Merge pull request #2859 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

@@ -13,43 +13,51 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
-src/COMPRESS/*        @akohlmey
+src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
 src/MESSAGE/*         @sjplimp
+src/MLIAP/*           @athomps
+src/SNAP/*            @athomps
 src/SPIN/*            @julient31
-src/USER-CGDNA/*      @ohenrich
-src/USER-CGSDK/*      @akohlmey
-src/USER-COLVARS/*    @giacomofiorin
-src/USER-INTEL/*      @wmbrownintel
-src/USER-MANIFOLD/*   @Pakketeretet2
-src/USER-MEAMC/*      @martok
-src/USER-MESONT/*     @iafoss
-src/USER-MOFFF/*      @hheenen
-src/USER-MOLFILE/*    @akohlmey
-src/USER-NETCDF/*     @pastewka
-src/USER-PLUMED/*     @gtribello
-src/USER-PHONON/*     @lingtikong
-src/USER-PTM/*        @pmla
-src/USER-OMP/*        @akohlmey
-src/USER-QMMM/*       @akohlmey
-src/USER-REAXC/*      @hasanmetin
-src/USER-SCAFACOS/*   @rhalver
-src/USER-TALLY/*      @akohlmey
-src/USER-UEF/*        @danicholson
-src/USER-VTK/*        @rbberger
-
+src/BROWNIAN/*        @samueljmcameron
+src/CG-DNA/*          @ohenrich
+src/CG-SDK/*          @akohlmey
+src/COLVARS/*         @giacomofiorin
+src/DIELECTRIC/*      @ndtrung81
+src/FEP/*             @agiliopadua
+src/ML-HDNNP/*        @singraber
+src/INTEL/*           @wmbrownintel
+src/MANIFOLD/*        @Pakketeretet2
+src/MDI/*             @taylor-a-barnes
+src/MEAM/*            @martok
+src/MESONT/*          @iafoss
+src/MOFFF/*           @hheenen
+src/MOLFILE/*         @akohlmey
+src/NETCDF/*          @pastewka
+src/ML-PACE/*         @yury-lysogorskiy
+src/PLUMED/*          @gtribello
+src/PHONON/*          @lingtikong
+src/PTM/*             @pmla
+src/OPENMP/*          @akohlmey
+src/QMMM/*            @akohlmey
+src/REAXFF/*          @hasanmetin @stanmoore1
+src/REACTION/*        @jrgissing
+src/SCAFACOS/*        @rhalver
+src/TALLY/*           @akohlmey
+src/UEF/*             @danicholson
+src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
 src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/USER-REACTION/fix_bond_react.*  @jrgissing
-src/USER-MISC/*_grem.*              @dstelter92
-src/USER-MISC/compute_stress_mop*.* @RomainVermorel
+src/REPLICA/*_grem.*                @dstelter92
+src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
+src/MISC/*_tracker.*                @jtclemm
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -73,6 +81,7 @@ src/kspace.*              @sjplimp
 src/lmptyp.h              @sjplimp
 src/library.*             @sjplimp
 src/main.cpp              @sjplimp
+src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
 src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
@@ -101,7 +110,6 @@ src/thermo.*              @sjplimp
 src/universe.*            @sjplimp
 src/update.*              @sjplimp
 src/variable.*            @sjplimp
-src/verlet.*              @sjplimp
 src/velocity.*            @sjplimp
 src/write_data.*          @sjplimp
 src/write_restart.*       @sjplimp
@@ -114,6 +122,7 @@ src/info.*                @akohlmey @rbberger
 src/timer.*               @akohlmey
 src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
+src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
@@ -122,15 +131,17 @@ 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 +153,7 @@ fortran/*             @akohlmey
 doc/utils/*/*         @rbberger
 doc/Makefile          @rbberger
 doc/README            @rbberger
+examples/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/CONTRIBUTING.md

@@ -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
@@ -17,20 +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/clang.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_*
@@ -43,6 +44,8 @@ Thumbs.db
 /build*
 /CMakeCache.txt
 /CMakeFiles/
+/Testing
 /Makefile
+/Testing
 /cmake_install.cmake
 /lmp

.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

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)
@@ -72,7 +77,7 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
     set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
@@ -86,6 +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                                                   #
 ########################################################################
@@ -104,11 +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})
@@ -116,17 +138,92 @@ install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
-set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
-  GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
-  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
-  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-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
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  H5MD
+  INTERLAYER
+  KIM
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
-set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
+set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
 
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
@@ -137,7 +234,7 @@ endforeach()
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
 
-if(PKG_USER-ADIOS)
+if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
@@ -147,7 +244,6 @@ if(PKG_USER-ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
@@ -155,8 +251,11 @@ else()
 endif()
 
 if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
-  if((CMAKE_SYSTEM_NAME STREQUAL Windows) AND CMAKE_CROSSCOMPILING)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
     target_link_libraries(lammps PUBLIC MPI::MPI_CXX)
   else()
@@ -190,7 +289,7 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
 target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
 else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@@ -206,12 +305,16 @@ endif()
 
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
-pkg_depends(MLIAP SNAP)
+pkg_depends(ML-IAP ML-SNAP)
 pkg_depends(MPIIO MPI)
-pkg_depends(USER-ATC MANYBODY)
-pkg_depends(USER-LB MPI)
-pkg_depends(USER-PHONON KSPACE)
-pkg_depends(USER-SCAFACOS MPI)
+pkg_depends(ATC MANYBODY)
+pkg_depends(LATBOLTZ MPI)
+pkg_depends(PHONON KSPACE)
+pkg_depends(SCAFACOS MPI)
+pkg_depends(DIELECTRIC KSPACE)
+pkg_depends(DIELECTRIC EXTRA-PAIR)
+pkg_depends(CG-DNA MOLECULE)
+pkg_depends(CG-DNA ASPHERE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -232,8 +335,10 @@ if(BUILD_OMP)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
 
-  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
-      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+  if(((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM") OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@@ -245,69 +350,7 @@ 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)
@@ -327,6 +370,8 @@ if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   endif()
 endif()
 
+# tweak jpeg library names to avoid linker errors with MinGW cross-compilation
+set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
 option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
@@ -358,7 +403,7 @@ 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")
@@ -369,7 +414,7 @@ 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")
@@ -386,8 +431,8 @@ 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()
@@ -480,11 +525,10 @@ 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)
@@ -496,9 +540,9 @@ 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})
@@ -506,13 +550,13 @@ 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 ${LAPACK_LIBRARIES})
   if(BUILD_MPI)
@@ -524,15 +568,15 @@ if(PKG_USER-ATC)
   target_compile_definitions(atc PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 endif()
 
-if(PKG_USER-H5MD)
-  include(Packages/USER-H5MD)
+if(PKG_H5MD)
+  include(Packages/H5MD)
 endif()
 
 ######################################################################
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -555,7 +599,7 @@ endif()
 # and the MPI library - if use - has to be linked right before those
 # and after everything else that is compiled locally
 ######################################################################
-if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
   target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
@@ -604,8 +648,8 @@ 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
@@ -683,7 +727,7 @@ 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
@@ -716,7 +760,7 @@ 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()
@@ -730,7 +774,7 @@ 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}")
@@ -761,15 +805,15 @@ 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}
@@ -799,9 +843,12 @@ 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 "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}")
@@ -811,7 +858,7 @@ 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: ${KOKKOS_ARCH}")
@@ -831,7 +878,7 @@ if(PKG_KSPACE)
   endif()
   if(PKG_KOKKOS)
     if(Kokkos_ENABLE_CUDA)
-      if (${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

@@ -55,8 +55,8 @@ if(BUILD_DOC)
     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/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
+  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"

cmake/Modules/FindN2P2.cmake

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

cmake/Modules/GTest.cmake

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

cmake/Modules/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()
 
@@ -104,3 +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/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.06.30.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "f9e55dd550cfbf77f46507adf7cb8fd2" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 

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

@@ -48,7 +48,7 @@ if(GPU_API STREQUAL "CUDA")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
   file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
-  if (GPU_LIB_OLD_CUBIN_HEADERS)
+  if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
       "Please run\n"
@@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
   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)
@@ -145,9 +145,16 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
+  # 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)
+  if(USE_STATIC_OPENCL_LOADER)
     include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)
@@ -289,18 +296,18 @@ elseif(GPU_API STREQUAL "HIP")
 
         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()

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)
@@ -40,10 +40,10 @@ endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
   if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
-    message(FATAL_ERROR "USER-INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
+    message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
   endif()
 else()
-  message(WARNING "USER-INTEL gives best performance with Intel compilers")
+  message(WARNING "INTEL gives best performance with Intel compilers")
 endif()
 
 find_package(TBB_MALLOC QUIET)
@@ -52,7 +52,7 @@ if(TBB_MALLOC_FOUND)
 else()
   target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    message(WARNING "USER-INTEL with Intel compilers should use TBB malloc libraries")
+    message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
   endif()
 endif()
 
@@ -65,12 +65,12 @@ else()
 endif()
 
 if((NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "64") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "128") AND (NOT ${LAMMPS_MEMALIGN} STREQUAL "256"))
-  message(FATAL_ERROR "USER-INTEL only supports memory alignment of 64, 128 or 256 on this platform")
+  message(FATAL_ERROR "INTEL only supports memory alignment of 64, 128 or 256 on this platform")
 endif()
 
 if(INTEL_ARCH STREQUAL "KNL")
   if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-    message(FATAL_ERROR "Must use Intel compiler with USER-INTEL for KNL architecture")
+    message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
   endif()
   set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
   set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
@@ -79,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
 else()
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     include(CheckCXXCompilerFlag)
-    foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
-      check_cxx_compiler_flag("${_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()
@@ -89,26 +91,26 @@ else()
 endif()
 
 # collect sources
-set(USER-INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-INTEL)
-set(USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/fix_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/fix_nh_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/intel_buffers.cpp
-                       ${USER-INTEL_SOURCES_DIR}/nbin_intel.cpp
-                       ${USER-INTEL_SOURCES_DIR}/npair_intel.cpp)
+set(INTEL_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/INTEL)
+set(INTEL_SOURCES ${INTEL_SOURCES_DIR}/fix_intel.cpp
+                       ${INTEL_SOURCES_DIR}/fix_nh_intel.cpp
+                       ${INTEL_SOURCES_DIR}/intel_buffers.cpp
+                       ${INTEL_SOURCES_DIR}/nbin_intel.cpp
+                       ${INTEL_SOURCES_DIR}/npair_intel.cpp)
 
-set_property(GLOBAL PROPERTY "USER-INTEL_SOURCES" "${USER-INTEL_SOURCES}")
+set_property(GLOBAL PROPERTY "INTEL_SOURCES" "${INTEL_SOURCES}")
 
-# detect styles which have a USER-INTEL version
-RegisterStylesExt(${USER-INTEL_SOURCES_DIR} intel USER-INTEL_SOURCES)
-RegisterNBinStyle(${USER-INTEL_SOURCES_DIR}/nbin_intel.h)
-RegisterNPairStyle(${USER-INTEL_SOURCES_DIR}/npair_intel.h)
-RegisterFixStyle(${USER-INTEL_SOURCES_DIR}/fix_intel.h)
+# detect styles which have a INTEL version
+RegisterStylesExt(${INTEL_SOURCES_DIR} intel INTEL_SOURCES)
+RegisterNBinStyle(${INTEL_SOURCES_DIR}/nbin_intel.h)
+RegisterNPairStyle(${INTEL_SOURCES_DIR}/npair_intel.h)
+RegisterFixStyle(${INTEL_SOURCES_DIR}/fix_intel.h)
 
-get_property(USER-INTEL_SOURCES GLOBAL PROPERTY USER-INTEL_SOURCES)
+get_property(INTEL_SOURCES GLOBAL PROPERTY INTEL_SOURCES)
 if(PKG_KSPACE)
-  list(APPEND USER-INTEL_SOURCES ${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
-  RegisterIntegrateStyle(${USER-INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
+  RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
-target_sources(lammps PRIVATE ${USER-INTEL_SOURCES})
-target_include_directories(lammps PRIVATE ${USER-INTEL_SOURCES_DIR})
+target_sources(lammps PRIVATE ${INTEL_SOURCES})
+target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -37,8 +37,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "4c84698917c93a18985b311bb6caf84f" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -58,7 +58,7 @@ if(DOWNLOAD_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()
@@ -79,6 +79,7 @@ target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
 set(KOKKOS_PKG_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/KOKKOS)
 set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_kokkos.cpp
+                       ${KOKKOS_PKG_SOURCES_DIR}/atom_map_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
@@ -99,7 +100,7 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
-    if(NOT ${FFT} STREQUAL "KISS")
+    if(NOT (FFT STREQUAL "KISS"))
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()
@@ -116,7 +117,7 @@ RegisterNBinStyle(${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/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

@@ -1,4 +1,4 @@
-if(LAMMPS_SIZES STREQUAL BIGBIG)
+if(LAMMPS_SIZES STREQUAL "BIGBIG")
   message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
 option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -0,0 +1,127 @@
+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/ML-QUIP.cmake

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

cmake/Modules/Packages/MOLFILE.cmake

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

cmake/Modules/Packages/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}/reaxff_bond_orders_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_hydrogen_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_nonbonded_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_bonds_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_init_md_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_torsion_angles_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_forces_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_multi_body_omp.cpp
+                                 ${OPENMP_SOURCES_DIR}/reaxff_valence_angles_omp.cpp)
+  endif()
+
+  target_sources(lammps PRIVATE ${OPENMP_SOURCES})
+  target_include_directories(lammps PRIVATE ${OPENMP_SOURCES_DIR})

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
+
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
 

cmake/Modules/Packages/QEQ.cmake

@@ -1,18 +1,13 @@
 # Fix qeq/fire requires MANYBODY (i.e. COMB and COMB3) to be installed
 set(QEQ_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/QEQ)
-file(GLOB QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix*.h)
-file(GLOB QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix*.cpp)
 
+get_property(hlist GLOBAL PROPERTY FIX)
 if(NOT PKG_MANYBODY)
-  list(REMOVE_ITEM QEQ_HEADERS ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
-  list(REMOVE_ITEM QEQ_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  list(REMOVE_ITEM hlist ${QEQ_SOURCES_DIR}/fix_qeq_fire.h)
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${QEQ_SOURCES_DIR}/fix_qeq_fire.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES ${LAMMPS_SOURCES})
 endif()
-set_property(GLOBAL PROPERTY "QEQ_SOURCES" "${QEQ_SOURCES}")
+set_property(GLOBAL PROPERTY FIX "${hlist}")
 
-foreach(MY_HEADER ${QEQ_HEADERS})
-  AddStyleHeader(${MY_HEADER} FIX)
-endforeach()
-
-get_property(QEQ_SOURCES GLOBAL PROPERTY QEQ_SOURCES)
-target_sources(lammps PRIVATE ${QEQ_SOURCES})
 target_include_directories(lammps PRIVATE ${QEQ_SOURCES_DIR})

cmake/Modules/Packages/USER-OMP.cmake

@@ -1,40 +0,0 @@
-  set(USER-OMP_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-OMP)
-  set(USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/thr_data.cpp
-                       ${USER-OMP_SOURCES_DIR}/thr_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_nh_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/fix_nh_sphere_omp.cpp
-                       ${USER-OMP_SOURCES_DIR}/domain_omp.cpp)
-  target_compile_definitions(lammps PRIVATE -DLMP_USER_OMP)
-  set_property(GLOBAL PROPERTY "OMP_SOURCES" "${USER-OMP_SOURCES}")
-
-  # detects styles which have USER-OMP version
-  RegisterStylesExt(${USER-OMP_SOURCES_DIR} omp OMP_SOURCES)
-  RegisterFixStyle(${USER-OMP_SOURCES_DIR}/fix_omp.h)
-
-  get_property(USER-OMP_SOURCES GLOBAL PROPERTY OMP_SOURCES)
-
-  # manually add package dependent source files from USER-OMP that do not provide styles
-
-  if(PKG_ASPHERE)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_nh_asphere_omp.cpp)
-  endif()
-
-  if(PKG_RIGID)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/fix_rigid_nh_omp.cpp)
-  endif()
-
-  if(PKG_USER-REAXC)
-    list(APPEND USER-OMP_SOURCES ${USER-OMP_SOURCES_DIR}/reaxc_bond_orders_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_hydrogen_bonds_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_nonbonded_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_bonds_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_init_md_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_torsion_angles_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_forces_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_multi_body_omp.cpp
-                                 ${USER-OMP_SOURCES_DIR}/reaxc_valence_angles_omp.cpp)
-  endif()
-
-  target_sources(lammps PRIVATE ${USER-OMP_SOURCES})
-  target_include_directories(lammps PRIVATE ${USER-OMP_SOURCES_DIR})

cmake/Modules/Packages/USER-QUIP.cmake

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

cmake/Modules/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

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

cmake/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 +1,96 @@
-# preset that turns on all existing packages off. can be used to reset
+# Preset that turns on all existing packages off. Can be used to reset
 # an existing package selection without losing any other settings
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC 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
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -1,19 +1,98 @@
-# preset that turns on all existing packages. using the combination
-# this preset followed by the nolib.cmake preset should configure a
-# LAMMPS binary, with as many packages included, that can be compiled
+# Preset that turns on all existing packages. Using the combination
+# of this preset followed by the nolib.cmake preset should configure
+# a LAMMPS binary, with as many packages included, that can be compiled
 # with just a working C++ compiler and an MPI library.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC 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
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  H5MD
+  INTEL
+  INTERLAYER
+  KIM
+  KOKKOS
+  KSPACE
+  LATBOLTZ
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MESSAGE
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-PACE
+  ML-QUIP
+  ML-RANN
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  MOLFILE
+  MPIIO
+  MSCG
+  NETCDF
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  PLUMED
+  POEMS
+  PTM
+  PYTHON
+  QEQ
+  QMMM
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SCAFACOS
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  VTK
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/clang.cmake

@@ -1,13 +1,26 @@
 # preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
 
+# prefer flang over gfortran, if available
+find_program(CLANG_FORTRAN NAMES flang gfortran f95)
+set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
 set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=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 +1,76 @@
-set(WIN_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-                 GRANULAR KSPACE LATTE MANYBODY MC MISC MLIAP MOLECULE OPT
-                 PERI POEMS QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-                 USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-                 USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF
-                 USER-FEP USER-INTEL USER-MANIFOLD USER-MEAMC USER-MESODPD
-                 USER-MESONT USER-MISC USER-MGPT USER-MOFFF USER-MOLFILE USER-OMP
-                 USER-PHONON USER-PTM USER-QTB USER-REACTION USER-REAXC
-                 USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
-                 USER-YAFF)
+set(WIN_PACKAGES
+  ASPHERE
+  ATC
+  AWPMD
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-DUMP
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GPU
+  GRANULAR
+  INTEL
+  INTERLAYER
+  KSPACE
+  LATTE
+  MACHDYN
+  MANIFOLD
+  MANYBODY
+  MC
+  MDI
+  MEAM
+  MESONT
+  MGPT
+  MISC
+  ML-HDNNP
+  ML-IAP
+  ML-SNAP
+  ML-RANN
+  MOFFF
+  MOLECULE
+  MOLFILE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  POEMS
+  PTM
+  QEQ
+  QTB
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SMTBQ
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${WIN_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
@@ -16,7 +79,7 @@ endforeach()
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
   set(PKG_MPIIO ON CACHE BOOL "" FORCE)
-  set(PKG_USER-LB ON CACHE BOOL "" FORCE)
+  set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)

cmake/presets/most.cmake

@@ -2,13 +2,65 @@
 # external libraries. Compared to all_on.cmake some more unusual packages
 # are removed. The resulting binary should be able to run most inputs.
 
-set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
-        GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
-        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
-        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
-        USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
+set(ALL_PACKAGES
+  ASPHERE
+  BOCS
+  BODY
+  BROWNIAN
+  CG-DNA
+  CG-SDK
+  CLASS2
+  COLLOID
+  COLVARS
+  COMPRESS
+  CORESHELL
+  DIELECTRIC
+  DIFFRACTION
+  DIPOLE
+  DPD-BASIC
+  DPD-MESO
+  DPD-REACT
+  DPD-SMOOTH
+  DRUDE
+  EFF
+  EXTRA-COMPUTE
+  EXTRA-FIX
+  EXTRA-MOLECULE
+  EXTRA-PAIR
+  FEP
+  GRANULAR
+  INTERLAYER
+  KSPACE
+  MACHDYN
+  MANYBODY
+  MC
+  MEAM
+  MISC
+  ML-IAP
+  ML-SNAP
+  MOFFF
+  MOLECULE
+  OPENMP
+  OPT
+  ORIENT
+  PERI
+  PHONON
+  PLUGIN
+  POEMS
+  PYTHON
+  QEQ
+  REACTION
+  REAXFF
+  REPLICA
+  RIGID
+  SHOCK
+  SPH
+  SPIN
+  SRD
+  TALLY
+  UEF
+  VORONOI
+  YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -1,10 +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

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

cmake/presets/pedantic.cmake

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

doc/Makefile

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

doc/README

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

doc/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 "8 April 2021" "2021-04-08"
+.TH LAMMPS "30 July 2021" "2021-07-30"
 .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

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

doc/src/Build_basics.rst

@@ -90,7 +90,7 @@ standard. A more detailed discussion of that is below.
       directory, or ``make`` from the ``src/STUBS`` dir.  If the build
       fails, you may need to edit the ``STUBS/Makefile`` for your
       platform.  The stubs library does not provide MPI/IO functions
-      required by some LAMMPS packages, e.g. ``MPIIO`` or ``USER-LB``,
+      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -120,19 +120,19 @@ self-installed MPICH or OpenMPI, so you should study the provided
 documentation to find out how to build and link with it.
 
 The majority of OpenMP (threading) support in LAMMPS is provided by the
-``USER-OMP`` package; see the :doc:`Speed_omp`
-page for details. The ``USER-INTEL`` package also includes OpenMP
-threading (it is compatible with ``USER-OMP`` and will usually fall
-back on styles from that package, if a ``USER-INTEL`` does not exist)
+``OPENMP`` package; see the :doc:`Speed_omp`
+page for details. The ``INTEL`` package also includes OpenMP
+threading (it is compatible with ``OPENMP`` and will usually fall
+back on styles from that package, if a ``INTEL`` does not exist)
 and adds vectorization support when compiled with compatible compilers,
 in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
 package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
 support included as well.  These are commands in the ``MPIIO``,
-``SNAP``, ``USER-DIFFRACTION``, and ``USER-DPD`` packages.  In addition
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  In addition
 some packages support OpenMP threading indirectly through the libraries
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``USER-COLVARS``.
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
 See the :doc:`Packages details <Packages_details>` page for more
 info on these packages and the pages for their respective commands
 for OpenMP threading info.
@@ -176,7 +176,7 @@ performance.  Vendor provided compilers for a specific hardware can
 produce faster code than open-source compilers like the GNU compilers.
 On the most common x86 hardware most popular C++ compilers are quite
 similar in performance of C/C++ code at high optimization levels.  When
-using the ``USER-INTEL`` package, there is a distinct advantage in using
+using the ``INTEL`` package, there is a distinct advantage in using
 the `Intel C++ compiler <intel_>`_ due to much improved vectorization
 through SSE and AVX instructions on compatible hardware as the source
 code includes changes and Intel compiler specific directives to enable
@@ -325,9 +325,9 @@ LAMMPS.
          .. code-block:: bash
 
             Makefile.opt                   # OPT package
-            Makefile.omp                   # USER-OMP package
-            Makefile.intel_cpu             # USER-INTEL package for CPUs
-            Makefile.intel_coprocessor     # USER-INTEL package for KNLs
+            Makefile.omp                   # OPENMP package
+            Makefile.intel_cpu             # INTEL package for CPUs
+            Makefile.intel_coprocessor     # INTEL package for KNLs
             Makefile.gpu                   # GPU package
             Makefile.kokkos_cuda_mpi       # KOKKOS package for GPUs
             Makefile.kokkos_omp            # KOKKOS package for CPUs (OpenMP)

doc/src/Build_cmake.rst

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

doc/src/Build_development.rst

@@ -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

@@ -31,34 +31,37 @@ This is the list of packages that may require additional steps.
 .. table_from_list::
    :columns: 6
 
+   * :ref:`ADIOS <adios>`
+   * :ref:`ATC <atc>`
+   * :ref:`AWPMD <awpmd>`
+   * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
    * :ref:`GPU <gpu>`
+   * :ref:`H5MD <h5md>`
+   * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
+   * :ref:`MACHDYN <machdyn>`
+   * :ref:`MDI <mdi>`
+   * :ref:`MESONT <mesont>`
    * :ref:`MESSAGE <message>`
-   * :ref:`MLIAP <mliap>`
+   * :ref:`ML-HDNNP <ml-hdnnp>`
+   * :ref:`ML-IAP <mliap>`
+   * :ref:`ML-PACE <ml-pace>`
+   * :ref:`ML-QUIP <ml-quip>`
+   * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
+   * :ref:`NETCDF <netcdf>`
+   * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
+   * :ref:`PLUMED <plumed>`
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
+   * :ref:`QMMM <qmmm>`
+   * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
-   * :ref:`USER-ADIOS <user-adios>`
-   * :ref:`USER-ATC <user-atc>`
-   * :ref:`USER-AWPMD <user-awpmd>`
-   * :ref:`USER-COLVARS <user-colvars>`
-   * :ref:`USER-H5MD <user-h5md>`
-   * :ref:`USER-INTEL <user-intel>`
-   * :ref:`USER-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:`VTK <vtk>`
 
 ----------
 
@@ -71,7 +74,8 @@ To build with this package you must have the `zlib compression library
 <https://zlib.net>`_ available on your system to build dump styles with
 a '/gz' suffix.  There are also styles using the
 `Zstandard <https://facebook.github.io/zstd/>`_ library which have a
-'/zstd' suffix.
+'/zstd' suffix.  The zstd library version must be at least 1.4.  Older
+versions use an incompatible API and thus LAMMPS will fail to compile.
 
 .. tabs::
 
@@ -454,6 +458,9 @@ They must be specified in uppercase.
    *  - ZEN2
       - HOST
       - AMD Zen2 class CPU (AVX 2)
+   *  - ZEN3
+      - HOST
+      - AMD Zen3 class CPU (AVX 2)
    *  - ARMV80
       - HOST
       - ARMv8.0 Compatible CPU
@@ -466,6 +473,9 @@ 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)
@@ -538,6 +548,9 @@ 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
@@ -546,12 +559,12 @@ 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::
 
@@ -610,7 +623,7 @@ 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:
@@ -799,16 +812,17 @@ be installed on your system.
 
 .. _mliap:
 
-MLIAP package
+ML-IAP package
 ---------------------------
 
-Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
-package.  There will be an error message if this requirement is not satisfied.
-Using the *mliappy* model also requires enabling Python support, which
-in turn requires the :ref:`PYTHON <PKG-PYTHON>`
-package **and** requires you have the `cython <https://cython.org>`_ software
-installed and with it a working ``cythonize`` command.  This feature requires
-compiling LAMMPS with Python version 3.6 or later.
+Building the ML-IAP package requires including the :ref:`ML-SNAP
+<PKG-ML-SNAP>` package.  There will be an error message if this requirement
+is not satisfied.  Using the *mliappy* model also requires enabling
+Python support, which in turn requires to include the :ref:`PYTHON
+<PKG-PYTHON>` package **and** requires to have the `cython
+<https://cython.org>`_ software installed and with it a working
+``cythonize`` command.  This feature requires compiling LAMMPS with
+Python version 3.6 or later.
 
 .. tabs::
 
@@ -822,9 +836,9 @@ compiling LAMMPS with Python version 3.6 or later.
       suitable Python version and the ``cythonize`` command and choose
       the default accordingly.  During the build procedure the provided
       .pyx file(s) will be automatically translated to C++ code and compiled.
-      Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
+      Please do **not** run ``cythonize`` manually in the ``src/ML-IAP`` folder,
       as that can lead to compilation errors if Python support is not enabled.
-      If you did by accident, please remove the generated .cpp and .h files.
+      If you did it by accident, please remove the generated .cpp and .h files.
 
    .. tab:: Traditional make
 
@@ -833,15 +847,16 @@ compiling LAMMPS with Python version 3.6 or later.
       the ``cythonize`` command in case the corresponding .pyx file(s) were
       modified.  You may need to modify ``lib/python/Makefile.lammps``
       if the LAMMPS build fails.
-      To manually enforce building MLIAP with Python support enabled,
-      you can add
-      ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
-      You may have to manually run the ``cythonize`` command on .pyx file(s)
-      in the ``src`` folder, if this is not automatically done during
-      installing the MLIAP package.  Please do **not** run ``cythonize``
-      in the ``src/MLIAP`` folder, as that can lead to compilation errors
-      if Python support is not enabled.
-      If you did by accident, please remove the generated .cpp and .h files.
+
+      To enable building the ML-IAP package with Python support enabled,
+      you need to add ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in
+      your machine makefile.  You may have to manually run the
+      ``cythonize`` command on .pyx file(s) in the ``src`` folder, if
+      this is not automatically done during installing the ML-IAP
+      package.  Please do **not** run ``cythonize`` in the ``src/ML-IAP``
+      folder, as that can lead to compilation errors if Python support
+      is not enabled.  If you did this by accident, please remove the
+      generated .cpp and .h files.
 
 ----------
 
@@ -1042,12 +1057,12 @@ binary package provided by your operating system.
 
 ----------
 
-.. _user-adios:
+.. _adios:
 
-USER-ADIOS package
+ADIOS package
 -----------------------------------
 
-The USER-ADIOS package requires the `ADIOS I/O library
+The ADIOS package requires the `ADIOS I/O library
 <https://github.com/ornladios/ADIOS2>`_, version 2.3.1 or newer. Make
 sure that you have ADIOS built either with or without MPI to match if
 you build LAMMPS with or without MPI.  ADIOS compilation settings for
@@ -1063,38 +1078,38 @@ systems.
       .. code-block:: bash
 
          -D ADIOS2_DIR=path        # path is where ADIOS 2.x is installed
-         -D PKG_USER-ADIOS=yes
+         -D PKG_ADIOS=yes
 
    .. tab:: Traditional make
 
-      Turn on the USER-ADIOS package before building LAMMPS. If the
+      Turn on the ADIOS package before building LAMMPS. If the
       ADIOS 2.x software is installed in PATH, there is nothing else to
       do:
 
       .. code-block:: bash
 
-         $ make yes-user-adios
+         $ make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         $ ADIOS2_DIR=path make yes-user-adios   # path is where ADIOS 2.x is installed
+         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
-.. _user-atc:
+.. _atc:
 
-USER-ATC package
+ATC package
 -------------------------------
 
-The USER-ATC package requires the MANYBODY package also be installed.
+The ATC package requires the MANYBODY package also be installed.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-ATC=yes``
+      No additional settings are needed besides ``-D PKG_ATC=yes``
       and ``-D PKG_MANYBODY=yes``.
 
    .. tab:: Traditional make
@@ -1137,16 +1152,16 @@ The USER-ATC package requires the MANYBODY package also be installed.
 
 ----------
 
-.. _user-awpmd:
+.. _awpmd:
 
-USER-AWPMD package
+AWPMD package
 ------------------
 
 .. tabs::
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-AQPMD=yes``.
+      No additional settings are needed besides ``-D PKG_AQPMD=yes``.
 
    .. tab:: Traditional make
 
@@ -1188,9 +1203,9 @@ USER-AWPMD package
 
 ----------
 
-.. _user-colvars:
+.. _colvars:
 
-USER-COLVARS package
+COLVARS package
 ---------------------------------------
 
 This package includes the `Colvars library
@@ -1204,7 +1219,7 @@ be built for the most part with all major versions of the C++ language.
 
       This is the recommended build procedure for using Colvars in
       LAMMPS. No additional settings are normally needed besides
-      ``-D PKG_USER-COLVARS=yes``.
+      ``-D PKG_COLVARS=yes``.
 
    .. tab:: Traditional make
 
@@ -1247,9 +1262,49 @@ 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
@@ -1257,7 +1312,7 @@ USER-PLUMED package
 Before building LAMMPS with this package, you must first build PLUMED.
 PLUMED can be built as part of the LAMMPS build or installed separately
 from LAMMPS using the generic `PLUMED installation instructions <plumedinstall_>`_.
-The USER-PLUMED package has been tested to work with Plumed versions
+The PLUMED package has been tested to work with Plumed versions
 2.4.x, 2.5.x, and 2.6.x and will error out, when trying to run calculations
 with a different version of the Plumed kernel.
 
@@ -1293,7 +1348,7 @@ LAMMPS build.
 
    .. tab:: CMake build
 
-      When the ``-D PKG_USER-PLUMED=yes`` flag is included in the cmake
+      When the ``-D PKG_PLUMED=yes`` flag is included in the cmake
       command you must ensure that GSL is installed in locations that
       are specified in your environment.  There are then two additional
       variables that control the manner in which PLUMED is obtained and
@@ -1326,7 +1381,7 @@ LAMMPS build.
 
    .. tab:: Traditional make
 
-      PLUMED needs to be installed before the USER-PLUMED package is
+      PLUMED needs to be installed before the PLUMED package is
       installed so that LAMMPS can find the right settings when
       compiling and linking the LAMMPS executable.  You can either
       download and build PLUMED inside the LAMMPS plumed library folder
@@ -1351,12 +1406,12 @@ LAMMPS build.
       build to use. A new file ``lib/plumed/Makefile.lammps`` is also
       created with settings suitable for LAMMPS to compile and link
       PLUMED using the desired linkage mode. After this step is
-      completed, you can install the USER-PLUMED package and compile
+      completed, you can install the PLUMED package and compile
       LAMMPS in the usual manner:
 
       .. code-block:: bash
 
-         $ make yes-user-plumed
+         $ make yes-plumed
          $ make machine
 
       Once this compilation completes you should be able to run LAMMPS
@@ -1371,15 +1426,15 @@ LAMMPS build.
 
       If you want to change the linkage mode, you have to re-run "make
       lib-plumed" with the desired settings **and** do a re-install if
-      the USER-PLUMED package with "make yes-user-plumed" to update the
+      the PLUMED package with "make yes-plumed" to update the
       required makefile settings with the changes in the lib/plumed
       folder.
 
 ----------
 
-.. _user-h5md:
+.. _h5md:
 
-USER-H5MD package
+H5MD package
 ---------------------------------
 
 To build with this package you must have the HDF5 software package
@@ -1390,7 +1445,7 @@ the HDF5 library.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-H5MD=yes``.
+      No additional settings are needed besides ``-D PKG_H5MD=yes``.
 
       This should auto-detect the H5MD library on your system.  Several
       advanced CMake H5MD options exist if you need to specify where it
@@ -1422,24 +1477,78 @@ the HDF5 library.
 
 ----------
 
-.. _user-intel:
+.. _ml-hdnnp:
 
-USER-INTEL package
+ML-HDNNP package
+----------------
+
+To build with the ML-HDNNP package it is required to download and build the
+external `n2p2 <https://github.com/CompPhysVienna/n2p2>`_ library ``v2.1.4``
+(or higher). The LAMMPS build process offers an automatic download and
+compilation of *n2p2* or allows you to choose the installation directory of
+*n2p2* manually. Please see the boxes below for the CMake and traditional build
+system for detailed information.
+
+In case of a manual installation of *n2p2* you only need to build the *n2p2* core
+library ``libnnp`` and interface library ``libnnpif``. When using GCC it should
+suffice to execute ``make libnnpif`` in the *n2p2* ``src`` directory. For more
+details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
+<https://compphysvienna.github.io/n2p2/topics/build.html>`_.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_N2P2=value    # download n2p2 for build, value = no (default) or yes
+         -D N2P2_DIR=path          # n2p2 base directory (only needed if a custom location)
+
+      If ``DOWNLOAD_N2P2`` is set, the *n2p2* library will be downloaded and
+      built inside the CMake build directory.  If the *n2p2* library is already
+      on your system (in a location CMake cannot find it), set the ``N2P2_DIR``
+      to path where *n2p2* is located. If *n2p2* is located directly in
+      ``lib/hdnnp/n2p2`` it will be automatically found by CMake.
+
+   .. tab:: Traditional make
+
+      You can download and build the *n2p2* library manually if you prefer;
+      follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
+      one step from the ``lammps/src`` dir, using a command like these, which
+      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
+
+      .. code-block:: bash
+
+         $ make lib-hdnnp             # print help message
+         $ make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
+         $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
+         $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+
+      Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
+      ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
+      ``n2p2/include``, ``n2p2/lib`` and ``n2p2/lib/Makefile.lammps-extra``,
+      respectively. When LAMMPS is built in ``src`` it will use these links.
+
+----------
+
+.. _intel:
+
+INTEL package
 -----------------------------------
 
 To build with this package, you must choose which hardware you want to
 build for, either x86 CPUs or Intel KNLs in offload mode.  You should
-also typically :ref:`install the USER-OMP package <user-omp>`, as it can be
-used in tandem with the USER-INTEL package to good effect, as explained
+also typically :ref:`install the OPENMP package <openmp>`, as it can be
+used in tandem with the INTEL package to good effect, as explained
 on the :doc:`Speed_intel` page.
 
 When using Intel compilers version 16.0 or later is required.  You can
 also use the GNU or Clang compilers and they will provide performance
-improvements over regular styles and USER-OMP styles, but less so than
+improvements over regular styles and OPENMP styles, but less so than
 with the Intel compilers.  Please also note, that some compilers have
 been found to apply memory alignment constraints incompletely or
 incorrectly and thus can cause segmentation faults in otherwise correct
-code when using features from the USER-INTEL package.
+code when using features from the INTEL package.
 
 
 .. tabs::
@@ -1456,7 +1565,7 @@ code when using features from the USER-INTEL package.
       Choose which hardware to compile for in Makefile.machine via the
       following settings.  See ``src/MAKE/OPTIONS/Makefile.intel_cpu*``
       and ``Makefile.knl`` files for examples. and
-      ``src/USER-INTEL/README`` for additional information.
+      ``src/INTEL/README`` for additional information.
 
       For CPUs:
 
@@ -1492,9 +1601,38 @@ 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
@@ -1507,7 +1645,7 @@ they will be downloaded the first time this package is installed.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-MESONT=yes``
+      No additional settings are needed besides ``-D PKG_MESONT=yes``
 
    .. tab:: Traditional make
 
@@ -1534,9 +1672,9 @@ they will be downloaded the first time this package is installed.
 
 ----------
 
-.. _user-molfile:
+.. _molfile:
 
-USER-MOLFILE package
+MOLFILE package
 ---------------------------------------
 
 .. tabs::
@@ -1546,9 +1684,9 @@ USER-MOLFILE package
       .. code-block:: bash
 
          -D MOLFILE_INCLUDE_DIR=path   # (optional) path where VMD molfile plugin headers are installed
-         -D PKG_USER-MOLFILE=yes
+         -D PKG_MOLFILE=yes
 
-      Using ``-D PKG_USER-MOLFILE=yes`` enables the package, and setting
+      Using ``-D PKG_MOLFILE=yes`` enables the package, and setting
       ``-D MOLFILE_INCLUDE_DIR`` allows to provide a custom location for
       the molfile plugin header files. These should match the ABI of the
       plugin files used, and thus one typically sets them to include
@@ -1572,9 +1710,9 @@ USER-MOLFILE package
 
 ----------
 
-.. _user-netcdf:
+.. _netcdf:
 
-USER-NETCDF package
+NETCDF package
 -------------------------------------
 
 To build with this package you must have the NetCDF library installed
@@ -1584,7 +1722,7 @@ on your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-NETCDF=yes``.
+      No additional settings are needed besides ``-D PKG_NETCDF=yes``.
 
       This should auto-detect the NETCDF library if it is installed on
       your system at standard locations.  Several advanced CMake NETCDF
@@ -1603,9 +1741,9 @@ on your system.
 
 ----------
 
-.. _user-omp:
+.. _openmp:
 
-USER-OMP package
+OPENMP package
 -------------------------------
 
 .. tabs::
@@ -1613,13 +1751,13 @@ USER-OMP package
    .. tab:: CMake build
 
       No additional settings are required besides ``-D
-      PKG_USER-OMP=yes``.  If CMake detects OpenMP compiler support, the
-      USER-OMP code will be compiled with multi-threading support
+      PKG_OPENMP=yes``.  If CMake detects OpenMP compiler support, the
+      OPENMP code will be compiled with multi-threading support
       enabled, otherwise as optimized serial code.
 
    .. tab:: Traditional make
 
-      To enable multi-threading support in the USER-OMP package (and
+      To enable multi-threading support in the OPENMP package (and
       other styles supporting OpenMP) the following compile and link
       flags must be added to your Makefile.machine file.  See
       ``src/MAKE/OPTIONS/Makefile.omp`` for an example.
@@ -1636,12 +1774,12 @@ USER-OMP package
 
 ----------
 
-.. _user-qmmm:
+.. _qmmm:
 
-USER-QMMM package
+QMMM package
 ---------------------------------
 
-For using LAMMPS to do QM/MM simulations via the USER-QMMM package you
+For using LAMMPS to do QM/MM simulations via the QMMM package you
 need to build LAMMPS as a library.  A LAMMPS executable with :doc:`fix
 qmmm <fix_qmmm>` included can be built, but will not be able to do a
 QM/MM simulation on as such.  You must also build a QM code - currently
@@ -1664,11 +1802,11 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       libqmmm.a) are not included in the static LAMMPS library and
       (currently) not installed, while their code is included in the
       shared LAMMPS library.  Thus a typical command line to configure
-      building LAMMPS for USER-QMMM would be:
+      building LAMMPS for QMMM would be:
 
       .. code-block:: bash
 
-         cmake -C ../cmake/presets/minimal.cmake -D PKG_USER-QMMM=yes \
+         cmake -C ../cmake/presets/basic.cmake -D PKG_QMMM=yes \
              -D BUILD_LIB=yes -DBUILD_SHARED_LIBS=yes ../cmake
 
       After completing the LAMMPS build and also configuring and
@@ -1711,16 +1849,16 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
 ----------
 
-.. _user-quip:
+.. _ml-quip:
 
-USER-QUIP package
+ML-QUIP package
 ---------------------------------
 
 To build with this package, you must download and build the QUIP
 library.  It can be obtained from GitHub.  For support of GAP
 potentials, additional files with specific licensing conditions need
-to be downloaded and configured.  See step 1 and step 1.1 in the
-``lib/quip/README`` file for details on how to do this.
+to be downloaded and configured.  The automatic download will from
+within CMake will download the non-commercial use version.
 
 .. tabs::
 
@@ -1728,11 +1866,14 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
       .. code-block:: bash
 
+         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
          -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
 
-      CMake will **not** download and build the QUIP library.  But once you have
-      done that, a CMake build of LAMMPS with ``-D PKG_USER-QUIP=yes`` should
-      work.  Set the ``QUIP_LIBRARY`` variable if CMake cannot find the QUIP library.
+      CMake will try to download and build the QUIP library from GitHub, if it is not
+      found on the local machine. This requires to have git installed. It will use the same compilers
+      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      and installed QUIP library and CMake cannot find it.
 
    .. tab:: Traditional make
 
@@ -1746,9 +1887,9 @@ to be downloaded and configured.  See step 1 and step 1.1 in the
 
 ----------
 
-.. _user-scafacos:
+.. _scafacos:
 
-USER-SCAFACOS package
+SCAFACOS package
 -----------------------------------------
 
 To build with this package, you must download and build the
@@ -1793,9 +1934,9 @@ To build with this package, you must download and build the
 
 ----------
 
-.. _user-smd:
+.. _machdyn:
 
-USER-SMD package
+MACHDYN package
 -------------------------------
 
 To build with this package, you must download the Eigen3 library.
@@ -1837,9 +1978,9 @@ Eigen3 is a template library, so you do not need to build it.
 
 ----------
 
-.. _user-vtk:
+.. _vtk:
 
-USER-VTK package
+VTK package
 -------------------------------
 
 To build with this package you must have the VTK library installed on
@@ -1849,7 +1990,7 @@ your system.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_USER-VTK=yes``.
+      No additional settings are needed besides ``-D PKG_VTK=yes``.
 
       This should auto-detect the VTK library if it is installed on your
       system at standard locations.  Several advanced VTK options exist

doc/src/Build_make.rst

@@ -117,10 +117,10 @@ settings may become outdated:
 
    make mac             # build serial LAMMPS on a Mac
    make mac_mpi         # build parallel LAMMPS on a Mac
-   make intel_cpu       # build with the USER-INTEL package optimized for CPUs
-   make knl             # build with the USER-INTEL package optimized for KNLs
+   make intel_cpu       # build with the INTEL package optimized for CPUs
+   make knl             # build with the INTEL package optimized for KNLs
    make opt             # build with the OPT package optimized for CPUs
-   make omp             # build with the USER-OMP package optimized for OpenMP
+   make omp             # build with the OPENMP package optimized for OpenMP
    make kokkos_omp      # build with the KOKKOS package for OpenMP
    make kokkos_cuda_mpi # build with the KOKKOS package for GPUs
    make kokkos_phi      # build with the KOKKOS package for KNLs

doc/src/Build_manual.rst

@@ -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
 --------------------
@@ -215,9 +204,9 @@ be multiple tests run automatically:
 
   .. parsed-literal::
 
-     Found 33 standard and 41 user packages
-     Standard package NEWPACKAGE missing in Packages_standard.rst
-     Standard package NEWPACKAGE missing in Packages_details.rst
+     Found 88 packages
+     Package NEWPACKAGE missing in Packages_list.rst
+     Package NEWPACKAGE missing in Packages_details.rst
 
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
@@ -257,4 +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

@@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
    * :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>`

doc/src/Commands_bond.rst

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

doc/src/Commands_category.rst

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

doc/src/Commands_compute.rst

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

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>`
@@ -152,11 +157,15 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair/tracker <fix_pair_tracker>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
+   * :doc:`polarize/bem/gmres <fix_polarize>`
+   * :doc:`polarize/bem/icc <fix_polarize>`
+   * :doc:`polarize/functional <fix_polarize>`
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
@@ -170,14 +179,14 @@ OPT.
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
-   * :doc:`qeq/reax (ko) <fix_qeq_reax>`
+   * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
    * :doc:`rattle <fix_shake>`
-   * :doc:`reax/c/bonds (k) <fix_reaxc_bonds>`
-   * :doc:`reax/c/species (k) <fix_reaxc_species>`
+   * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
+   * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rhok <fix_rhok>`

doc/src/Commands_input.rst

@@ -50,6 +50,6 @@ values are not desired, the :doc:`processors <processors>` and
 tell LAMMPS how to map processors to the simulation box.
 
 Many input script errors are detected by LAMMPS and an ERROR or
-WARNING message is printed.  The :doc:`Errors <Errors>` doc page gives
+WARNING message is printed.  The :doc:`Errors <Errors>` page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.

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::
@@ -28,12 +28,16 @@ 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>`
    * :doc:`pppm/dipole/spin <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`pppm/disp (io) <kspace_style>`
    * :doc:`pppm/disp/tip4p (o) <kspace_style>`
+   * :doc:`pppm/disp/dielectric <kspace_style>`
    * :doc:`pppm/stagger <kspace_style>`
    * :doc:`pppm/tip4p (o) <kspace_style>`
+   * :doc:`pppm/dielectric <kspace_style>`
    * :doc:`scafacos <kspace_style>`

doc/src/Commands_pair.rst

@@ -16,7 +16,7 @@ Pair_style potentials
 
 All LAMMPS :doc:`pair_style <pair_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
-parenthesis: g = GPU, i = USER-INTEL, k = KOKKOS, o = USER-OMP, t =
+parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
@@ -26,10 +26,10 @@ 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>`
-   *
-   *
+   * :doc:`tracker <pair_tracker>`
    *
    *
    *
@@ -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>`
@@ -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>`
@@ -160,6 +170,7 @@ OPT.
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
+   * :doc:`lj/long/coul/long/dielectric <pair_dielectric>`
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
@@ -168,7 +179,7 @@ OPT.
    * :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>`
@@ -179,7 +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>`
@@ -215,6 +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>`
@@ -222,7 +234,8 @@ OPT.
    * :doc:`polymorphic <pair_polymorphic>`
    * :doc:`python <pair_python>`
    * :doc:`quip <pair_quip>`
-   * :doc:`reax/c (ko) <pair_reaxc>`
+   * :doc:`rann <pair_rann>`
+   * :doc:`reaxff (ko) <pair_reaxff>`
    * :doc:`rebo (io) <pair_airebo>`
    * :doc:`resquared (go) <pair_resquared>`
    * :doc:`sdpd/taitwater/isothermal <pair_sdpd_taitwater_isothermal>`

doc/src/Commands_parse.rst

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

doc/src/Commands_removed.rst

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

doc/src/Developer_org.rst

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

@@ -59,31 +59,25 @@ Members of ``lammpsplugin_t``
    * - author
      - String with the name and email of the author
    * - creator.v1
-     - Pointer to factory function for pair, bond, angle, dihedral, or improper styles
+     - 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
-   * - creator.v3
-     - Pointer to factory function for command 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.
-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.
-The "creator.v3" element takes the same arguments as "creator.v3" but is
-specific to creating command styles: the factory function has to instantiate
-the command style locally passing the LAMMPS pointer as argument and then
-call its "command" member function with the number and list of arguments.
-The factory function pointer needs to be cast to the
-``lammpsplugin_factory3`` type before assignment.
+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
 ^^^^^^^^^^^^^^^^^^
@@ -123,12 +117,12 @@ function would look like this:
 
 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`` pointer type.  It returns a
+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``, must be unique inside
-the entire LAMMPS executable.
+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
 ^^^^^^^^^^^^^^^^^
@@ -169,9 +163,9 @@ Below is an example for that:
 
 Command style example
 ^^^^^^^^^^^^^^^^^^^^^
-For command styles there is a third variant of factory function as
+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 also be within the same
+implementation of the plugin class may be within the same source
 file as the plugin interface code:
 
 .. code-block:: C++
@@ -180,15 +174,15 @@ file as the plugin interface code:
 
    #include "comm.h"
    #include "error.h"
-   #include "pointers.h"
+   #include "command.h"
    #include "version.h"
 
    #include <cstring>
 
    namespace LAMMPS_NS {
-     class Hello : protected Pointers {
+     class Hello : public Command {
       public:
-       Hello(class LAMMPS *lmp) : Pointers(lmp) {};
+       Hello(class LAMMPS *lmp) : Command(lmp) {};
        void command(int, char **);
      };
    }
@@ -202,10 +196,9 @@ file as the plugin interface code:
         utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
    }
 
-   static void hellocreator(LAMMPS *lmp, int argc, char **argv)
+   static void hellocreator(LAMMPS *lmp)
    {
-     Hello hello(lmp);
-     hello.command(argc,argv);
+     return new Hello(lmp);
    }
 
    extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
@@ -216,9 +209,9 @@ file as the plugin interface code:
      plugin.version = LAMMPS_VERSION;
      plugin.style   = "command";
      plugin.name    = "hello";
-     plugin.info    = "Hello world command v1.0";
+     plugin.info    = "Hello world command v1.1";
      plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
-     plugin.creator.v3 = (lammpsplugin_factory3 *) &hellocreator;
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
      plugin.handle  = handle;
      (*register_plugin)(&plugin,lmp);
    }

doc/src/Developer_unittest.rst

@@ -404,8 +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.

doc/src/Developer_utils.rst

@@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
 reduces redundant implementations and encourages consistent behavior.
 
-I/O with status check
-^^^^^^^^^^^^^^^^^^^^^
+I/O with status check and similar functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-These are wrappers around the corresponding C library calls like
-``fgets()`` or ``fread()``.  They will check if there were errors
-on reading or an unexpected end-of-file state was reached.  In that
-case, the functions will stop the calculation with an error message,
-indicating the name of the problematic file, if possible.
+The the first two functions are wrappers around the corresponding C
+library calls ``fgets()`` or ``fread()``.  They will check if there
+were errors on reading or an unexpected end-of-file state was reached.
+In that case, the functions will stop with an error message, indicating
+the name of the problematic file, if possible unless the *error* argument
+is a NULL pointer.
+
+The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
+but it will read in a whole line (i.e. until the end of line or end
+of file), but store only as many characters as will fit into the buffer
+including a final newline character and the terminating NULL byte.
+If the line in the file is longer it will thus be truncated in the buffer.
+This function is used by :cpp:func:`read_lines_from_file` to read individual
+lines but make certain they follow the size constraints.
+
+The :cpp:func:`read_lines_from_file` function will read the requested
+number of lines of a maximum length into a buffer and will return 0
+if successful or 1 if not. It also guarantees that all lines are
+terminated with a newline character and the entire buffer with a
+NULL character.
 
 ----------
 
@@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible.
 .. doxygenfunction:: sfread
    :project: progguide
 
+.. doxygenfunction:: fgets_trunc
+   :project: progguide
+
+.. doxygenfunction:: read_lines_from_file
+   :project: progguide
+
 ----------
 
 String to number conversions with validity check
@@ -164,7 +185,10 @@ Argument processing
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+   :project: progguide
+
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
 .. doxygenfunction:: getsyserror

doc/src/Developer_write.rst

@@ -59,7 +59,7 @@ of each timestep. First of all, implement a constructor:
    }
 
 In the constructor you should parse your fix arguments which are
-specified in the script. All fixes have pretty the same syntax:
+specified in the script. All fixes have pretty much the same syntax:
 ``fix <fix-ID> <fix group> <fix name> <fix arguments ...>``. The
 first 3 parameters are parsed by Fix base class constructor, while
 ``<fix arguments>`` should be parsed by you. In our case, we need to

doc/src/Errors.rst

@@ -1,11 +1,11 @@
 Errors
 ******
 
-These doc pages describe the errors you can encounter when using
-LAMMPS.  The common problems include conceptual issues.  The messages
-and warnings doc pages give complete lists of all the messages the
-code may generate (except those generated by USER packages), with
-additional details for many of them.
+These doc pages describe many of the error and warning message you can
+encounter when using LAMMPS.  The common problems include conceptual
+issues.  The messages and warnings doc pages give complete lists of all
+the messages the code may generate, with additional details for many of
+them.
 
 .. toctree::
    :maxdepth: 1

doc/src/Errors_bugs.rst

@@ -5,8 +5,8 @@ If you are confident that you have found a bug in LAMMPS, please follow
 the steps outlined below:
 
  * Check the `New features and bug fixes
-   <https://lammps.sandia.gov/bug.html>`_ section of the `LAMMPS WWW site
-   <https://lammps.sandia.gov>`_ or the
+   <https://www.lammps.org/bug.html>`_ section of the `LAMMPS WWW site
+   <https://www.lammps.org>`_ or the
    `GitHub Releases page <https://github.com/lammps/lammps/releases>`_ to
    see if the bug has already been addressed in a patch release.
  * Check that your issue can be reproduced with the latest development
@@ -17,8 +17,9 @@ the steps outlined below:
    if your issue has already been reported and if it is still open.
  * Check the `GitHub Pull Requests page <https://github.com/lammps/lammps/pulls>`_
    to see if there is already a fix for your bug pending.
- * Check the `mailing list archives <https://lammps.sandia.gov/mail.html>`_
-   to see if the issue has been discussed before.
+ * Check the `mailing list archives <https://www.lammps.org/mail.html>`_ or
+   the `LAMMPS forum <https://www.lammps.org/forum.html>`_ to see if the
+   issue has been discussed before.
 
 If none of these steps yields any useful information, please file a new
 bug report on the `GitHub Issue page <https://github.com/lammps/lammps/issues>`_.

doc/src/Errors_common.rst

@@ -39,7 +39,7 @@ figure out your physics or numerical mistakes, like choosing too big a
 timestep, specifying erroneous force field coefficients, or putting 2
 atoms on top of each other!  If you run into errors that LAMMPS
 does not catch that you think it should flag, please send an email to
-the `developers <https://lammps.sandia.gov/authors.html>`_.
+the `developers <https://www.lammps.org/authors.html>`_.
 
 If you get an error message about an invalid command in your input
 script, you can determine what command is causing the problem by