ``-D PKG_ATC=yes``
       and ``-D PKG_MANYBODY=yes``.
 
    .. tab:: Traditional make
@@ -1145,16 +1152,16 @@ The USER-ATC package requires the MANYBODY package also be installed.
 
 ----------
 
-.. _user-awpmd:
+.. _awpmd:
 
-USER-AWPMD package
+AWPMD package
 ------------------
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
+      No additional settings are needed besides ``-D PKG_AQPMD=yes``.
 
    .. tab:: Traditional make
 
@@ -1196,9 +1203,9 @@ USER-AWPMD package
 
 ----------
 
-.. _user-colvars:
+.. _colvars:
 
-USER-COLVARS package
+COLVARS package
 ---------------------------------------
 
 This package includes the `Colvars library
@@ -1212,7 +1219,7 @@ be built for the most part with all major versions of the C++ language.
 
       This is the recommended build procedure for using Colvars in
       LAMMPS. No additional settings are normally needed besides
-      ``-D PKG_USER-COLVARS=yes``.
+      ``-D PKG_COLVARS=yes``.
 
    .. tab:: Traditional make
 
@@ -1255,9 +1262,9 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
-.. _user-pace:
+.. _ml-pace:
 
-USER-PACE package
+ML-PACE package
 -----------------------------
 
 This package requires a library that can be downloaded and built
@@ -1270,8 +1277,8 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
    .. tab:: CMake build
 
       By default the library will be downloaded from the git repository
-      and built automatically when the USER-PACE package is enabled with
-      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      and built automatically when the ML-PACE package is enabled with
+      ``-D PKG_ML-PACE=yes``.  The location for the sources may be
       customized by setting the variable ``PACELIB_URL`` when
       configuring with CMake (e.g. to use a local archive on machines
       without internet access).  Since CMake checks the validity of the
@@ -1282,7 +1289,7 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
    .. tab:: Traditional make
 
-      You can download and build the USER-PACE library
+      You can download and build the ML-PACE library
       in one step from the ``lammps/src`` dir, using these commands,
       which invoke the ``lib/pace/Install.py`` script.
 
@@ -1295,9 +1302,9 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
 ----------
 
-.. _user-plumed:
+.. _plumed:
 
-USER-PLUMED package
+PLUMED package
 -------------------------------------
 
 .. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
@@ -1305,7 +1312,7 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
-The USER-PLUMED package has been tested to work with Plumed versions
+The PLUMED package has been tested to work with Plumed versions
 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
 with a different version of the Plumed kernel.
 
@@ -1341,7 +1348,7 @@ LAMMPS build.
 
    .. tab:: CMake build
 
-      When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
+      When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
       command you must ensure that GSL is installed in locations that
       are specified in your environment.  There are then two additional
       variables that control the manner in which PLUMED is obtained and
@@ -1374,7 +1381,7 @@ LAMMPS build.
 
    .. tab:: Traditional make
 
-      PLUMED needs to be installed before the USER-PLUMED package is
+      PLUMED needs to be installed before the PLUMED package is
       installed so that LAMMPS can find the right settings when
       compiling and linking the LAMMPS executable.  You can either
       download and build PLUMED inside the LAMMPS plumed library folder
@@ -1399,12 +1406,12 @@ LAMMPS build.
       build to use. A new file ``lib/plumed/Makefile.lammps`` is also
       created with settings suitable for LAMMPS to compile and link
       PLUMED using the desired linkage mode. After this step is
-      completed, you can install the USER-PLUMED package and compile
+      completed, you can install the PLUMED package and compile
       LAMMPS in the usual manner:
 
       .. code-block:: bash
 
-         $ make yes-user-plumed
+         $ make yes-plumed
          $ make machine
 
       Once this compilation completes you should be able to run LAMMPS
@@ -1419,15 +1426,15 @@ LAMMPS build.
 
       If you want to change the linkage mode, you have to re-run "make
       lib-plumed" with the desired settings **and** do a re-install if
-      the USER-PLUMED package with "make yes-user-plumed" to update the
+      the PLUMED package with "make yes-plumed" to update the
       required makefile settings with the changes in the lib/plumed
       folder.
 
 ----------
 
-.. _user-h5md:
+.. _h5md:
 
-USER-H5MD package
+H5MD package
 ---------------------------------
 
 To build with this package you must have the HDF5 software package
@@ -1438,7 +1445,7 @@ the HDF5 library.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
+      No additional settings are needed besides ``-D PKG_H5MD=yes``.
 
       This should auto-detect the H5MD library on your system.  Several
       advanced CMake H5MD options exist if you need to specify where it
@@ -1470,24 +1477,78 @@ the HDF5 library.
 
 ----------
 
-.. _user-intel:
+.. _ml-hdnnp:
 
-USER-INTEL package
+ML-HDNNP package
+----------------
+
+To build with the ML-HDNNP package it is required to download and build the
+external `n2p2 <https://github.com/CompPhysVienna/n2p2>`_ library ``v2.1.4``
+(or higher). The LAMMPS build process offers an automatic download and
+compilation of *n2p2* or allows you to choose the installation directory of
+*n2p2* manually. Please see the boxes below for the CMake and traditional build
+system for detailed information.
+
+In case of a manual installation of *n2p2* you only need to build the *n2p2* core
+library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
+suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
+details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
+<https://compphysvienna.github.io/n2p2/topics/build.html>`_.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_N2P2=value    # download n2p2 for build, value = no (default) or yes
+         -D N2P2_DIR=path          # n2p2 base directory (only needed if a custom location)
+
+      If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
+      built inside the CMake build directory.  If the *n2p2* library is already
+      on your system (in a location CMake cannot find it), set the ``N2P2_DIR``
+      to path where *n2p2* is located. If *n2p2* is located directly in
+      ``lib/hdnnp/n2p2`` it will be automatically found by CMake.
+
+   .. tab:: Traditional make
+
+      You can download and build the *n2p2* library manually if you prefer;
+      follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
+      one step from the ``lammps/src`` dir, using a command like these, which
+      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         $ make lib-hdnnp             # print help message
+         $ make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
+         $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
+         $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+
+      Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
+      ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
+      ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
+      respectively. When LAMMPS is built in ``src`` it will use these links.
+
+----------
+
+.. _intel:
+
+INTEL package
 -----------------------------------
 
 To build with this package, you must choose which hardware you want to
 build for, either x86 CPUs or Intel KNLs in offload mode.  You should
-also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
-used in tandem with the USER-INTEL package to good effect, as explained
+also typically :ref:`install the OPENMP package <openmp>`, as it can be
+used in tandem with the INTEL package to good effect, as explained
 on the :doc:`Speed_intel` page.
 
 When using Intel compilers version 16.0 or later is required.  You can
 also use the GNU or Clang compilers and they will provide performance
-improvements over regular styles and USER-OMP styles, but less so than
+improvements over regular styles and OPENMP styles, but less so than
 with the Intel compilers.  Please also note, that some compilers have
 been found to apply memory alignment constraints incompletely or
 incorrectly and thus can cause segmentation faults in otherwise correct
-code when using features from the USER-INTEL package.
+code when using features from the INTEL package.
 
 
 .. tabs::
@@ -1504,7 +1565,7 @@ code when using features from the USER-INTEL package.
       Choose which hardware to compile for in Makefile.machine via the
       following settings.  See ``src/MAKE/OPTIONS/Makefile.intel_cpu*``
       and ``Makefile.knl`` files for examples. and
-      ``src/USER-INTEL/README`` for additional information.
+      ``src/INTEL/README`` for additional information.
 
       For CPUs:
 
@@ -1540,9 +1601,9 @@ TBB and MKL.
 
 ----------
 
-.. _user-mdi:
+.. _mdi:
 
-USER-MDI package
+MDI package
 -----------------------------
 
 .. tabs::
@@ -1569,9 +1630,9 @@ USER-MDI package
 
 ----------
 
-.. _user-mesont:
+.. _mesont:
 
-USER-MESONT package
+MESONT package
 -------------------------
 
 This package includes a library written in Fortran 90 in the
@@ -1584,7 +1645,7 @@ they will be downloaded the first time this package is installed.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
+      No additional settings are needed besides ``-D PKG_MESONT=yes``
 
    .. tab:: Traditional make
 
@@ -1611,9 +1672,9 @@ they will be downloaded the first time this package is installed.
 
 ----------
 
-.. _user-molfile:
+.. _molfile:
 
-USER-MOLFILE package
+MOLFILE package
 ---------------------------------------
 
 .. tabs::
@@ -1623,9 +1684,9 @@ USER-MOLFILE package
       .. code-block:: bash
 
          -D MOLFILE_INCLUDE_DIR=path   # (optional) path where VMD molfile plugin headers are installed
-         -D PKG_USER-MOLFILE=yes
+         -D PKG_MOLFILE=yes
 
-      Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting
+      Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
       ``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for
       the molfile plugin header files. These should match the ABI of the
       plugin files used, and thus one typically sets them to include
@@ -1649,9 +1710,9 @@ USER-MOLFILE package
 
 ----------
 
-.. _user-netcdf:
+.. _netcdf:
 
-USER-NETCDF package
+NETCDF package
 -------------------------------------
 
 To build with this package you must have the NetCDF library installed
@@ -1661,7 +1722,7 @@ on your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
+      No additional settings are needed besides ``-D PKG_NETCDF=yes``.
 
       This should auto-detect the NETCDF library if it is installed on
       your system at standard locations.  Several advanced CMake NETCDF
@@ -1680,9 +1741,9 @@ on your system.
 
 ----------
 
-.. _user-omp:
+.. _openmp:
 
-USER-OMP package
+OPENMP package
 -------------------------------
 
 .. tabs::
@@ -1690,13 +1751,13 @@ USER-OMP package
    .. tab:: CMake build
 
       No additional settings are required besides ``-D
-      PKG_USER-OMP=yes``.  If CMake detects OpenMP compiler support, the
-      USER-OMP code will be compiled with multi-threading support
+      PKG_OPENMP=yes``.  If CMake detects OpenMP compiler support, the
+      OPENMP code will be compiled with multi-threading support
       enabled, otherwise as optimized serial code.
 
    .. tab:: Traditional make
 
-      To enable multi-threading support in the USER-OMP package (and
+      To enable multi-threading support in the OPENMP package (and
       other styles supporting OpenMP) the following compile and link
       flags must be added to your Makefile.machine file.  See
       ``src/MAKE/OPTIONS/Makefile.omp`` for an example.
@@ -1713,12 +1774,12 @@ USER-OMP package
 
 ----------
 
-.. _user-qmmm:
+.. _qmmm:
 
-USER-QMMM package
+QMMM package
 ---------------------------------
 
-For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
+For using LAMMPS to do QM/MM simulations via the QMMM package you
 need to build LAMMPS as a library.  A LAMMPS executable with :doc:`fix
 qmmm <fix_qmmm>` included can be built, but will not be able to do a
 QM/MM simulation on as such.  You must also build a QM code - currently
@@ -1741,11 +1802,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       libqmmm.a) are not included in the static LAMMPS library and
       (currently) not installed, while their code is included in the
       shared LAMMPS library.  Thus a typical command line to configure
-      building LAMMPS for USER-QMMM would be:
+      building LAMMPS for QMMM would be:
 
       .. code-block:: bash
 
-         cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
+         cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \
              -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
 
       After completing the LAMMPS build and also configuring and
@@ -1788,16 +1849,16 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _user-quip:
+.. _ml-quip:
 
-USER-QUIP package
+ML-QUIP package
 ---------------------------------
 
 To build with this package, you must download and build the QUIP
 library.  It can be obtained from GitHub.  For support of GAP
 potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  See step 1 and step 1.1 in the
-``lib/quip/README`` file for details on how to do this.
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
 
 .. tabs::
 
@@ -1805,11 +1866,14 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
       .. code-block:: bash
 
+         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
          -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
-      CMake will **not** download and build the QUIP library.  But once you have
-      done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
-      work.  Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
+      CMake will try to download and build the QUIP library from GitHub, if it is not
+      found on the local machine. This requires to have git installed. It will use the same compilers
+      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      and installed QUIP library and CMake cannot find it.
 
    .. tab:: Traditional make
 
@@ -1823,9 +1887,9 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
 ----------
 
-.. _user-scafacos:
+.. _scafacos:
 
-USER-SCAFACOS package
+SCAFACOS package
 -----------------------------------------
 
 To build with this package, you must download and build the
@@ -1870,9 +1934,9 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _user-smd:
+.. _machdyn:
 
-USER-SMD package
+MACHDYN package
 -------------------------------
 
 To build with this package, you must download the Eigen3 library.
@@ -1914,9 +1978,9 @@ Eigen3 is a template library, so you do not need to build it.
 
 ----------
 
-.. _user-vtk:
+.. _vtk:
 
-USER-VTK package
+VTK package
 -------------------------------
 
 To build with this package you must have the VTK library installed on
@@ -1926,7 +1990,7 @@ your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
+      No additional settings are needed besides ``-D PKG_VTK=yes``.
 
       This should auto-detect the VTK library if it is installed on your
       system at standard locations.  Several advanced VTK options exist

doc/src/Build_make.rst

@@ -117,10 +117,10 @@ settings may become outdated:
 
    make mac             # build serial LAMMPS on a Mac
    make mac_mpi         # build parallel LAMMPS on a Mac
-   make intel_cpu       # build with the USER-INTEL package optimized for CPUs
-   make knl             # build with the USER-INTEL package optimized for KNLs
+   make intel_cpu       # build with the INTEL package optimized for CPUs
+   make knl             # build with the 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 omp             # build with the OPENMP 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_manual.rst

@@ -22,35 +22,23 @@ files. Here is a list with descriptions:
    .gitignore       # list of files and folders to be ignored by git
    doxygen-warn.log # logfile with warnings from running doxygen
    github-development-workflow.md   # notes on the LAMMPS development workflow
-   include-file-conventions.md      # notes on LAMMPS' include file conventions
 
 If you downloaded LAMMPS as a tarball from `the LAMMPS website <lws_>`_,
 the html folder and the PDF files should be included.
 
 If you downloaded LAMMPS from the public git repository, then the HTML
-and PDF files are not included.  Instead you need to create them, in one
-of two ways:
-
-a. You can "fetch" the current HTML and PDF files from the LAMMPS web
-   site.  Just type ``make fetch``.  This should download a ``html_www``
-   directory and a ``Manual_www.pdf`` file.  Note that if new LAMMPS features
-   have been added more recently than the date of your LAMMPS version, 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 or PDF files yourself, by typing ``make html``
-   or ``make pdf`` in the ``doc`` folder.  This requires various tools
-   and files.  Some of them have to be installed (see below).  For the
-   rest the build process will attempt to download and install them into
-   a python virtual environment and local folders.
+and PDF files are not included.  You can build the HTML or PDF files yourself,
+by typing ``make html``  or ``make pdf`` in the ``doc`` folder.  This requires
+various tools and files.  Some of them have to be installed (see below).  For
+the rest the build process will attempt to download and install them into
+a python virtual environment and local folders.
 
 A current version of the manual (latest patch release, aka unstable
 branch) is is available online at:
-`https://lammps.sandia.gov/doc/Manual.html
-<https://lammps.sandia.gov/doc/Manual.html>`_ A version of the manual
-corresponding to the ongoing development (aka master branch) is
-available online at: `https://docs.lammps.org/
-<https://docs.lammps.org/>`_
+`https://docs.lammps.org/Manual.html <https://docs.lammps.org/Manual.html>`_.
+A version of the manual corresponding to the ongoing development (aka master branch)
+is available online at: `https://docs.lammps.org/latest/
+<https://docs.lammps.org/latest/>`_
 
 Build using GNU make
 --------------------
@@ -86,8 +74,8 @@ folder.  The following ``make`` commands are available:
 .. code-block:: bash
 
    make html          # generate HTML in html dir using Sphinx
-   make pdf           # generate PDF  as Manual.pdf using Sphinx and pdflatex
-   make fetch         # fetch HTML pages and PDF files from LAMMPS web site
+   make pdf           # generate PDF  as Manual.pdf using Sphinx and PDFLaTeX
+   make fetch         # fetch HTML pages and PDF files from LAMMPS website
                       #  and unpack into the html_www folder and Manual_www.pdf
    make epub          # generate LAMMPS.epub in ePUB format using Sphinx
    make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
@@ -215,9 +203,9 @@ be multiple tests run automatically:
 
   .. parsed-literal::
 
-     Found 33 standard and 41 user packages
-     Standard package NEWPACKAGE missing in Packages_standard.rst
-     Standard package NEWPACKAGE missing in Packages_details.rst
+     Found 88 packages
+     Package NEWPACKAGE missing in Packages_list.rst
+     Package NEWPACKAGE missing in Packages_details.rst
 
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
@@ -257,4 +245,4 @@ the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
 
 .. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
 
-.. _lws: https://lammps.sandia.gov
+.. _lws: https://www.lammps.org

doc/src/Build_package.rst

@@ -30,17 +30,37 @@ steps, as explained on the :doc:`Build extras <Build_extras>` 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-PACE <user-pace>`   | :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>`         |                              |                                |                                      |
-+--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+.. table_from_list::
+   :columns: 6
+
+   * :ref:`ADIOS <adios>`
+   * :ref:`ATC <atc>`
+   * :ref:`AWPMD <awpmd>`
+   * :ref:`COLVARS <colvars>`
+   * :ref:`COMPRESS <compress>`
+   * :ref:`GPU <gpu>`
+   * :ref:`H5MD <h5md>`
+   * :ref:`INTEL <intel>`
+   * :ref:`KIM <kim>`
+   * :ref:`KOKKOS <kokkos>`
+   * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`MESSAGE <message>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
+   * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
+   * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
+   * :ref:`POEMS <poems>`
+   * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`SCAFACOS <scafacos>`
+   * :ref:`VORONOI <voronoi>`
+   * :ref:`VTK <vtk>`
 
 The mechanism for including packages is simple but different for CMake
 versus make.
@@ -58,14 +78,10 @@ versus make.
       .. code-block:: csh
 
          -D PKG_MANYBODY=yes
-         -D PKG_USER-INTEL=yes
+         -D PKG_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.
+      All packages are included the same way.  See the shortcut section
+      below for how to install many packages at once with CMake.
 
       .. note::
 
@@ -89,12 +105,10 @@ versus make.
       .. code-block:: bash
 
          make no-rigid
-         make yes-user-intel
+         make yes-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.
+      All packages are included the same way.  See the shortcut section
+      below for how to install many packages at once with make.
 
       .. note::
 
@@ -126,7 +140,7 @@ other files dependent on that package are also excluded.
 
 .. note::
 
-   By default no package is installed.  Prior to August 2018, however,
+   By default no packages are installed.  Prior to August 2018, however,
    if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
    were pre-installed via the traditional make procedure in the ``src``
    directory.  That is no longer the case, so that CMake will build
@@ -153,7 +167,7 @@ one of them as a starting point and customize it to your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/minimal.cmake  [OPTIONS] ../cmake  # enable just a few core packages
+    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake  # enable just a few core packages
     cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
     cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
     cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
@@ -208,10 +222,10 @@ These commands install/un-install sets of packages:
 
     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-basic                      # install a few commonly used packages'
+    make no-basic                       # remove a few commonly used packages'
+    make yes-most                       # install most packages w/o libs'
+    make no-most                        # remove most packages w/o libs'
     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
@@ -225,15 +239,14 @@ package`` will list all the these commands.
    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
+   src/KSPACE, src/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.
+updating LAMMPS via git.
 
 Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
@@ -245,10 +258,10 @@ 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.
+files from the package sub-directories if the package is installed.  It
+should be used after the checkout has been :doc:`updated or changed
+withy git <Install_git>`, this will only update the files in the package
+sub-directories, but not the copies in the src folder.
 
 Type ``make package-overwrite`` to overwrite files in the package
 sub-directories with src files.

doc/src/Build_settings.rst

@@ -64,14 +64,15 @@ LAMMPS can use them if they are available on your system.
       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
+      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
       the FFT library, you can set these variables to assist:
 
       .. code-block:: bash
 
          -D FFTW3_INCLUDE_DIR=path   # path to FFTW3 include files
          -D FFTW3_LIBRARY=path       # path to FFTW3 libraries
-         -D FFT_FFTW_THREADS=on      # enable using threaded FFTW3 libraries
+         -D FFTW3_OMP_LIBRARY=path   # path to FFTW3 OpenMP wrapper libraries
+         -D FFT_FFTW_THREADS=on      # enable using OpenMP threaded FFTW3 libraries
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
@@ -242,8 +243,8 @@ does not support 64-bit integers or incurs performance penalties when
 using them.
 
 These are limits for the core of the LAMMPS code, specific features or
-some styles may impose additional limits.  The :ref:`USER-ATC
-<PKG-USER-ATC>` package cannot be compiled with the "bigbig" setting.
+some styles may impose additional limits.  The :ref:`ATC
+<PKG-ATC>` package cannot be compiled with the "bigbig" setting.
 Also, there are limitations when using the library interface where some
 functions with known issues have been replaced by dummy calls printing a
 corresponding error message rather than crashing randomly or corrupting

doc/src/Commands_bond.rst

@@ -18,7 +18,7 @@ Bond_style potentials
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -57,7 +57,7 @@ Angle_style potentials
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -99,7 +99,7 @@ Dihedral_style potentials
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -135,7 +135,7 @@ Improper_style potentials
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::

doc/src/Commands_category.rst

@@ -2,7 +2,7 @@ Commands by category
 ====================
 
 This page lists most of the LAMMPS commands, grouped by category.  The
-:doc:`General commands <Commands_all>` doc page lists all general commands
+:doc:`General commands <Commands_all>` page lists all general commands
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 

doc/src/Commands_compute.rst

@@ -16,8 +16,8 @@ Compute commands
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
-additional letters in parenthesis: g = GPU, i = USER-INTEL, k =
-KOKKOS, o = USER-OMP, t = OPT.
+additional letters in parenthesis: g = GPU, i = INTEL, k =
+KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
    :columns: 5
@@ -47,17 +47,20 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
    * :doc:`dilatation/atom <compute_dilatation_atom>`
+   * :doc:`dipole <compute_dipole>`
    * :doc:`dipole/chunk <compute_dipole_chunk>`
    * :doc:`displace/atom <compute_displace_atom>`
    * :doc:`dpd <compute_dpd>`
    * :doc:`dpd/atom <compute_dpd_atom>`
    * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
+   * :doc:`efield/atom <compute_efield_atom>`
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
    * :doc:`erotate/sphere <compute_erotate_sphere>`
    * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
+   * :doc:`fabric <compute_fabric>`
    * :doc:`fep <compute_fep>`
    * :doc:`force/tally <compute_tally>`
    * :doc:`fragment/atom <compute_cluster_atom>`
@@ -69,6 +72,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`gyration/shape/chunk <compute_gyration_shape_chunk>`
    * :doc:`heat/flux <compute_heat_flux>`
    * :doc:`heat/flux/tally <compute_tally>`
+   * :doc:`heat/flux/virial/tally <compute_tally>`
    * :doc:`hexorder/atom <compute_hexorder_atom>`
    * :doc:`hma <compute_hma>`
    * :doc:`improper <compute_improper>`
@@ -148,7 +152,7 @@ KOKKOS, o = USER-OMP, t = OPT.
    * :doc:`temp/chunk <compute_temp_chunk>`
    * :doc:`temp/com <compute_temp_com>`
    * :doc:`temp/cs <compute_temp_cs>`
-   * :doc:`temp/deform <compute_temp_deform>`
+   * :doc:`temp/deform (k) <compute_temp_deform>`
    * :doc:`temp/deform/eff <compute_temp_deform_eff>`
    * :doc:`temp/drude <compute_temp_drude>`
    * :doc:`temp/eff <compute_temp_eff>`

doc/src/Commands_fix.rst

@@ -16,7 +16,7 @@ Fix commands
 
 An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -148,7 +148,7 @@ OPT.
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`
    * :doc:`nvt/manifold/rattle <fix_nvt_manifold_rattle>`
-   * :doc:`nvt/sllod (io) <fix_nvt_sllod>`
+   * :doc:`nvt/sllod (iko) <fix_nvt_sllod>`
    * :doc:`nvt/sllod/eff <fix_nvt_sllod_eff>`
    * :doc:`nvt/sphere (o) <fix_nvt_sphere>`
    * :doc:`nvt/uef <fix_nh_uef>`
@@ -157,11 +157,15 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
+   * :doc:`polarize/bem/gmres <fix_polarize>`
+   * :doc:`polarize/bem/icc <fix_polarize>`
+   * :doc:`polarize/functional <fix_polarize>`
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
@@ -175,14 +179,14 @@ OPT.
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
-   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
    * :doc:`rattle <fix_shake>`
-   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
-   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
+   * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rhok <fix_rhok>`
@@ -232,6 +236,7 @@ OPT.
    * :doc:`ti/spring <fix_ti_spring>`
    * :doc:`tmd <fix_tmd>`
    * :doc:`ttm <fix_ttm>`
+   * :doc:`ttm/grid <fix_ttm>`
    * :doc:`ttm/mod <fix_ttm>`
    * :doc:`tune/kspace <fix_tune_kspace>`
    * :doc:`vector <fix_vector>`

doc/src/Commands_input.rst

@@ -1,55 +1,75 @@
 LAMMPS input scripts
 ====================
 
-LAMMPS executes by reading commands from a input script (text file),
-one line at a time.  When the input script ends, LAMMPS exits.  Each
-command causes LAMMPS to take some action.  It may set an internal
-variable, read in a file, or run a simulation.  Most commands have
-default settings, which means you only need to use the command if you
-wish to change the default.
+LAMMPS executes calculations by reading commands from a input script (text file), one
+line at a time.  When the input script ends, LAMMPS exits.  This is different
+from programs that read and process the entire input before starting a calculation.
+
+Each command causes LAMMPS to take some immediate action without regard
+for any commands that may be processed later. Commands may set an
+internal variable, read in a file, or run a simulation.  These actions
+can be grouped into three categories:
+
+a) commands that change a global setting (examples: timestep, newton,
+   echo, log, thermo, restart),
+b) commands that add, modify, remove, or replace "styles" that are
+   executed during a "run" (examples: pair_style, fix, compute, dump,
+   thermo_style, pair_modify), and
+c) commands that execute a "run" or perform some other computation or
+   operation (examples: print, run, minimize, temper, write_dump, rerun,
+   read_data, read_restart)
+
+Commands in category a) have default settings, which means you only
+need to use the command if you wish to change the defaults.
 
 In many cases, the ordering of commands in an input script is not
-important.  However the following rules apply:
+important, but can have consequences when the global state is changed
+between commands in the c) category. The following rules apply:
 
 (1) LAMMPS does not read your entire input script and then perform a
-simulation with all the settings.  Rather, the input script is read
-one line at a time and each command takes effect when it is read.
-Thus this sequence of commands:
+    simulation with all the settings.  Rather, the input script is read
+    one line at a time and each command takes effect when it is read.
+    Thus this sequence of commands:
 
-.. code-block:: LAMMPS
+    .. code-block:: LAMMPS
 
-   timestep 0.5
-   run      100
-   run      100
+       timestep 0.5
+       run      100
+       run      100
 
-does something different than this sequence:
+    does something different than this sequence:
 
-.. code-block:: LAMMPS
+    .. code-block:: LAMMPS
 
-   run      100
-   timestep 0.5
-   run      100
+       run      100
+       timestep 0.5
+       run      100
 
-In the first case, the specified timestep (0.5 fs) is used for two
-simulations of 100 timesteps each.  In the second case, the default
-timestep (1.0 fs) is used for the first 100 step simulation and a 0.5 fs
-timestep is used for the second one.
+    In the first case, the specified timestep (0.5 fs) is used for two
+    simulations of 100 timesteps each.  In the second case, the default
+    timestep (1.0 fs) is used for the first 100 step simulation and a
+    0.5 fs timestep is used for the second one.
 
 (2) Some commands are only valid when they follow other commands.  For
-example you cannot set the temperature of a group of atoms until atoms
-have been defined and a group command is used to define which atoms
-belong to the group.
+    example you cannot set the temperature of a group of atoms until
+    atoms have been defined and a group command is used to define which
+    atoms belong to the group.
 
 (3) Sometimes command B will use values that can be set by command A.
-This means command A must precede command B in the input script if it
-is to have the desired effect.  For example, the
-:doc:`read_data <read_data>` command initializes the system by setting
-up the simulation box and assigning atoms to processors.  If default
-values are not desired, the :doc:`processors <processors>` and
-:doc:`boundary <boundary>` commands need to be used before read_data to
-tell LAMMPS how to map processors to the simulation box.
+    This means command A must precede command B in the input script if
+    it is to have the desired effect.  For example, the :doc:`read_data
+    <read_data>` command initializes the system by setting up the
+    simulation box and assigning atoms to processors.  If default values
+    are not desired, the :doc:`processors <processors>` and
+    :doc:`boundary <boundary>` commands need to be used before read_data
+    to tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
+
+You can use the :ref:`-skiprun <skiprun>` command line flag
+to have LAMMPS skip the execution of any "run", "minimize", or similar
+commands to check the entire input for correct syntax to avoid crashes
+on typos or syntax errors in long runs.

doc/src/Commands_kspace.rst

@@ -16,7 +16,7 @@ KSpace solvers
 
 All LAMMPS :doc:`kspace_style <kspace_style>` solvers.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -24,16 +24,21 @@ OPT.
 
    * :doc:`ewald (o) <kspace_style>`
    * :doc:`ewald/disp <kspace_style>`
+   * :doc:`ewald/disp/dipole <kspace_style>`
    * :doc:`ewald/dipole <kspace_style>`
    * :doc:`ewald/dipole/spin <kspace_style>`
    * :doc:`msm (o) <kspace_style>`
    * :doc:`msm/cg (o) <kspace_style>`
+   * :doc:`msm/dielectric <kspace_style>`
    * :doc:`pppm (giko) <kspace_style>`
    * :doc:`pppm/cg (o) <kspace_style>`
    * :doc:`pppm/dipole <kspace_style>`
    * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/disp (io) <kspace_style>`
    * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/disp/dielectric <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`scafacos <kspace_style>`

doc/src/Commands_pair.rst

@@ -16,7 +16,7 @@ Pair_style potentials
 
 All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -29,7 +29,7 @@ OPT.
    * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
-   *
+   * :doc:`tracker <pair_tracker>`
    *
    *
    *
@@ -69,13 +69,16 @@ OPT.
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
    * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/dielectric <pair_dielectric>`
    * :doc:`coul/cut/global (o) <pair_coul>`
    * :doc:`coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
    * :doc:`coul/dsf (gko) <pair_coul>`
+   * :doc:`coul/exclude <pair_coul>`
    * :doc:`coul/long (gko) <pair_coul>`
    * :doc:`coul/long/cs (g) <pair_cs>`
+   * :doc:`coul/long/dielectric <pair_dielectric>`
    * :doc:`coul/long/soft (o) <pair_fep_soft>`
    * :doc:`coul/msm (o) <pair_coul>`
    * :doc:`coul/slater/cut <pair_coul_slater>`
@@ -118,6 +121,7 @@ OPT.
    * :doc:`gw/zbl <pair_gw>`
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`hdnnp <pair_hdnnp>`
    * :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
    * :doc:`kolmogorov/crespi/z <pair_kolmogorov_crespi_z>`
@@ -142,13 +146,17 @@ OPT.
    * :doc:`lj/cubic (go) <pair_lj_cubic>`
    * :doc:`lj/cut (gikot) <pair_lj>`
    * :doc:`lj/cut/coul/cut (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/cut/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/coul/debye (gko) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/debye/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/dsf (gko) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long (gikot) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/long/cs <pair_cs>`
+   * :doc:`lj/cut/coul/long/dielectric (o) <pair_dielectric>`
    * :doc:`lj/cut/coul/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
+   * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
    * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
@@ -163,6 +171,7 @@ OPT.
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/coul/long/dielectric <pair_dielectric>`
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
@@ -182,7 +191,7 @@ OPT.
    * :doc:`lubricateU/poly <pair_lubricateU>`
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
-   * :doc:`meam/c <pair_meamc>`
+   * :doc:`meam <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
@@ -226,7 +235,8 @@ OPT.
    * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
-   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`rann <pair_rann>`
+   * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Commands_parse.rst

@@ -47,7 +47,7 @@ LAMMPS:
    named "x" followed by an "x" character.
 
    How the variable is converted to a text string depends on what style
-   of variable it is; see the :doc:`variable <variable>` doc page for
+   of variable it is; see the :doc:`variable <variable>` page for
    details.  It can be a variable that stores multiple text strings, and
    return one of them.  The returned text string can be multiple "words"
    (space separated) which will then be interpreted as multiple
@@ -164,7 +164,7 @@ LAMMPS:
    allowed, but that should be sufficient for most use cases.
 
 .. admonition:: ASCII versus UTF-8
-        :class: note
+   :class: note
 
    LAMMPS expects and processes 7-bit ASCII format text internally.
    Many modern environments use UTF-8 encoding, which is a superset

doc/src/Commands_removed.rst

@@ -25,23 +25,20 @@ The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`
 MEAM package
 ------------
 
-The MEAM package has been removed since it was superseded by the
-:ref:`USER-MEAMC package <PKG-USER-MEAMC>`. The code in
-the USER-MEAMC package is a translation of the Fortran code of MEAM into C++,
-which removes several restrictions (e.g. there can be multiple instances
-in hybrid pair styles) and allows for some optimizations leading
-to better performance.  The new pair style :doc:`meam/c <pair_meamc>` has
-the exact same syntax as the old "meam" pair style and thus pair style
-meam is an alias to the new style and backward
-compatibility of old inputs is preserved.
+The MEAM package in Fortran has been replaced by a C++ implementation.
+The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
+Fortran code of MEAM into C++, which removes several restrictions
+(e.g. there can be multiple instances in hybrid pair styles) and allows
+for some optimizations leading to better performance.  The pair style
+:doc:`meam <pair_meam>` has the exact same syntax.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`USER-REAXC package <PKG-USER-REAXC>`.  The USER-REAXC
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
 package has been tested to yield equivalent results to the REAX package,
-offers better performance, supports OpenMP multi-threading via USER-OMP,
+offers better performance, supports OpenMP multi-threading via OPENMP,
 and GPU and threading parallelization through KOKKOS.  The new pair styles
 are not syntax compatible with the removed reax pair style, so input
 files will have to be adapted.

doc/src/Developer.rst

@@ -11,6 +11,7 @@ of time and requests from the LAMMPS user community.
    :maxdepth: 1
 
    Developer_org
+   Developer_parallel
    Developer_flow
    Developer_write
    Developer_notes

doc/src/Developer_org.rst

@@ -17,7 +17,7 @@ currently supports building with :doc:`conventional makefiles
 differ in how packages are enabled or disabled for inclusion into a
 LAMMPS binary so they cannot be mixed.  The source files for each
 package are in all-uppercase sub-directories of the ``src`` folder, for
-example ``src/MOLECULE`` or ``src/USER-MISC``.  The ``src/STUBS``
+example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
 sub-directory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
 directory and its sub-directories contain makefiles with settings and

doc/src/Developer_par_comm.rst

@@ -0,0 +1,120 @@
+Communication
+^^^^^^^^^^^^^
+
+Following the partitioning scheme in use all per-atom data is
+distributed across the MPI processes, which allows LAMMPS to handle very
+large systems provided it uses a correspondingly large number of MPI
+processes.  Since The per-atom data (atom IDs, positions, velocities,
+types, etc.)  To be able to compute the short-range interactions MPI
+processes need not only access to data of atoms they "own" but also
+information about atoms from neighboring sub-domains, in LAMMPS referred
+to as "ghost" atoms.  These are copies of atoms storing required
+per-atom data for up to the communication cutoff distance. The green
+dashed-line boxes in the :ref:`domain-decomposition` figure illustrate
+the extended ghost-atom sub-domain for one processor.
+
+This approach is also used to implement periodic boundary
+conditions: atoms that lie within the cutoff distance across a periodic
+boundary are also stored as ghost atoms and taken from the periodic
+replication of the sub-domain, which may be the same sub-domain, e.g. if
+running in serial.  As a consequence of this, force computation in
+LAMMPS is not subject to minimum image conventions and thus cutoffs may
+be larger than half the simulation domain.
+
+.. _ghost-atom-comm:
+.. figure:: img/ghost-comm.png
+   :align: center
+
+   ghost atom communication
+
+   This figure shows the ghost atom communication patterns between
+   sub-domains for "brick" (left) and "tiled" communication styles for
+   2d simulations.  The numbers indicate MPI process ranks.  Here the
+   sub-domains are drawn spatially separated for clarity.  The
+   dashed-line box is the extended sub-domain of processor 0 which
+   includes its ghost atoms.  The red- and blue-shaded boxes are the
+   regions of communicated ghost atoms.
+
+Efficient communication patterns are needed to update the "ghost" atom
+data, since that needs to be done at every MD time step or minimization
+step.  The diagrams of the `ghost-atom-comm` figure illustrate how ghost
+atom communication is performed in two stages for a 2d simulation (three
+in 3d) for both a regular and irregular partitioning of the simulation
+box.  For the regular case (left) atoms are exchanged first in the
+*x*-direction, then in *y*, with four neighbors in the grid of processor
+sub-domains.
+
+In the *x* stage, processor ranks 1 and 2 send owned atoms in their
+red-shaded regions to rank 0 (and vice versa).  Then in the *y* stage,
+ranks 3 and 4 send atoms in their blue-shaded regions to rank 0, which
+includes ghost atoms they received in the *x* stage.  Rank 0 thus
+acquires all its ghost atoms; atoms in the solid blue corner regions
+are communicated twice before rank 0 receives them.
+
+For the irregular case (right) the two stages are similar, but a
+processor can have more than one neighbor in each direction.  In the
+*x* stage, MPI ranks 1,2,3 send owned atoms in their red-shaded regions to
+rank 0 (and vice versa).  These include only atoms between the lower
+and upper *y*-boundary of rank 0's sub-domain.  In the *y* stage, ranks
+4,5,6 send atoms in their blue-shaded regions to rank 0.  This may
+include ghost atoms they received in the *x* stage, but only if they
+are needed by rank 0 to fill its extended ghost atom regions in the
++/-*y* directions (blue rectangles).  Thus in this case, ranks 5 and
+6 do not include ghost atoms they received from each other (in the *x*
+stage) in the atoms they send to rank 0.  The key point is that while
+the pattern of communication is more complex in the irregular
+partitioning case, it can still proceed in two stages (three in 3d)
+via atom exchanges with only neighboring processors.
+
+When attributes of owned atoms are sent to neighboring processors to
+become attributes of their ghost atoms, LAMMPS calls this a "forward"
+communication.  On timesteps when atoms migrate to new owning processors
+and neighbor lists are rebuilt, each processor creates a list of its
+owned atoms which are ghost atoms in each of its neighbor processors.
+These lists are used to pack per-atom coordinates (for example) into
+message buffers in subsequent steps until the next reneighboring.
+
+A "reverse" communication is when computed ghost atom attributes are
+sent back to the processor who owns the atom.  This is used (for
+example) to sum partial forces on ghost atoms to the complete force on
+owned atoms.  The order of the two stages described in the
+:ref:`ghost-atom-comm` figure is inverted and the same lists of atoms
+are used to pack and unpack message buffers with per-atom forces.  When
+a received buffer is unpacked, the ghost forces are summed to owned atom
+forces.  As in forward communication, forces on atoms in the four blue
+corners of the diagrams are sent, received, and summed twice (once at
+each stage) before owning processors have the full force.
+
+These two operations are used many places within LAMMPS aside from
+exchange of coordinates and forces, for example by manybody potentials
+to share intermediate per-atom values, or by rigid-body integrators to
+enable each atom in a body to access body properties.  Here are
+additional details about how these communication operations are
+performed in LAMMPS:
+
+- When exchanging data with different processors, forward and reverse
+  communication is done using ``MPI_Send()`` and ``MPI_IRecv()`` calls.
+  If a processor is "exchanging" atoms with itself, only the pack and
+  unpack operations are performed, e.g. to create ghost atoms across
+  periodic boundaries when running on a single processor.
+
+- For forward communication of owned atom coordinates, periodic box
+  lengths are added and subtracted when the receiving processor is
+  across a periodic boundary from the sender.  There is then no need to
+  apply a minimum image convention when calculating distances between
+  atom pairs when building neighbor lists or computing forces.
+
+- The cutoff distance for exchanging ghost atoms is typically equal to
+  the neighbor cutoff.  But it can also chosen to be longer if needed,
+  e.g. half the diameter of a rigid body composed of multiple atoms or
+  over 3x the length of a stretched bond for dihedral interactions.  It
+  can also exceed the periodic box size.  For the regular communication
+  pattern (left), if the cutoff distance extends beyond a neighbor
+  processor's sub-domain, then multiple exchanges are performed in the
+  same direction.  Each exchange is with the same neighbor processor,
+  but buffers are packed/unpacked using a different list of atoms. For
+  forward communication, in the first exchange a processor sends only
+  owned atoms.  In subsequent exchanges, it sends ghost atoms received
+  in previous exchanges.  For the irregular pattern (right) overlaps of
+  a processor's extended ghost-atom sub-domain with all other processors
+  in each dimension are detected.

doc/src/Developer_par_long.rst

@@ -0,0 +1,188 @@
+Long-range interactions
+^^^^^^^^^^^^^^^^^^^^^^^
+
+For charged systems, LAMMPS can compute long-range Coulombic
+interactions via the FFT-based particle-particle/particle-mesh (PPPM)
+method implemented in :doc:`kspace style pppm and its variants
+<kspace_style>`.  For that Coulombic interactions are partitioned into
+short- and long-range components.  The short-ranged portion is computed
+in real space as a loop over pairs of charges within a cutoff distance,
+using neighbor lists.  The long-range portion is computed in reciprocal
+space using a kspace style.  For the PPPM implementation the simulation
+cell is overlaid with a regular FFT grid in 3d. It proceeds in several stages:
+
+a) each atom's point charge is interpolated to nearby FFT grid points,
+b) a forward 3d FFT is performed,
+c) a convolution operation is performed in reciprocal space,
+d) one or more inverse 3d FFTs are performed, and
+e) electric field values from grid points near each atom are interpolated to compute
+   its forces.
+
+For any of the spatial-decomposition partitioning schemes each processor
+owns the brick-shaped portion of FFT grid points contained within its
+sub-domain.  The two interpolation operations use a stencil of grid
+points surrounding each atom.  To accommodate the stencil size, each
+processor also stores a few layers of ghost grid points surrounding its
+brick.  Forward and reverse communication of grid point values is
+performed similar to the corresponding :doc:`atom data communication
+<Developer_par_comm>`.  In this case, electric field values on owned
+grid points are sent to neighboring processors to become ghost point
+values.  Likewise charge values on ghost points are sent and summed to
+values on owned points.
+
+For triclinic simulation boxes, the FFT grid planes are parallel to
+the box faces, but the mapping of charge and electric field values
+to/from grid points is done in reduced coordinates where the tilted
+box is conceptually a unit cube, so that the stencil and FFT
+operations are unchanged.  However the FFT grid size required for a
+given accuracy is larger for triclinic domains than it is for
+orthogonal boxes.
+
+.. _fft-parallel:
+.. figure:: img/fft-decomp-parallel.png
+   :align: center
+
+   parallel FFT in PPPM
+
+   Stages of a parallel FFT for a simulation domain overlaid
+   with an 8x8x8 3d FFT grid, partitioned across 64 processors.
+   Within each of the 4 diagrams, grid cells of the same color are
+   owned by a single processor; for simplicity only cells owned by 4
+   or 8 of the 64 processors are colored.  The two images on the left
+   illustrate brick-to-pencil communication.  The two images on the
+   right illustrate pencil-to-pencil communication, which in this
+   case transposes the *y* and *z* dimensions of the grid.
+
+Parallel 3d FFTs require substantial communication relative to their
+computational cost.  A 3d FFT is implemented by a series of 1d FFTs
+along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus the FFT
+grid cannot be decomposed like atoms into 3 dimensions for parallel
+processing of the FFTs but only in 1 (as planes) or 2 (as pencils)
+dimensions and in between the steps the grid needs to be transposed to
+have the FFT grid portion "owned" by each MPI process complete in the
+direction of the 1d FFTs it has to perform. LAMMPS uses the
+pencil-decomposition algorithm as shown in the :ref:`fft-parallel` figure.
+
+Initially (far left), each processor owns a brick of same-color grid
+cells (actually grid points) contained within in its sub-domain.  A
+brick-to-pencil communication operation converts this layout to 1d
+pencils in the *x*-dimension (center left).  Again, cells of the same
+color are owned by the same processor.  Each processor can then compute
+a 1d FFT on each pencil of data it wholly owns using a call to the
+configured FFT library.  A pencil-to-pencil communication then converts
+this layout to pencils in the *y* dimension (center right) which
+effectively transposes the *x* and *y* dimensions of the grid, followed
+by 1d FFTs in *y*.  A final transpose of pencils from *y* to *z* (far
+right) followed by 1d FFTs in *z* completes the forward FFT.  The data
+is left in a *z*-pencil layout for the convolution operation.  One or
+more inverse FFTs then perform the sequence of 1d FFTs and communication
+steps in reverse order; the final layout of resulting grid values is the
+same as the initial brick layout.
+
+Each communication operation within the FFT (brick-to-pencil or
+pencil-to-pencil or pencil-to-brick) converts one tiling of the 3d grid
+to another, where a tiling in this context means an assignment of a
+small brick-shaped subset of grid points to each processor, the union of
+which comprise the entire grid.  The parallel `fftMPI library
+<https://lammps.github.io/fftmpi/>`_ written for LAMMPS allows arbitrary
+definitions of the tiling so that an irregular partitioning of the
+simulation domain can use it directly.  Transforming data from one
+tiling to another is implemented in `fftMPI` using point-to-point
+communication, where each processor sends data to a few other
+processors, since each tile in the initial tiling overlaps with a
+handful of tiles in the final tiling.
+
+The transformations could also be done using collective communication
+across all $P$ processors with a single call to ``MPI_Alltoall()``, but
+this is typically much slower.  However, for the specialized brick and
+pencil tiling illustrated in :ref:`fft-parallel` figure, collective
+communication across the entire MPI communicator is not required.  In
+the example an :math:`8^3` grid with 512 grid cells is partitioned
+across 64 processors; each processor owns a 2x2x2 3d brick of grid
+cells.  The initial brick-to-pencil communication (upper left to upper
+right) only requires collective communication within subgroups of 4
+processors, as illustrated by the 4 colors.  More generally, a
+brick-to-pencil communication can be performed by partitioning *P*
+processors into :math:`P^{\frac{2}{3}}` subgroups of
+:math:`P^{\frac{1}{3}}` processors each.  Each subgroup performs
+collective communication only within its subgroup.  Similarly,
+pencil-to-pencil communication can be performed by partitioning *P*
+processors into :math:`P^{\frac{1}{2}}` subgroups of
+:math:`P^{\frac{1}{2}}` processors each.  This is illustrated in the
+figure for the :math:`y \Rightarrow z` communication (center).  An
+eight-processor subgroup owns the front *yz* plane of data and performs
+collective communication within the subgroup to transpose from a
+*y*-pencil to *z*-pencil layout.
+
+LAMMPS invokes point-to-point communication by default, but also
+provides the option of partitioned collective communication when using a
+:doc:`kspace_modify collective yes <kspace_modify>` command to switch to
+that mode.  In the latter case, the code detects the size of the
+disjoint subgroups and partitions the single *P*-size communicator into
+multiple smaller communicators, each of which invokes collective
+communication.  Testing on a large IBM Blue Gene/Q machine at Argonne
+National Labs showed a significant improvement in FFT performance for
+large processor counts; partitioned collective communication was faster
+than point-to-point communication or global collective communication
+involving all *P* processors.
+
+Here are some additional details about FFTs for long-range and related
+grid/particle operations that LAMMPS supports:
+
+- The fftMPI library allows each grid dimension to be a multiple of
+  small prime factors (2,3,5), and allows any number of processors to
+  perform the FFT.  The resulting brick and pencil decompositions are
+  thus not always as well-aligned but the size of subgroups of
+  processors for the two modes of communication (brick/pencil and
+  pencil/pencil) still scale as :math:`O(P^{\frac{1}{3}})` and
+  :math:`O(P^{\frac{1}{2}})`.
+
+- For efficiency in performing 1d FFTs, the grid transpose
+  operations illustrated in Figure \ref{fig:fft} also involve
+  reordering the 3d data so that a different dimension is contiguous
+  in memory.  This reordering can be done during the packing or
+  unpacking of buffers for MPI communication.
+
+- For large systems and particularly a large number of MPI processes,
+  the dominant cost for parallel FFTs is often the communication, not
+  the computation of 1d FFTs, even though the latter scales as :math:`N
+  \log(N)` in the number of grid points *N* per grid direction.  This is
+  due to the fact that only a 2d decomposition into pencils is possible
+  while atom data (and their corresponding short-range force and energy
+  computations) can be decomposed efficiently in 3d.
+
+  This can be addressed by reducing the number of MPI processes involved
+  in the MPI communication by using :doc:`hybrid MPI + OpenMP
+  parallelization <Speed_omp>`.  This will use OpenMP parallelization
+  inside the MPI domains and while that may have a lower parallel
+  efficiency, it reduces the communication overhead.
+
+  As an alternative it is also possible to start a :ref:`multi-partition
+  <partition>` calculation and then use the :doc:`verlet/split
+  integrator <run_style>` to perform the PPPM computation on a
+  dedicated, separate partition of MPI processes.  This uses an integer
+  "1:*p*" mapping of *p* sub-domains of the atom decomposition to one
+  sub-domain of the FFT grid decomposition and where pairwise non-bonded
+  and bonded forces and energies are computed on the larger partition
+  and the PPPM kspace computation concurrently on the smaller partition.
+
+- LAMMPS also implements PPPM-based solvers for other long-range
+  interactions, dipole and dispersion (Lennard-Jones), which can be used
+  in conjunction with long-range  Coulombics for point charges.
+
+- LAMMPS implements a ``GridComm`` class which overlays the simulation
+  domain with a regular grid, partitions it across processors in a
+  manner consistent with processor sub-domains, and provides methods for
+  forward and reverse communication of owned and ghost grid point
+  values.  It is used for PPPM as an FFT grid (as outlined above) and
+  also for the MSM algorithm which uses a cascade of grid sizes from
+  fine to coarse to compute long-range Coulombic forces.  The GridComm
+  class is also useful for models where continuum fields interact with
+  particles.  For example, the two-temperature model (TTM) defines heat
+  transfer between atoms (particles) and electrons (continuum gas) where
+  spatial variations in the electron temperature are computed by finite
+  differences of a discretized heat equation on a regular grid.  The
+  :doc:`fix ttm/grid <fix_ttm>` command uses the ``GridComm`` class
+  internally to perform its grid operations on a distributed grid
+  instead of the original :doc:`fix ttm <fix_ttm>` which uses a
+  replicated grid.