Merge pull request #2822 from akohlmey/next_patch_release

Step version strings for next patch release

.gitattributes

@@ -1,3 +1,5 @@
 .gitattributes export-ignore
 .gitignore export-ignore
 .github export-ignore
+.lgtm.yml export-ignore
+SECURITY.md export-ignore

.github/CODEOWNERS

@@ -13,33 +13,42 @@ 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
+src/REACTION/*   @jrgissing
+src/SCAFACOS/*   @rhalver
+src/TALLY/*      @akohlmey
+src/UEF/*        @danicholson
+src/VTK/*        @rbberger
 
 
 # individual files in packages
@@ -47,7 +56,6 @@ 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
 
@@ -122,15 +130,17 @@ tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
 tools/code_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 +152,7 @@ fortran/*             @akohlmey
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+examples/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/CONTRIBUTING.md

@@ -26,11 +26,11 @@ __
 
 ## 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 the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+> **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.
 
 ## How Can I Contribute?
 
-There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+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
 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
@@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not
 
 If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
 
+The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort  towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
+
 ### Reporting Bugs
 
 While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
@@ -72,13 +74,13 @@ Here is a checklist of steps you need to follow to submit a single file or user
 * 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.
+* 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 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 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
+* 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 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/PACKAGES 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.
+* 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/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.
 

.github/codeql/cpp.yml

@@ -0,0 +1,4 @@
+paths:
+ - src
+ - lib
+ - tools

.github/codeql/python.yml

@@ -0,0 +1,5 @@
+paths:
+ - python/lammps
+
+queries:
+ - uses: security-and-quality

.github/workflows/codeql-analysis.yml

@@ -31,16 +31,18 @@ jobs:
       uses: github/codeql-action/init@v1
       with:
         languages: ${{ matrix.language }}
+        config-file: ./.github/codeql/${{ matrix.language }}.yml
 
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      if: ${{ matrix.language == 'cpp' }}
+      run: mkdir build
 
     - name: Building LAMMPS via CMake
       if: ${{ matrix.language == 'cpp' }}
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
+        cmake -C ../cmake/presets/most.cmake ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/unittest-macos.yml

@@ -10,6 +10,8 @@ jobs:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: macos-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
@@ -17,18 +19,36 @@ jobs:
       with:
         fetch-depth: 2
 
+    - name: Install ccache
+      run: brew install ccache
+
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: macos-ccache-${{ github.sha }}
+        restore-keys: macos-ccache-
 
     - name: Building LAMMPS via CMake
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
-              -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
+        ccache -z
+        cmake -C ../cmake/presets/clang.cmake \
+              -C ../cmake/presets/most.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D ENABLE_TESTING=on \
+              -D BUILD_SHARED_LIBS=on \
+              -D LAMMPS_EXCEPTIONS=on \
+              ../cmake
         cmake --build . --parallel 2
+        ccache -s
 
     - name: Run Tests
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       shell: bash
       run: ctest -V

.gitignore

@@ -12,6 +12,7 @@
 *.sif
 *.dll
 *.pyc
+a.out
 __pycache__
 
 Obj_*

.lgtm.yml

@@ -0,0 +1,14 @@
+extraction:
+  cpp:
+    configure:
+      command:
+      - "mkdir build"
+      - "cd build"
+      - "cmake -G Ninja -C ../cmake/presets/most.cmake ../cmake"
+    index:
+      build_command:
+      - "cd build"
+      - "ninja"
+  python:
+    python_setup:
+      version: 3

LICENSE

@@ -1,6 +1,6 @@
 GNU GENERAL PUBLIC LICENSE
 
-Version 2, June 1991 
+Version 2, June 1991
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -301,9 +301,8 @@ one line to give the program's name and an idea of what it does.
 Copyright (C) yyyy  name of author
 
 This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or (at
-your option) any later version.
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of

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:
 

SECURITY.md

@@ -0,0 +1,35 @@
+# Security Policy
+
+LAMMPS is designed as a user-level application to conduct computer
+simulations for research using classical mechanics.  As such LAMMPS
+depends to some degrees on users providing correctly formatted input and
+LAMMPS needs to read and write files based on uncontrolled user input.
+As a parallel application for use in high-performance computing
+environments, performance critical steps are also done without checking
+data.
+
+LAMMPS also is interfaced to a number of external libraries, including
+libraries with experimental research software, that are not validated
+and tested by the LAMMPS developers, so it is easy to import bad
+behavior from calling functions in one of those libraries.
+
+Thus is is quite easy to crash LAMMPS through malicious input and do all
+kinds of filesystem manipulations.  And because of that LAMMPS should
+**NEVER** be compiled or **run** as superuser, either from a "root" or
+"administrator" account directly or indirectly via "sudo" or "su".
+
+Therefore what could be seen as a security vulnerability is usually
+either a user mistake or a bug in the code.  Bugs can be reported in
+the LAMMPS project
+[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+
+
+# Version Updates
+
+LAMMPS follows continuous release development model.  We aim to keep all
+release versions (stable or patch) fully functional and employ a variety
+of automatic testing procedures to detect failures of existing
+functionality from adding new features before releases are made.  Thus
+bugfixes and updates are only integrated into the current development
+branch and thus the next (patch) release and users are recommended to
+update regularly.

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/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)
@@ -22,11 +27,23 @@ set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
+set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
+set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
+set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty")
+mark_as_advanced(LAMMPS_DOWNLOADS_URL)
+
 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 )
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
+option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
+if(LAMMPS_INSTALL_RPATH)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
@@ -60,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
   set(CMAKE_CXX_FLAGS "${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")
@@ -74,6 +91,11 @@ set(CMAKE_CXX_STANDARD 11)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 
+# 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                                                   #
 ########################################################################
@@ -92,11 +114,23 @@ 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})
@@ -104,17 +138,86 @@ 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
-  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-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)
+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
+  FEP
+  GRANULAR
+  H5MD
+  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
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  USER-MISC
+  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)
@@ -125,7 +228,7 @@ 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
@@ -139,12 +242,13 @@ if(NOT CMAKE_CROSSCOMPILING)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
   # 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()
@@ -156,8 +260,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
@@ -179,7 +282,7 @@ 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")
@@ -195,12 +298,13 @@ 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)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -221,8 +325,10 @@ 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.
@@ -234,69 +340,7 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-# Compiler specific features for testing
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC --coverage)
-      target_link_options(lammps PUBLIC --coverage)
-    endif()
-  endif()
-endif()
-
-#######################################
-# add custom target for IWYU analysis
-#######################################
-set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
-mark_as_advanced(ENABLE_IWYU)
-if(ENABLE_IWYU)
-  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)
-    add_custom_target(
-      iwyu
-      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
-      COMMENT "Running IWYU")
-    add_dependencies(iwyu lammps)
-  else()
-    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
-      "and the iwyu-tool/iwyu_tool script installed in your PATH")
-  endif()
-endif()
-
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
-mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
-set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
-validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
-string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
-if(NOT ENABLE_SANITIZER STREQUAL "none")
-  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-    endif()
-  else()
-    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
-    set(ENABLE_SANITIZER "none")
-  endif()
-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)
@@ -347,7 +391,7 @@ 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")
@@ -358,7 +402,7 @@ 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")
@@ -375,8 +419,8 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+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})
   endif()
@@ -469,11 +513,10 @@ 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)
@@ -485,9 +528,9 @@ 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})
@@ -495,13 +538,13 @@ 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 ${LAPACK_LIBRARIES})
   if(BUILD_MPI)
@@ -513,26 +556,38 @@ if(PKG_USER-ATC)
   target_compile_definitions(atc PRIVATE -DLAMMPS_${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()
 endforeach()
 
+if(PKG_PLUGIN)
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
+endif()
+
 ######################################################################
 # the windows version of LAMMPS requires a couple extra libraries
 # and the MPI library - if use - has to be linked right before those
 # and after everything else that is compiled locally
 ######################################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
@@ -581,8 +636,8 @@ 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
@@ -660,7 +715,7 @@ 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
@@ -693,7 +748,7 @@ 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()
@@ -707,7 +762,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Operating System: ${CMAKE_SYSTEM_NAME}
+   Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    Build type:       ${CMAKE_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -738,15 +793,15 @@ 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}
@@ -776,11 +831,12 @@ if(BUILD_MPI)
 endif()
 if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
--- GPU API:          ${GPU_API}")
+-- GPU API:                  ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU architecture: ${GPU_ARCH}")
-  elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
+    message(STATUS "CUDA Compiler:            ${CUDA_NVCC_EXECUTABLE}")
+    message(STATUS "GPU default architecture: ${GPU_ARCH}")
+    message(STATUS "GPU binning with CUDPP:   ${CUDPP_OPT}")
+    message(STATUS "CUDA MPS support:         ${CUDA_MPS_SUPPORT}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")
@@ -790,7 +846,7 @@ if(PKG_GPU)
       message(STATUS "HIP GPU sorting: off")
     endif()
   endif()
-  message(STATUS "GPU precision:    ${GPU_PREC}")
+  message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
@@ -810,7 +866,7 @@ if(PKG_KSPACE)
   endif()
   if(PKG_KOKKOS)
     if(Kokkos_ENABLE_CUDA)
-      if (${FFT} STREQUAL "KISS")
+      if(FFT STREQUAL "KISS")
         message(STATUS "Kokkos FFT: KISS")
       else()
         message(STATUS "Kokkos FFT: cuFFT")

cmake/Modules/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/Documentation.cmake

@@ -50,16 +50,20 @@ if(BUILD_DOC)
     OUTPUT ${DOC_BUILD_DIR}/requirements.txt
     DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
     COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
+  mark_as_advanced(MATHJAX_URL)
+
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
+    file(DOWNLOAD ${MATHJAX_URL}
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
+      EXPECTED_MD5 ${MATHJAX_MD5})
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
     file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

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)
@@ -8,10 +8,12 @@ endif()
 
 include(ExternalProject)
 set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
 mark_as_advanced(GTEST_URL)
+mark_as_advanced(GTEST_MD5)
 ExternalProject_Add(googletest
-                    URL ${GTEST_URL}
-                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
+                    URL             ${GTEST_URL}
+                    URL_MD5         ${GTEST_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}
@@ -20,10 +22,10 @@ ExternalProject_Add(googletest
                                     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
                                     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
                                     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
                     LOG_DOWNLOAD ON
                     LOG_CONFIGURE ON
                     LOG_BUILD ON
@@ -39,10 +41,10 @@ file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
 file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
 
 ExternalProject_Get_Property(googletest BINARY_DIR)
-set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
-set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 # Prevent GoogleTest from overriding our compiler/linker options
 # when building with Visual Studio

cmake/Modules/GenerateOpenCLHeader.cmake

@@ -0,0 +1,3 @@
+# utility script to call WriteOpenCLHeader function
+include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
+WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

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()
 
@@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
   if (EXISTS "${pkgfolder}/potentials.txt")
-    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)
@@ -105,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
     endforeach()
   endif()
 endfunction(FetchPotentials)
+
+# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
+if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
+  file(STRINGS /etc/os-release distro REGEX "^NAME=")
+  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
+  string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
+  set(CMAKE_LINUX_DISTRO ${distro})
+  set(CMAKE_DISTRO_VERSION ${disversion})
+endif()

cmake/Modules/MPI4WIN.cmake

@@ -1,16 +1,25 @@
 # Download and configure custom MPICH files for Windows
 message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
 include(ExternalProject)
 if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
-    URL_MD5 4939fdb59d13182fd5dd65211e469f14
+    URL     ${MPICH2_WIN64_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 else()
   ExternalProject_Add(mpi4win_build
-    URL https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
-    URL_MD5 a61d153500dce44e21b755ee7257e031
+    URL     ${MPICH2_WIN32_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
     BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 endif()

cmake/Modules/OpenCLLoader.cmake

@@ -0,0 +1,50 @@
+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")
+mark_as_advanced(OPENCL_LOADER_URL)
+mark_as_advanced(OPENCL_LOADER_MD5)
+
+include(ExternalProject)
+ExternalProject_Add(opencl_loader
+                    URL             ${OPENCL_LOADER_URL}
+                    URL_MD5         ${OPENCL_LOADER_MD5}
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
+set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
+
+ExternalProject_Get_Property(opencl_loader BINARY_DIR)
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
+
+find_package(Threads QUIET)
+if(NOT WIN32)
+  set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
+else()
+  set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
+endif()
+
+add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+add_dependencies(OpenCL::OpenCL opencl_loader)
+
+set_target_properties(OpenCL::OpenCL PROPERTIES
+  IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
+  INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
+  INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
+
+

cmake/Modules/OpenCLUtils.cmake

@@ -1,10 +1,8 @@
-function(GenerateOpenCLHeader varname outfile files)
-    message("Creating ${outfile}...")
+function(WriteOpenCLHeader varname outfile files)
     file(WRITE ${outfile} "const char * ${varname} = \n")
-    math(EXPR ARG_END   "${ARGC}-1")
+    separate_arguments(files)
 
-    foreach(IDX RANGE 2 ${ARG_END})
-        list(GET ARGV ${IDX} filename)
+    foreach(filename ${files})
         file(READ ${filename} content)
         string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
     endforeach()
 
     file(APPEND ${outfile} ";\n")
+endfunction(WriteOpenCLHeader)
+
+function(GenerateOpenCLHeader varname outfile files)
+    list(REMOVE_AT ARGV 0 1)
+    add_custom_command(OUTPUT ${outfile}
+      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+                               -D VARNAME=${varname}
+                               -D HEADER_FILE=${outfile}
+                               -D SOURCE_FILES="${ARGV}"
+                               -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
+      DEPENDS ${ARGV}
+      COMMENT "Generating ${outfile}...")
 endfunction(GenerateOpenCLHeader)

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

@@ -1,7 +1,9 @@
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
-                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.h
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.cpp)
 target_compile_definitions(lammps PRIVATE -DLMP_GPU)
 
 set(GPU_API "opencl" CACHE STRING "API used by GPU package")
@@ -33,7 +35,7 @@ if(GPU_API STREQUAL "CUDA")
   if(NOT BIN2C)
     message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
   endif()
-  option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+  option(CUDPP_OPT "Enable GPU binning via CUDAPP (should be off for modern GPUs)" OFF)
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
     if(CUDPP_OPT)
@@ -46,7 +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"
@@ -97,19 +99,23 @@ if(GPU_API STREQUAL "CUDA")
   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 and 8.6) is supported by CUDA 11 and later
+  # 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] -gencode arch=compute_86,code=[sm_86,compute_86]")
+    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()
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
     message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -125,7 +131,7 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -139,27 +145,20 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-    # download and unpack support binaries for compilation of windows binaries.
-    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
-    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
-            EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
-    if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
-    elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
-    endif()
-    set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+  # the static OpenCL loader doesn't seem to work on macOS. use the system provided
+  # version by default instead (for as long as it will be available)
+  if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(_opencl_static_default OFF)
+  else()
+    set(_opencl_static_default ON)
+  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)
+    include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)
   endif()
-  set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-  set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-  set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-  validate_option(OCL_TUNE OCL_TUNE_VALUES)
-  string(TOUPPER ${OCL_TUNE} OCL_TUNE)
 
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@@ -203,7 +202,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
   target_link_libraries(lammps PRIVATE gpu)
@@ -211,6 +210,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
+  add_dependencies(ocl_get_devices OpenCL::OpenCL)
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
@@ -225,7 +225,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(NOT DEFINED HIP_PLATFORM)
       if(NOT DEFINED ENV{HIP_PLATFORM})
-          set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
+          set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation")
       else()
           set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
       endif()
@@ -233,7 +233,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc")
+  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
@@ -291,23 +291,23 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc")
+    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()
     elseif(HIP_PLATFORM STREQUAL "nvcc")
         add_custom_command(OUTPUT ${CUBIN_FILE}
-          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
+          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
           DEPENDS ${CU_FILE}
           COMMENT "Generating ${CU_NAME}.cubin")
     endif()
@@ -345,11 +345,16 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
+        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
+        mark_as_advanced(CUB_URL)
+        mark_as_advanced(CUB_MD5)
+
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          GIT_REPOSITORY https://github.com/NVlabs/cub
-          TIMEOUT 5
+          URL     ${CUB_URL}
+          URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
           BUILD_COMMAND ""
@@ -361,7 +366,7 @@ elseif(GPU_API STREQUAL "HIP")
       else()
         find_package(CUB)
         if(NOT CUB_FOUND)
-          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it")
         endif()
       endif()
 
@@ -388,18 +393,21 @@ elseif(GPU_API STREQUAL "HIP")
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
     target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
+  elseif(HIP_PLATFORM STREQUAL "amd")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)
 endif()
 
-# GPU package
-FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-# detects styles which have GPU version
+# detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 

cmake/Modules/Packages/INTEL.cmake

@@ -5,7 +5,7 @@ endif()
 
 target_compile_definitions(lammps PRIVATE -DLMP_USER_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)
@@ -30,15 +30,20 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
   endif()
 endif()
 if(INTEL_LRT_MODE STREQUAL "C++11")
-  target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+  if(Threads_FOUND)
+    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+    target_link_libraries(lammps PRIVATE Threads::Threads)
+  else()
+    message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+  endif()
 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)
@@ -47,7 +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()
 
@@ -60,12 +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  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
   set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
@@ -74,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
 else()
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     include(CheckCXXCompilerFlag)
-    foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
-      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
-      if(COMPILER_SUPPORTS${_FLAG})
+    foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+      string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
+      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
+      if(COMPILER_SUPPORTS${_FLAGX})
+          separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
           target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()
@@ -84,26 +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/KIM.cmake

@@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
   include(ExternalProject)
   enable_language(C)
   enable_language(Fortran)
+  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
+  set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
+  mark_as_advanced(KIM_URL)
+  mark_as_advanced(KIM_MD5)
   ExternalProject_Add(kim_build
-    URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
-    URL_MD5 ae1ddda2ef7017ea07934e519d023dca
+    URL     ${KIM_URL}
+    URL_MD5 ${KIM_MD5}
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@@ -69,14 +73,14 @@ if(DOWNLOAD_KIM)
     BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
     )
 else()
-  if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
+  if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
     # For kim-api >= 2.2.0
-    find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
+    find_package(KIM-API 2.2.0 CONFIG REQUIRED)
     target_link_libraries(lammps PRIVATE KIM-API::kim-api)
   else()
     # For kim-api 2.1.3 (consistent with previous version of this file)
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
     target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
   endif()
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -37,9 +37,13 @@ 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/3.4.01.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
-    URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
-    URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
+    URL     ${KOKKOS_URL}
+    URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -51,10 +55,12 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
+  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.3.01 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()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -66,6 +72,7 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
+  target_link_libraries(lmp PRIVATE kokkos)
 endif()
 target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
 
@@ -92,7 +99,7 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
-    if(NOT ${FFT} STREQUAL "KISS")
+    if(NOT (FFT STREQUAL "KISS"))
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()
@@ -109,7 +116,7 @@ RegisterNBinStyle(${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)

cmake/Modules/Packages/LATTE.cmake

@@ -15,10 +15,14 @@ endif()
 option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
 if(DOWNLOAD_LATTE)
   message(STATUS "LATTE download requested - we will build our own")
+  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
+  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
+  mark_as_advanced(LATTE_URL)
+  mark_as_advanced(LATTE_MD5)
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
-    URL_MD5 820e73a457ced178c08c71389a385de7
+    URL     ${LATTE_URL}
+    URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

cmake/Modules/Packages/MACHDYN.cmake

@@ -7,10 +7,14 @@ 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")
+  mark_as_advanced(EIGEN3_URL)
+  mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
-    URL_MD5 9e30f67e8531477de4117506fe44669b
+    URL     ${EIGEN3_URL}
+    URL_MD5 ${EIGEN3_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)

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_USER_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

cmake/Modules/Packages/MESSAGE.cmake

@@ -1,10 +1,9 @@
-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)
-file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+file(GLOB_RECURSE cslib_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -0,0 +1,127 @@
+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} -DMPICH_SKIP_MPICXX=1")
+      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} -DMPICH_SKIP_MPICXX=1")
+      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}")
+
+  # 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

@@ -0,0 +1,25 @@
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+
+# download library sources to build folder
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
+
+# uncompress downloaded sources
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+  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 ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
+target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/MOLFILE.cmake

@@ -1,9 +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})
-# no need to link with -ldl on windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+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

@@ -7,10 +7,15 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  mark_as_advanced(MSCG_URL)
+  mark_as_advanced(MSCG_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(mscg_build
-    URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
-    URL_MD5 8c45e269ee13f60b303edd7823866a91
+    URL     ${MSCG_URL}
+    URL_MD5 ${MSCG_MD5}
     SOURCE_SUBDIR src/CMake
     CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

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
+                       ${OPENMP_SOURCES_DIR}/domain_omp.cpp)
+  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
+  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${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}/reaxc_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
+  endif()
+
+  target_sources(lammps PRIVATE ${OPENMP_SOURCES})
+  target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR})

cmake/Modules/Packages/PLUMED.cmake

@@ -53,10 +53,17 @@ if(DOWNLOAD_PLUMED)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
     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")
+
+  mark_as_advanced(PLUMED_URL)
+  mark_as_advanced(PLUMED_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz
-    URL_MD5 95f29dd0c067577f11972ff90dfc7d12
+    URL     ${PLUMED_URL}
+    URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
@@ -65,6 +72,7 @@ if(DOWNLOAD_PLUMED)
                                              ${PLUMED_CONFIG_OMP}
                                              CXX=${PLUMED_CONFIG_CXX}
                                              CC=${PLUMED_CONFIG_CC}
+    PATCH_COMMAND sed -i "/^#include <algorithm>/a #include <limits>" <SOURCE_DIR>/src/lepton/Operation.h
     BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
   )
   ExternalProject_get_property(plumed_build INSTALL_DIR)

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

@@ -14,15 +14,19 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  mark_as_advanced(SCAFACOS_URL)
+  mark_as_advanced(SCAFACOS_MD5)
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
-  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+  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)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
-    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    URL     ${SCAFACOS_URL}
+    URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

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/VORONOI.cmake

@@ -7,6 +7,11 @@ endif()
 option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
 if(DOWNLOAD_VORO)
   message(STATUS "Voro++ download requested - we will build our own")
+  set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball")
+  set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball")
+  mark_as_advanced(VORO_URL)
+  mark_as_advanced(VORO_MD5)
+
   include(ExternalProject)
 
   if(BUILD_SHARED_LIBS)
@@ -22,8 +27,8 @@ if(DOWNLOAD_VORO)
   endif()
 
   ExternalProject_Add(voro_build
-    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
-    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+    URL     ${VORO_URL}
+    URL_MD5 ${VORO_MD5}
     PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${VORO_BUILD_OPTIONS}

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

@@ -16,11 +16,14 @@ if(ENABLE_TESTING)
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
-  # check if a faster linker is available.
-  # only verified with GNU and Clang compilers and new CMake
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+  # 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)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@@ -53,3 +56,76 @@ if(ENABLE_TESTING)
   get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
   add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
 endif()
+
+# Compiler specific features for testing
+if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+#######################################
+# add custom target for IWYU analysis
+#######################################
+set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
+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")))
+    message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
+  endif()
+  # detect the "native" header folder so we can include them first
+  execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
+  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)
+    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
+      COMMENT "Running IWYU")
+    add_dependencies(iwyu lammps)
+  else()
+    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
+      "and the iwyu-tool/iwyu_tool script installed in your PATH")
+  endif()
+endif()
+
+#######################################
+# select code sanitizer options
+#######################################
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+endif()

cmake/Modules/Tools.cmake

@@ -45,7 +45,7 @@ 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

@@ -2,17 +2,32 @@ message(STATUS "Downloading and building YAML library")
 
 include(ExternalProject)
 set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
 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           bb15429d8fb787e7d3f1c83ae129a999
+                    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=${CMAKE_C_COMPILER}
-                                      --prefix=<INSTALL_DIR> --disable-shared
-                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
+                                      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      "")
 
 ExternalProject_Get_Property(libyaml INSTALL_DIR)
@@ -23,7 +38,7 @@ set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
 file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
 file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
 
-set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 add_library(Yaml::Yaml UNKNOWN IMPORTED)
 set_target_properties(Yaml::Yaml PROPERTIES

cmake/Modules/generate_lmpgitversion.cmake

@@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}

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 +1,90 @@
-# 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 MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-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
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  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
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  USER-MISC
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,19 +1,92 @@
-# 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 MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-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
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  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
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  USER-MISC
+  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=f95" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f95" 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

@@ -2,10 +2,22 @@
 
 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" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
 set(OpenMP_C "gcc" CACHE STRING "" 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 +1,69 @@
-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
+  FEP
+  GPU
+  GRANULAR
+  INTEL
+  KSPACE
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  OPENMP
+  OPT
+  PERI
+  PHONON
+  POEMS
+  PTM
+  QEQ
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  USER-MISC
+  VORONOI
+  YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -16,7 +72,7 @@ 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 +2,59 @@
 # 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
-        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        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
+  FEP
+  GRANULAR
+  KSPACE
+  MACHDYN
+  MANYBODY
+  MC
+  MEAM
+  MISC
+  ML-IAP
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  OPENMP
+  OPT
+  PERI
+  PHONON
+  PLUGIN
+  POEMS
+  PYTHON
+  QEQ
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SPH
+  SPIN
+  SRD
+  UEF
+  USER-MISC
+  VORONOI
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -1,10 +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 MPIIO MSCG PYTHON
-        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-MESONT USER-NETCDF 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

@@ -0,0 +1,28 @@
+# 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)
+set(OpenMP_C "icx" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" 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
@@ -47,6 +46,8 @@ HAS_PDFLATEX = YES
 endif
 endif
 
+# override settings for PIP commands
+# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
 #SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
 
@@ -57,7 +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
 
 # ------------------------------------------
 
@@ -66,7 +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)"
@@ -183,13 +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 ;\
@@ -211,6 +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
@@ -228,15 +224,15 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install --upgrade pip; \
-		pip install -r $(BUILDDIR)/utils/requirements.txt; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 https://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/graphviz/lammps-classes.dot

@@ -18,8 +18,8 @@ digraph lammps {
     Up [shape=box label="Update" color=blue]
     Un [shape=box label="Universe" color=blue]
     Ti [shape=box label="Timer" color=blue]
-    Lt [label="Lattice"]
     Rg [label="Region" color=red]
+    Lt [label="Lattice"]
     Rb [shape=box label="RegionBlock"]
     Rs [shape=box label="RegionSphere"]
     Av [label="AtomVec" color=red]
@@ -34,6 +34,7 @@ digraph lammps {
     Du [label="Dump" color=red]
     Fi [label="Fix" color=red]
     Cp [label="Compute" color=red]
+    Cm [label="Command" color=red]
     Th [label="Thermo"]
     Va [label="Variable"]
     Ew [shape=box label="Ewald"]
@@ -71,16 +72,19 @@ digraph lammps {
     Dg [shape=box label="DumpCFG"]
     Ve [shape=box label="Verlet"]
     Rr [shape=box label="Respa"]
+    Ru [shape=box label="Run"]
+    Se [shape=box label="Set"]
     Pt [shape=box label="PPPMTIP4P"]
     Vs [shape=box label="VerletSplit"]
     Ro [shape=box label="RespaOMP"]
     Mc [shape=box label="MinCG"]
     Mf [shape=box label="MinFire"]
     La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
-    Do -> {Lt Rg} [penwidth=2]
+    Do -> {Rg Lt} [penwidth=2]
     Rg -> {Rb Rs} [style=dashed penwidth=2]
     Co -> {Cb Ct} [style=dashed penwidth=2]
-    In -> Va [penwidth=2]
+    In -> {Va Cm} [penwidth=2]
+    Cm -> {Ru Se} [style=dashed penwidth=2]
     Mo -> {Fi Cp} [penwidth=2]
     Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
     Ks -> {Ew Pp} [style=dashed penwidth=2]

doc/include-file-conventions.md

@@ -122,7 +122,7 @@ recorded compilation commands information when typing `make iwyu`.
 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
+for example to the REAXFF, or the 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 "10 February 2021" "2021-02-10"
+.TH LAMMPS "2 July 2021" "2021-07-2"
 .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
@@ -135,7 +135,7 @@ 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.

doc/src/Bibliography.rst

@@ -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_basics.rst

@@ -1,7 +1,7 @@
 Basic build options
 ===================
 
-The following topics are covered on this page, for building both with
+The following topics are covered on this page, for building with both
 CMake and make:
 
 * :ref:`Serial vs parallel build <serial>`
@@ -90,12 +90,12 @@ 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::
 
-         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
          called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
          operating system does not support ``gettimeofday()``, you will
          need to insert code to call another timer.  Note that the
@@ -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
@@ -234,6 +234,8 @@ LAMMPS.
          cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
          # Building with Intel Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         # Building with Intel oneAPI Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
          # Building with LLVM/Clang Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
          # Building with PGI/Nvidia Compilers:
@@ -243,8 +245,10 @@ LAMMPS.
       provided that can be loaded with
       `-C ../cmake/presets/clang.cmake`.  Similarly,
       `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
-      should switch the compiler to the PGI compilers.
+      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
+      will switch to the LLVM based oneAPI Intel compilers,
+      and `-C ../cmake/presets/pgi.cmake`
+      will switch the compiler to the PGI compilers.
 
       In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts. By
@@ -321,9 +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)
@@ -526,6 +530,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

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

@@ -28,6 +28,28 @@ variable VERBOSE set to 1:
 
 ----------
 
+.. _clang-tidy:
+
+Enable static code analysis with clang-tidy
+-------------------------------------------
+
+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
@@ -288,7 +310,7 @@ 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 +345,7 @@ 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
@@ -447,12 +469,24 @@ 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``.
+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 style.  The `clang-format` command bundled with Clang version 8.0
+or later is required.  The configuration is in files ``.clang-format``
+in the respective folders.  Since the modifications from `clang-format`
+can be significant and - especially for "legacy style code" - also is
+not always improving readability, a large number of files currently have
+a ``// clang-format off`` at the top, which will disable the processing.
+Over time, files will be refactored and updated to that `clang-format`
+may be applied to them (at least in part).
+
+If `clang-format` is available, the source code files in the ``unittest``
+tree can be updated to conform to the formatting settings using
+``make format-tests`` and the files in ``src`` with ``make format-src``.

doc/src/Build_extras.rst

@@ -37,28 +37,31 @@ This is the list of packages that may require additional steps.
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
    * :ref:`MESSAGE <message>`
-   * :ref:`MLIAP <mliap>`
+   * :ref:`ML-IAP <mliap>`
    * :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-MESONT <user-mesont>`
-   * :ref:`USER-MOLFILE <user-molfile>`
-   * :ref:`USER-NETCDF <user-netcdf>`
-   * :ref:`USER-PLUMED <user-plumed>`
-   * :ref:`USER-OMP <user-omp>`
-   * :ref:`USER-QMMM <user-qmmm>`
-   * :ref:`USER-QUIP <user-quip>`
-   * :ref:`USER-SCAFACOS <user-scafacos>`
-   * :ref:`USER-SMD <user-smd>`
-   * :ref:`USER-VTK <user-vtk>`
+   * :ref:`ADIOS <adios>`
+   * :ref:`ATC <atc>`
+   * :ref:`AWPMD <awpmd>`
+   * :ref:`COLVARS <colvars>`
+   * :ref:`H5MD <h5md>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`INTEL <intel>`
+   * :ref:`MDI <mdi>`
+   * :ref:`MESONT <mesont>`
+   * :ref:`MOLFILE <molfile>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`PLUMED <plumed>`
+   * :ref:`OPENMP <openmp>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`SCAFACOS <scafacos>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`VTK <vtk>`
 
 ----------
 
@@ -120,21 +123,21 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D OCL_TUNE=value            # hardware choice for GPU_API=opencl
-                                # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
+                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
-   -D CUDPP_OPT=value           # optimization setting for GPU_API=cuda
-                                # enables CUDA Performance Primitives Optimizations, must be "no" for CUDA_MPS_SUPPORT=yes
-                                # value = yes (default) or no
+   -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
+                                # enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
+                                # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
+                                      # value = yes (default) or no
 
 :code:`GPU_ARCH` settings for different GPU hardware is as follows:
 
@@ -161,19 +164,32 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
 using the traditional build procedure. CMake will detect files generated by that
 process and will terminate with an error and a suggestion for how to remove them.
 
+If you are compiling for OpenCL, the default setting is to download, build, and
+link with a static OpenCL ICD loader library and standard OpenCL headers.  This
+way no local OpenCL development headers or library needs to be present and only
+OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
+desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
 .. code:: bash
 
-   # AMDGPU target
+   # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
+.. code:: bash
+
+   # AMDGPU target (ROCm >= 4.1)
+   export HIP_PLATFORM=amd
+   cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
+   make -j 4
+
 .. code:: bash
 
    # CUDA target (not recommended, use GPU_ARCH=cuda)
@@ -224,11 +240,12 @@ GPU architectures as supported by the CUDA toolkit in use. This is done
 through using the "--gencode " flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
-To include CUDA performance primitives set the Makefile variable
-``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.
+To enable GPU binning via CUDA performance primitives set the Makefile variable
+``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.  This should **not** be used with
+most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you should **not** use
+``-DCUDA_PROXY``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
@@ -258,18 +275,18 @@ To build with this package, the KIM library with API v2 must be downloaded
 and built on your system. It must include the KIM models that you want to
 use with LAMMPS.
 
-If you would like to use the :doc:`kim_query <kim_commands>`
+If you would like to use the :doc:`kim query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-If you would like to use the :doc:`kim_property <kim_commands>`
+If you would like to use the :doc:`kim property <kim_commands>`
 command, you need to build LAMMPS with the PYTHON package installed
 and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
 for more details on this. After successfully building LAMMPS with Python, you
-also need to install the kim-property Python package, which can be easily done using
-*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
-``conda install kim-property`` if LAMMPS is built in Conda. More detailed
-information is available at:
+also need to install the ``kim-property`` Python package, which can be easily
+done using *pip* as ``pip install kim-property``, or from the *conda-forge*
+channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
+detailed information is available at:
 `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 
 In addition to installing the KIM API, it is also necessary to install the
@@ -309,7 +326,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
-      this in one step from the lammps/src dir, using a command like
+      this in one step from the lammps/src directory, using a command like
       these, which simply invoke the ``lib/kim/Install.py`` script with
       the specified args.
 
@@ -329,7 +346,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: make
 
-         LMP_INC =       -DLMP_NO_SSL_CHECK
+         LMP_INC = -DLMP_NO_SSL_CHECK
 
 Debugging OpenKIM web queries in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -377,10 +394,11 @@ Enabling the extra unit tests have some requirements,
   Conda. More detailed information is available at:
   `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 * It is also necessary to install
-  ``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
-  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
+  ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
+  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
+  ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
   See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
-  to learn how to install a pre-build binary of the OpenKIM Repository of
+  to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
   `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
   to learn how to install the specific KIM models.
@@ -439,6 +457,9 @@ 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
@@ -451,6 +472,9 @@ They must be specified in uppercase.
    *  - ARMV8_THUNDERX2
       - HOST
       - ARMv8 Cavium ThunderX2 CPU
+   *  - A64FX
+      - HOST
+      - ARMv8.2 with SVE Support
    *  - WSM
       - HOST
       - Intel Westmere CPU (SSE 4.2)
@@ -523,6 +547,9 @@ They must be specified in uppercase.
    *  - AMPERE80
       - GPU
       - NVIDIA Ampere generation CC 8.0 GPU
+   *  - AMPERE86
+      - GPU
+      - NVIDIA Ampere generation CC 8.6 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -531,12 +558,12 @@ They must be specified in uppercase.
       - AMD GPU MI50/MI60 GFX906
    *  - VEGA908
       - GPU
-      - AMD GPU GFX908
+      - AMD GPU MI100 GFX908
    *  - INTEL_GEN
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.3 of the Kokkos library.
+This list was last updated for version 3.4.1 of the Kokkos library.
 
 .. tabs::
 
@@ -595,7 +622,7 @@ This list was last updated for version 3.3 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:
@@ -784,16 +811,17 @@ 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::
 
@@ -807,9 +835,9 @@ 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
 
@@ -818,15 +846,16 @@ 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.
 
 ----------
 
@@ -1027,12 +1056,12 @@ 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
@@ -1048,38 +1077,38 @@ 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
@@ -1122,16 +1151,16 @@ 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
 
@@ -1173,9 +1202,9 @@ USER-AWPMD package
 
 ----------
 
-.. _user-colvars:
+.. _colvars:
 
-USER-COLVARS package
+COLVARS package
 ---------------------------------------
 
 This package includes the `Colvars library
@@ -1189,7 +1218,7 @@ 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
 
@@ -1232,9 +1261,49 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
-.. _user-plumed:
+.. _ml-pace:
 
-USER-PLUMED package
+ML-PACE package
+-----------------------------
+
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
+LAMMPS with this package. The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      By default the library will be downloaded from the git repository
+      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
+      archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
+      if you provide a different library version than what is downloaded
+      automatically.
+
+
+   .. tab:: Traditional make
+
+      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.
+
+      .. code-block:: bash
+
+         $ make lib-pace                          # print help message
+         $ make lib-pace args="-b"                # download and build the default version in lib/pace
+
+      You should not need to edit the ``lib/pace/Makefile.lammps`` file.
+
+----------
+
+.. _plumed:
+
+PLUMED package
 -------------------------------------
 
 .. _plumedinstall: https://plumed.github.io/doc-master/user-doc/html/_installation.html
@@ -1242,7 +1311,7 @@ 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.
 
@@ -1278,7 +1347,7 @@ 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
@@ -1311,7 +1380,7 @@ 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
@@ -1336,12 +1405,12 @@ 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
@@ -1356,15 +1425,15 @@ 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
@@ -1375,7 +1444,7 @@ 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
@@ -1407,24 +1476,78 @@ 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::
@@ -1441,7 +1564,7 @@ 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:
 
@@ -1477,9 +1600,38 @@ TBB and MKL.
 
 ----------
 
-.. _user-mesont:
+.. _mdi:
 
-USER-MESONT package
+MDI package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_MDI=value    # download MDI Library for build, value = no (default) or yes
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must build the MDI Library in
+      ``lib/mdi``\ .  You can do this by executing a command like one
+      of the following from the ``lib/mdi`` directory:
+
+      .. code-block:: bash
+
+         $ python Install.py -m gcc       # build using gcc compiler
+         $ python Install.py -m icc       # build using icc compiler
+
+      The build should produce two files: ``lib/mdi/includelink/mdi.h``
+      and ``lib/mdi/liblink/libmdi.so``\ .
+
+----------
+
+.. _mesont:
+
+MESONT package
 -------------------------
 
 This package includes a library written in Fortran 90 in the
@@ -1492,7 +1644,7 @@ 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
 
@@ -1519,9 +1671,9 @@ they will be downloaded the first time this package is installed.
 
 ----------
 
-.. _user-molfile:
+.. _molfile:
 
-USER-MOLFILE package
+MOLFILE package
 ---------------------------------------
 
 .. tabs::
@@ -1531,9 +1683,9 @@ 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
@@ -1557,9 +1709,9 @@ USER-MOLFILE package
 
 ----------
 
-.. _user-netcdf:
+.. _netcdf:
 
-USER-NETCDF package
+NETCDF package
 -------------------------------------
 
 To build with this package you must have the NetCDF library installed
@@ -1569,7 +1721,7 @@ 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
@@ -1588,9 +1740,9 @@ on your system.
 
 ----------
 
-.. _user-omp:
+.. _openmp:
 
-USER-OMP package
+OPENMP package
 -------------------------------
 
 .. tabs::
@@ -1598,13 +1750,13 @@ 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.
@@ -1621,12 +1773,12 @@ 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
@@ -1649,11 +1801,11 @@ 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
@@ -1696,9 +1848,9 @@ 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
@@ -1716,7 +1868,7 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
          -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
+      done that, a CMake build of LAMMPS with ``-D PKG_ML-QUIP=yes`` should
       work.  Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
 
    .. tab:: Traditional make
@@ -1731,9 +1883,9 @@ 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
@@ -1778,9 +1930,9 @@ 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.
@@ -1822,9 +1974,9 @@ 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
@@ -1834,7 +1986,7 @@ 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_link.rst

@@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library.  The ``library.h`` file includes ``mpi.h``
-   and uses definitions from it so those need to be available and
-   consistent.  When LAMMPS is compiled with the included STUBS MPI
-   library, then its ``mpi.h`` file needs to be included.  While it is
-   technically possible to use a full MPI library in the calling code
-   and link to a serial LAMMPS library compiled with MPI STUBS, it is
-   recommended to use the *same* MPI library for both, and then use
-   ``MPI_Comm_split()`` in the calling code to pass a suitable
-   communicator with a subset of MPI ranks to the function creating the
-   LAMMPS instance.
+   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   MPI support using the include STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
@@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
                       -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
                       -llammps_serial -lpoems -lmpi_stubs
@@ -174,7 +166,7 @@ the POEMS package installed becomes:
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
 
 Locating liblammps.so at runtime

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

@@ -28,29 +28,18 @@ 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
 --------------------
@@ -74,7 +63,11 @@ For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
 that virtual environment via the ``pip`` tool.  For rendering embedded
 LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
-engine needs to be downloaded.
+engine needs to be downloaded.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
+at beginning of the makefile.
 
 The actual translation is then done via ``make`` commands in the doc
 folder.  The following ``make`` commands are available:
@@ -108,7 +101,10 @@ installation of the HTML manual pages into the "install" step when
 installing LAMMPS after the CMake build via ``cmake --build . --target
 install``.  The documentation build is included in the default build
 target, but can also be requested independently with
-``cmake --build . --target doc``.
+``cmake --build . --target doc``.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable.
 
 .. code-block:: bash
 
@@ -208,7 +204,7 @@ be multiple tests run automatically:
 
   .. parsed-literal::
 
-     Found 33 standard and 41 user packages
+     Found 74 packages
      Standard package NEWPACKAGE missing in Packages_standard.rst
      Standard package NEWPACKAGE missing in Packages_details.rst
 
@@ -250,4 +246,4 @@ 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-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

@@ -64,7 +64,7 @@ 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
@@ -242,8 +242,8 @@ 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_all.rst

@@ -60,17 +60,14 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`include <include>`
    * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim_init <kim_commands>`
-   * :doc:`kim_interactions <kim_commands>`
-   * :doc:`kim_param <kim_commands>`
-   * :doc:`kim_property <kim_commands>`
-   * :doc:`kim_query <kim_commands>`
+   * :doc:`kim <kim_commands>`
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
+   * :doc:`mdi/engine <mdi_engine>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
    * :doc:`min_modify <min_modify>`
@@ -90,6 +87,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
+   * :doc:`plugin <plugin>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`

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::
@@ -126,7 +126,7 @@ OPT.
    * :doc:`quadratic (o) <dihedral_quadratic>`
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
-   * :doc:`table/cut <dihedral_table_cut>`
+   * :doc:`table/cut <dihedral_table>`
 
 .. _improper:
 
@@ -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_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>`

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::
@@ -39,6 +39,9 @@ OPT.
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
+   * :doc:`brownian <fix_brownian>`
+   * :doc:`brownian/asphere <fix_brownian>`
+   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
@@ -46,6 +49,7 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`client/md <fix_client_md>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -97,6 +101,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`mdi/engine <fix_mdi_engine>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`
@@ -114,7 +119,7 @@ OPT.
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
    * :doc:`nphug <fix_nphug>`
-   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt (giko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
    * :doc:`npt/cauchy <fix_npt_cauchy>`
@@ -122,8 +127,8 @@ OPT.
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
    * :doc:`numdiff <fix_numdiff>`
-   * :doc:`nve (iko) <fix_nve>`
-   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve (giko) <fix_nve>`
+   * :doc:`nve/asphere (gi) <fix_nve_asphere>`
    * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
    * :doc:`nve/awpmd <fix_nve_awpmd>`
    * :doc:`nve/body <fix_nve_body>`
@@ -138,7 +143,7 @@ OPT.
    * :doc:`nve/spin <fix_nve_spin>`
    * :doc:`nve/tri <fix_nve_tri>`
    * :doc:`nvk <fix_nvk>`
-   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt (giko) <fix_nh>`
    * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`
@@ -157,6 +162,9 @@ OPT.
    * :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>`

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::
@@ -28,6 +28,7 @@ OPT.
    * :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>`
@@ -36,4 +37,5 @@ OPT.
    * :doc:`pppm/disp/tip4p (o) <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::
@@ -26,6 +26,7 @@ OPT.
    * :doc:`zero <pair_zero>`
    * :doc:`hybrid (k) <pair_hybrid>`
    * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    *
@@ -33,7 +34,6 @@ OPT.
    *
    *
    *
-   *
    * :doc:`adp (o) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
@@ -69,12 +69,15 @@ 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/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>`
@@ -86,6 +89,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (gio) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/ext <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (go) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -115,6 +120,7 @@ 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>`
@@ -122,7 +128,7 @@ OPT.
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`line/lj <pair_line_lj>`
-   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
    * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
@@ -139,13 +145,17 @@ 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>`
@@ -160,14 +170,16 @@ 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>`
+   * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/sdk (gko) <pair_sdk>`
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
-   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
    * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
@@ -178,7 +190,7 @@ 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>`
@@ -186,7 +198,7 @@ OPT.
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap <pair_mliap>`
-   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -214,6 +226,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`pace <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -221,6 +234,7 @@ OPT.
    * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
+   * :doc:`rann <pair_rann>`
    * :doc:`reax/c (ko) <pair_reaxc>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`

doc/src/Commands_parse.rst

@@ -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

@@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_plugins
    Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_org.rst

@@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries
 which may have different conventions, all C and C++ header files have a
 ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
 ``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointer class
-or the MathVec functions.
+are implemented with only a ``.h`` file. Examples are the Pointers and
+Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in
 between runs.  For these an instance of the class is created, its
 command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
-run, or velocity command styles.
+run, set, or velocity command styles.
 
 For all those ``styles`` certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
@@ -175,11 +175,11 @@ follows:
 - The Input class reads and processes input input strings and files,
   stores variables, and invokes :doc:`commands <Commands_all>`.
 
-- As discussed above, command style classes are directly derived from
-  the Pointers class. They provide input script commands that perform
-  one-time operations before/after/between simulations or which invoke a
-  simulation.  They are instantiated from within the Input class,
-  invoked, then immediately destructed.
+- Command style classes are derived from the Command class. They provide
+  input script commands that perform one-time operations
+  before/after/between simulations or which invoke a simulation.  They
+  are usually instantiated from within the Input class, its ``command``
+  method invoked, and then immediately destructed.
 
 - The Finish class is instantiated to print statistics to the screen
   after a simulation is performed, by commands like run and minimize.

doc/src/Developer_plugins.rst

@@ -0,0 +1,251 @@
+Writing plugins
+---------------
+
+Plugins provide a mechanism to add functionality to a LAMMPS executable
+without recompiling LAMMPS.  The functionality for this and the
+:doc:`plugin command <plugin>` are implemented in the
+:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
+
+Plugins use the operating system's capability to load dynamic shared
+object (DSO) files in a way similar shared libraries and then reference
+specific functions in those DSOs.  Any DSO file with plugins has to include
+an initialization function with a specific name, "lammpsplugin_init", that
+has to follow specific rules described below.  When loading the DSO with
+the "plugin" command, this function is looked up and called and will then
+register the contained plugin(s) with LAMMPS.
+
+From the programmer perspective this can work because of the object
+oriented design of LAMMPS where all pair style commands are derived from
+the class Pair, all fix style commands from the class Fix and so on and
+usually only functions present in those base classes are called
+directly.  When a :doc:`pair_style` command or :doc:`fix` command is
+issued a new instance of such a derived class is created.  This is done
+by a so-called factory function which is mapped to the style name.  Thus
+when, for example, the LAMMPS processes the command ``pair_style lj/cut
+2.5``, LAMMPS will look up the factory function for creating the
+``PairLJCut`` class and then execute it.  The return value of that
+function is a ``Pair *`` pointer and the pointer will be assigned to the
+location for the currently active pair style.
+
+A DSO file with a plugin thus has to implement such a factory function
+and register it with LAMMPS so that it gets added to the map of available
+styles of the given category.  To register a plugin with LAMMPS an
+initialization function has to be present in the DSO file called
+``lammpsplugin_init`` which is called with three ``void *`` arguments:
+a pointer to the current LAMMPS instance, a pointer to the opened DSO
+handle, and a pointer to the registration function.  The registration
+function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
+with information about the plugin and a pointer to the current LAMMPS
+instance.  Please see below for an example of how the registration is
+done.
+
+Members of ``lammpsplugin_t``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Member
+     - Description
+   * - version
+     - LAMMPS Version string the plugin was compiled for
+   * - style
+     - Style of the plugin (pair, bond, fix, command, etc.)
+   * - name
+     - Name of the plugin style
+   * - info
+     - String with information about the plugin
+   * - author
+     - String with the name and email of the author
+   * - creator.v1
+     - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
+   * - creator.v2
+     - Pointer to factory function for compute, fix, or region styles
+   * - handle
+     - Pointer to the open DSO file handle
+
+Only one of the three alternate creator entries can be used at a time
+and which of those is determined by the style of plugin. The
+"creator.v1" element is for factory functions of supported styles
+computing forces (i.e.  command, pair, bond, angle, dihedral, or
+improper styles) and the function takes as single argument the pointer
+to the LAMMPS instance. The factory function is cast to the
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
+element is for factory functions creating an instance of a fix, compute,
+or region style and takes three arguments: a pointer to the LAMMPS
+instance, an integer with the length of the argument list and a ``char
+**`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before
+assignment.
+
+Pair style example
+^^^^^^^^^^^^^^^^^^
+
+As an example, a hypothetical pair style plugin "morse2" implemented in
+a class ``PairMorse2`` in the files ``pair_morse2.h`` and
+``pair_morse2.cpp`` with the factory function and initialization
+function would look like this:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "pair_morse2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Pair *morse2creator(LAMMPS *lmp)
+  {
+    return new PairMorse2(lmp);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "pair";
+    plugin.name    = "morse2";
+    plugin.info    = "Morse2 variant pair style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+The factory function in this example is called ``morse2creator()``.  It
+receives a pointer to the LAMMPS class as only argument and thus has to
+be assigned to the *creator.v1* member of the plugin struct and cast to
+the ``lammpsplugin_factory1`` function pointer type.  It returns a
+pointer to the allocated class instance derived from the ``Pair`` class.
+This function may be declared static to avoid clashes with other
+plugins.  The name of the derived class, ``PairMorse2``, however must be
+unique inside the entire LAMMPS executable.
+
+Fix style example
+^^^^^^^^^^^^^^^^^
+
+If the factory function would be for a fix or compute, which take three
+arguments (a pointer to the LAMMPS class, the number of arguments and the
+list of argument strings), then the pointer type is ``lammpsplugin_factory2``
+and it must be assigned to the *creator.v2* member of the plugin struct.
+Below is an example for that:
+
+.. code-block:: C++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "fix_nve2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+  {
+    return new FixNVE2(lmp,argc,argv);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "fix";
+    plugin.name    = "nve2";
+    plugin.info    = "NVE2 variant fix style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+Command style example
+^^^^^^^^^^^^^^^^^^^^^
+Command styles also use the first variant of factory function as
+demonstrated in the following example, which also shows that the
+implementation of the plugin class may be within the same source
+file as the plugin interface code:
+
+.. code-block:: C++
+
+   #include "lammpsplugin.h"
+
+   #include "comm.h"
+   #include "error.h"
+   #include "command.h"
+   #include "version.h"
+
+   #include <cstring>
+
+   namespace LAMMPS_NS {
+     class Hello : public Command {
+      public:
+       Hello(class LAMMPS *lmp) : Command(lmp) {};
+       void command(int, char **);
+     };
+   }
+
+   using namespace LAMMPS_NS;
+
+   void Hello::command(int argc, char **argv)
+   {
+      if (argc != 1) error->all(FLERR,"Illegal hello command");
+      if (comm->me == 0)
+        utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
+   }
+
+   static void hellocreator(LAMMPS *lmp)
+   {
+     return new Hello(lmp);
+   }
+
+   extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+   {
+     lammpsplugin_t plugin;
+     lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+     plugin.version = LAMMPS_VERSION;
+     plugin.style   = "command";
+     plugin.name    = "hello";
+     plugin.info    = "Hello world command v1.1";
+     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
+     plugin.handle  = handle;
+     (*register_plugin)(&plugin,lmp);
+   }
+
+Additional Details
+^^^^^^^^^^^^^^^^^^
+
+The initialization function **must** be called ``lammpsplugin_init``, it
+**must** have C bindings and it takes three void pointers as arguments.
+The first is a pointer to the LAMMPS class that calls it and it needs to
+be passed to the registration function.  The second argument is a
+pointer to the internal handle of the DSO file, this needs to be added
+to the plugin info struct, so that the DSO can be closed and unloaded
+when all its contained plugins are unloaded.  The third argument is a
+function pointer to the registration function and needs to be stored
+in a variable of ``lammpsplugin_regfunc`` type and then called with a
+pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
+instance as arguments to register a single plugin.  There may be multiple
+calls to multiple plugins in the same initialization function.
+
+To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
+with relevant info: current LAMMPS version string, kind of style, name of
+style, info string, author string, pointer to factory function, and the
+DSO handle.  The registration function is called with a pointer to the address
+of this struct and the pointer of the LAMMPS class.  The registration function
+will then add the factory function of the plugin style to the respective
+style map under the provided name.  It will also make a copy of the struct
+in a list of all loaded plugins and update the reference counter for loaded
+plugins from this specific DSO file.
+
+The pair style itself (i.e. the PairMorse2 class in this example) can be
+written just like any other pair style that is included in LAMMPS.  For
+a plugin, the use of the ``PairStyle`` macro in the section encapsulated
+by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
+name to the style name is done by the plugin registration function with
+the information from the ``lammpsplugin_t`` struct.  It may be included
+in case the new code is intended to be later included in LAMMPS directly.

doc/src/Developer_unittest.rst

@@ -4,10 +4,10 @@ Adding tests for unit testing
 This section discusses adding or expanding tests for the unit test
 infrastructure included into the LAMMPS source code distribution.
 Unlike example inputs, unit tests focus on testing the "local" behavior
-of individual features, tend to run very fast, and should be set up to
-cover as much of the added code as possible.  When contributing code to
-the distribution, the LAMMPS developers will appreciate if additions
-to the integrated unit test facility are included.
+of individual features, tend to run fast, and should be set up to cover
+as much of the added code as possible.  When contributing code to the
+distribution, the LAMMPS developers will appreciate if additions to the
+integrated unit test facility are included.
 
 Given the complex nature of MD simulations where many operations can
 only be performed when suitable "real" simulation environment has been
@@ -50,6 +50,9 @@ available:
    * - File name:
      - Test name:
      - Description:
+   * - ``test_argutils.cpp``
+     - ArgInfo
+     - Tests for ``ArgInfo`` class used by LAMMPS
    * - ``test_fmtlib.cpp``
      - FmtLib
      - Tests for ``fmtlib::`` functions used by LAMMPS
@@ -155,23 +158,27 @@ have the desired effect:
    {
        ASSERT_EQ(lmp->update->ntimestep, 0);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 10");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 10");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 10);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 0");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 0");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
+       TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
    }
 
-Please note the use of the (global) verbose variable to control whether
-the LAMMPS command will be silent by capturing the output or not.  In
-the default case, verbose == false, the test output will be compact and
-not mixed with LAMMPS output. However setting the verbose flag (via
-setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
-helpful to understand why tests fail unexpectedly.
+Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
+functions that will capture output from running LAMMPS.  This is normally
+discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
+environment variable, ``TEST_ARGS=-v``) it can be printed and used to
+understand why tests fail unexpectedly.
 
 Another complexity of these tests stems from the need to capture
 situations where LAMMPS will stop with an error, i.e. handle so-called
@@ -210,6 +217,12 @@ The following test programs are currently available:
    * - ``test_lattice_region.cpp``
      - LatticeRegion
      - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
+   * - ``test_groups.cpp``
+     - GroupTest
+     - Tests to validate the :doc:`group <group>` command
+   * - ``test_variables.cpp``
+     - VariableTest
+     - Tests to validate the :doc:`variable <variable>` command
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`
@@ -391,8 +404,8 @@ noise). Then it will restart from the previously generated restart and
 compare with the reference and also start from the data file.  A final
 check will use multi-cutoff r-RESPA (if supported by the pair style) at
 a 1:1 split and compare to the Verlet results.  These sets of tests are
-run with multiple test fixtures for accelerated styles (OPT, USER-OMP,
-USER-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
+run with multiple test fixtures for accelerated styles (OPT, OPENMP,
+INTEL) and for the latter two with 4 OpenMP threads enabled.  For
 these tests the relative error (epsilon) is lowered by a common factor
 due to the additional numerical noise, but the tests are still comparing
 to the same reference data.