sync with develop

LAMMPS feature release 2 August 2023

.github/CODEOWNERS

@@ -37,8 +37,7 @@ src/MESONT/*          @iafoss
 src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
-src/ML-POD/*          @exapde
-src/ML-UF3/*          @monk-04
+src/ML-POD/*          @exapde @rohskopf
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -50,7 +49,6 @@ src/PTM/*             @pmla
 src/QMMM/*            @akohlmey
 src/REACTION/*        @jrgissing
 src/REAXFF/*          @hasanmetin @stanmoore1
-src/RHEO/*            @jtclemm
 src/SCAFACOS/*        @rhalver
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
@@ -60,26 +58,16 @@ src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
-src/KOKKOS/pair_vashishta_kokkos.*  @andeplane @stanmoore1
-src/KOSSOS/pair_pod_kokkos.*        @exapde @stanmoore1
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
 src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
-src/MANYBODY/pair_nb3b_screened.*   @flodesani
 src/REPLICA/*_grem.*                @dstelter92
-src/EXTRA-COMMAND/geturl.*          @akohlmey
-src/EXTRA-COMMAND/group_ndx.*       @akohlmey
-src/EXTRA-COMMAND/ndx_group.*       @akohlmey
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
-src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
-src/REAXFF/compute_reaxff_atom.*    @rbberger
-src/KOKKOS/compute_reaxff_atom_kokkos.*    @rbberger
 src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
-src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
-src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -91,7 +79,7 @@ src/bond.*                @sjplimp
 src/comm*.*               @sjplimp
 src/compute.*             @sjplimp
 src/dihedral.*            @sjplimp
-src/domain.*              @sjplimp @stanmoore1
+src/domain.*              @sjplimp
 src/dump*.*               @sjplimp
 src/error.*               @sjplimp
 src/finish.*              @sjplimp
@@ -99,11 +87,9 @@ src/fix.*                 @sjplimp
 src/force.*               @sjplimp
 src/group.*               @sjplimp
 src/improper.*            @sjplimp
-src/info.*                @akohlmey
 src/kspace.*              @sjplimp
-src/lmptype.h             @sjplimp
-src/label_map.*           @jrgissing @akohlmey
-src/library.*             @sjplimp @akohlmey
+src/lmptyp.h              @sjplimp
+src/library.*             @sjplimp
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
@@ -111,12 +97,12 @@ src/modify.*              @sjplimp @stanmoore1
 src/molecule.*            @sjplimp
 src/my_page.h             @sjplimp
 src/my_pool_chunk.h       @sjplimp
-src/npair*.*              @sjplimp @jtclemm
-src/ntopo*.*              @sjplimp @jtclemm
-src/nstencil*.*           @sjplimp @jtclemm
-src/neighbor.*            @sjplimp @jtclemm
-src/nbin*.*               @sjplimp @jtclemm
-src/neigh_*.*             @sjplimp @jtclemm
+src/npair*.*              @sjplimp
+src/ntopo*.*              @sjplimp
+src/nstencil*.*           @sjplimp
+src/neighbor.*            @sjplimp
+src/nbin*.*               @sjplimp
+src/neigh_*.*             @sjplimp
 src/output.*              @sjplimp
 src/pair.*                @sjplimp
 src/rcb.*                 @sjplimp
@@ -149,7 +135,6 @@ src/timer.*               @akohlmey
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
-src/fix_press_langevin.*  @Bibobu
 
 # tools
 tools/coding_standard/* @akohlmey @rbberger
@@ -166,12 +151,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @akohlmey
+cmake/*               @rbberger
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @ellio167
+cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/CONTRIBUTING.md

@@ -5,9 +5,9 @@ Thank you for considering to contribute to the LAMMPS software project.
 The following is a set of guidelines as well as explanations of policies and work flows for contributing to the LAMMPS molecular dynamics software project. These guidelines focus on submitting issues or pull requests on the LAMMPS GitHub project.
 
 Thus please also have a look at:
-* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
+* [The guide for submitting new features in the LAMMPS manual](https://www.lammps.org/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://www.lammps.org/doc/Modify_style.html)
+* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 ## Table of Contents
 
@@ -27,17 +27,17 @@ __
 
 ## I don't want to read this whole thing I just have a question!
 
-> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). Before posting to the forum, please read the general [guidelines](https://www.lammps.org/guidelines.html) and the forum specific [suggestions](https://matsci.org/t/please-read-this-first-guidelines-and-suggestions-for-posting-lammps-questions/49913). Following those guidelines and suggestions will help greatly to get a helpful response.  *Always* mention which LAMMPS version you are using. The MatSci website may be also used for discussions that would be off-topic for the LAMMPS categories. Those will just have to be posted to a different category.
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be posted to a more general category.
 
 ## How Can I Contribute?
 
 There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list or the forum, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
-to one of the [LAMMPS core developers](https://www.lammps.org/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
 
 ### Discussing How To Use LAMMPS
 
 The LAMMPS mailing list is hosted at SourceForge. The mailing list began in 2005, and now includes tens of thousands of messages in thousands of threads. LAMMPS developers try to respond to posted questions in a timely manner, but there are no guarantees. Please consider that people live in different timezone and may not have time to answer e-mails outside of their work hours.
-You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://www.lammps.org/guidelines.html) to maximize your chances to receive a helpful response.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
 
 Anyone can browse/search previous questions/answers in the archives. You do not have to subscribe to the list to post questions, receive answers (to your questions), or browse/search the archives. You **do** need to subscribe to the list if you want emails for **all** the posts (as individual messages or in digest form), or to answer questions yourself. Feel free to sign up and help us out! Answering questions from fellow LAMMPS users is a great way to pay back the community for providing you a useful tool for free, and to pass on the advice you have received yourself to others. It improves your karma and helps you understand your own research better.
 
@@ -47,7 +47,7 @@ The LAMMPS Materials Science Discourse forum was created recently to facilitate
 
 ### 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://www.lammps.org/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
 
 When you click on the green "New Issue" button, you will be provided with a text field, where you can enter your message. That text field with contain a template with several headlines and some descriptions. Keep the headlines that are relevant to your reported potential bug and replace the descriptions with the information as suggested by the descriptions.
 You can also attach small text files (please add the file name extension `.txt` or it will be rejected), images, or small compressed text files (using gzip, do not use RAR or 7-ZIP or similar tools that are uncommon outside of Windows machines). In many cases, bugs are best illustrated by providing a small input deck (do **not** attach your entire production input, but remove everything that is not required to reproduce the issue, and scale down your system size, that the resulting calculation runs fast and can be run on small desktop quickly).
@@ -65,9 +65,9 @@ To be able to submit an issue on GitHub, you have to register for an account (fo
 
 We encourage users to submit new features or modifications for LAMMPS. Instructions, guidelines, requirements,
 and recommendations are in the following sections of the LAMMPS manual:
-* [The guide for submitting new features in the LAMMPS manual](https://docs.lammps.org/Modify_contribute.html)
-* [The guide on programming style and requirement in the LAMMPS manual](https://docs.lammps.org/Modify_requirements.html)
-* [The GitHub tutorial in the LAMMPS manual](http://docs.lammps.org/Howto_github.html)
+* [The guide for submitting new features in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The guide on programming style and requirement in the LAMMPS manual](https://lammps.sandia.gov/doc/Modify_contribute.html)
+* [The GitHub tutorial in the LAMMPS manual](http://lammps.sandia.gov/doc/Howto_github.html)
 
 
 ## GitHub Workflows
@@ -85,7 +85,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 ### Pull Requests
 
 Pull requests are the **only** way that changes get made to the LAMMPS distribution.  So also the LAMMPS core developers will submit pull requests for their own changes and discuss them on GitHub.  Thus if you submit a pull request it will be treated in a similar fashion. When you submit a pull request you may opt to submit a "Draft" pull request.  That means your changes are visible and will be subject to testing, but reviewers will not be (auto-)assigned and comments will take into account that this is not complete. On the other hand, this is a perfect way to ask the LAMMPS developers for comments on non-obvious changes and get feedback and possible suggestions for improvements or recommendations about what to avoid.
-Immediately after the submission, the LAMMPS continuing integration server at https://ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
+Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a number of tests: it will tests whether it compiles cleanly under various conditions, it will also do a check on whether your included documentation translates cleanly and run some unit tests and other checks. Whether these tests are successful or fail will be recorded.  If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again.  The test will be re-run each time the pull request is updated with a push to the remote branch on GitHub.  If you are unsure about what you need to change, ask a question in the discussion area of the pull request.
 Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission.  If you submitted a draft pull request, this will not happen unless you mark it "ready for review".  If you are not yet invited as a LAMMPS collaborator, and your contribution seems significant, you may also receive an invitation for collaboration on the LAMMPS repository.  As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.

.github/release_steps.md

@@ -1,108 +0,0 @@
-# LAMMPS Release Steps
-
-The following notes chronicle the current steps for preparing and publishing LAMMPS releases.  For
-definitions of LAMMPS versions and releases mean, please refer to [the corresponding section in the
-LAMMPS manual](https://docs.lammps.org/Manual_version.html).
-
-## LAMMPS Feature Release
-
-A LAMMPS feature release is currently prepared after about 500 to 750 commits to the 'develop'
-branch or after a period of four weeks up to two months.  This is not a fixed rule, though, since
-external circumstances can cause delays in preparing a release, or pull requests that are desired to
-be merged for the release are not yet completed.
-
-### Preparing a 'next\_release' branch
-
-Create a 'next\_release' branch off 'develop' and make the following changes:
-
-- set the LAMMPS\_VERSION define to the planned release date in src/version.h in the format
-  "D Mmm YYYY" or "DD Mmm YYYY"
-- remove the LAMMPS\_UPDATE define in src/version.h
-- update the release date in doc/lammps.1
-- update all TBD arguments for ..versionadded::, ..versionchanged:: ..deprecated:: to the
-  planned release date in the format "DMmmYYYY" or "DDMmmYYYY"
-- check release notes for merged new features and check if ..versionadded:: or ..versionchanged::
-  are missing and need to be added
-Submit this pull request, rebase if needed.  This is the last pull request merged for the release
-and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
-
-This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
-bugfix pull request should be created and merged to clear all tests.
-
-### Create release on GitHub
-
-When all pending pull requests for the release are merged and have cleared testing, the
-'next\_release' branch is merged into 'develop'.
-
-Check out 'develop' locally, pull the latest changes, merge them into 'release', apply a suitable
-release tag (for historical reasons the tag starts with "patch_" followed by the date, and finally
-push everything back to GitHub. Example:
-
-```
-git checkout develop
-git pull
-git checkout release
-git pull
-git merge --ff-only develop
-git tag -s -m "LAMMPS feature release 19 November 2024" patch_19Nov2024
-git push git@github.com:lammps/lammps.git --tags develop release
-```
-
-Go to https://github.com/lammps/lammps/releases and create a new (draft) release page or check the
-existing draft for any necessary changes from pull requests that were merged but are not listed.
-Then select the applied tag for the release in the "Choose a tag" dropdown list. Go to the bottom of
-the list and select the "Set as pre-release" checkbox.  The "Set as the latest release" button is
-reserved for stable releases and updates to them.
-
-If everything is in order, you can click on the "Publish release" button.  Otherwise, click on "Save
-draft" and finish pending tasks until you can return to edit the release page and publish it.
-
-### Update download website, prepare pre-compiled packages, update packages to GitHub
-
-Publishing the release on GitHub will trigger the Temple Jenkins cluster to update
-the https://docs.lammps.org/ website with the documentation for the new feature release
-and it will create a tarball for download (which contains the translated manual).
-
-Build a fully static LAMMPS installation using a musl-libc cross-compiler, install into a
-lammps-static folder, and create a tarball called lammps-linux-x86_64-19Nov2024.tar.gz (or using a
-corresponding date with a future release) from the lammps-static folder and upload it to GitHub
-with:
-
-```
-gh release upload patch_19Nov2024 ~/Downloads/lammps-linux-x86_64-19Nov2024.tar.gz
-```
-
-
-## LAMMPS Stable Release
-
-A LAMMPS stable release is prepared about once per year in the months July, August, or September.
-One (or two, if needed) feature releases before the stable release shall contain only bug fixes
-or minor feature updates in optional packages.  Also substantial changes to the core of the code
-shall be applied rather toward the beginning of a development cycle between two stable releases
-than toward the end.  The intention is to stablilize significant change to the core and have
-outside users and developers try them out during the development cycle; the sooner the changes
-are included, the better chances for spotting peripheral bugs and issues.
-
-### Prerequesites
-
-Before making a stable release all remaining backported bugfixes shall be released as a (final)
-stable update release (see below).
-
-A LAMMPS stable release process starts like a feature release (see above), only that this feature
-release is called a "Stable Release Candidate" and no assets are uploaded to GitHub.
-
-### Synchronize 'maintenance' branch with 'release'
-
-The state of the 'release' branch is then transferred to the 'maintenance' branch (which will
-have diverged significantly from 'release' due to the selectively backported bug fixes).
-
-### Fast-forward merge of 'maintenance' into 'stable' and apply tag
-
-At this point it should be possible to do a fast-forward merge of 'maintenance' to 'stable'
-and then apply the stable\_DMmmYYYY tag.
-
-### Push branches and tags
-
-
-
-## LAMMPS Stable Update Release

.github/workflows/check-cpp23.yml

@@ -1,92 +0,0 @@
-# GitHub action to build LAMMPS on Linux with gcc and C++23
-name: "Check for C++23 Compatibility"
-
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Build with C++23 support enabled
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache \
-                                libeigen3-dev \
-                                libcurl4-openssl-dev \
-                                mold \
-                                mpi-default-bin \
-                                mpi-default-dev \
-                                ninja-build \
-                                python3-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-cpp23-ccache-${{ github.sha }}
-        restore-keys: linux-cpp23-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install numpy
-        python3 -m pip install pyyaml
-        cmake -S cmake -B build \
-              -C cmake/presets/most.cmake \
-              -C cmake/presets/kokkos-openmp.cmake \
-              -D CMAKE_CXX_STANDARD=23 \
-              -D CMAKE_CXX_COMPILER=g++ \
-              -D CMAKE_C_COMPILER=gcc \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_BUILD_TYPE=Debug \
-              -D CMAKE_CXX_FLAGS_DEBUG="-Og -g" \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D BUILD_MPI=on \
-              -D BUILD_SHARED_LIBS=on \
-              -D BUILD_TOOLS=off \
-              -D ENABLE_TESTING=off \
-              -D MLIAP_ENABLE_ACE=on \
-              -D MLIAP_ENABLE_PYTHON=off \
-              -D PKG_AWPMD=on \
-              -D PKG_GPU=on \
-              -D GPU_API=opencl \
-              -D PKG_KOKKOS=on \
-              -D PKG_LATBOLTZ=on \
-              -D PKG_MDI=on \
-              -D PKG_MANIFOLD=on \
-              -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=off \
-              -D PKG_MOLFILE=on \
-              -D PKG_RHEO=on \
-              -D PKG_PTM=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QTB=on \
-              -D PKG_SMTBQ=on \
-              -G Ninja
-        cmake --build build
-        ccache -s

.github/workflows/check-vla.yml

@@ -1,89 +0,0 @@
-# GitHub action to build LAMMPS on Linux with gcc and -Werror=vla
-name: "Check for Variable Length Arrays"
-
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Build with -Werror=vla
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache \
-                                libeigen3-dev \
-                                libcurl4-openssl-dev \
-                                mold \
-                                mpi-default-bin \
-                                mpi-default-dev \
-                                ninja-build \
-                                python3-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-vla-ccache-${{ github.sha }}
-        restore-keys: linux-vla-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install numpy
-        python3 -m pip install pyyaml
-        cmake -S cmake -B build \
-              -C cmake/presets/most.cmake \
-              -D CMAKE_CXX_COMPILER=g++ \
-              -D CMAKE_C_COMPILER=gcc \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_BUILD_TYPE=Debug \
-              -D CMAKE_CXX_FLAGS_DEBUG="-Og -g -Werror=vla" \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D BUILD_MPI=on \
-              -D BUILD_SHARED_LIBS=off \
-              -D BUILD_TOOLS=off \
-              -D ENABLE_TESTING=off \
-              -D MLIAP_ENABLE_ACE=on \
-              -D MLIAP_ENABLE_PYTHON=off \
-              -D PKG_AWPMD=on \
-              -D PKG_GPU=on \
-              -D GPU_API=opencl \
-              -D PKG_LATBOLTZ=on \
-              -D PKG_MDI=on \
-              -D PKG_MANIFOLD=on \
-              -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=off \
-              -D PKG_MOLFILE=on \
-              -D PKG_RHEO=on \
-              -D PKG_PTM=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QTB=on \
-              -D PKG_SMTBQ=on \
-              -G Ninja
-        cmake --build build
-        ccache -s

.github/workflows/codeql-analysis.yml

@@ -25,17 +25,17 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v3
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -55,4 +55,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v3
+      uses: github/codeql-action/analyze@v2

.github/workflows/compile-msvc.yml

@@ -1,5 +1,5 @@
-# GitHub action to test LAMMPS on Windows with Visual C++
-name: "Windows Unit Tests"
+# GitHub action to build LAMMPS on Windows with Visual C++
+name: "Native Windows Compilation and Unit Tests"
 
 on:
   push:
@@ -11,59 +11,48 @@ on:
 
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
 jobs:
   build:
     name: Windows Compilation Test
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: windows-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
-    - name: Enable MSVC++
-      uses: lammps/setup-msvc-dev@v3
-      with:
-        arch: x64
-
-    - name: Install Ccache
-      run: |
-        choco install ccache ninja -y
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: win-unit-ccache-${{ github.sha }}
-        restore-keys: win-unit-ccache-
-
     - name: Select Python version
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v4
       with:
         python-version: '3.11'
 
     - name: Building LAMMPS via CMake
+      shell: bash
       run: |
-        ccache -z
         python3 -m pip install numpy
         python3 -m pip install pyyaml
-        cmake -C cmake\presets\windows.cmake -D CMAKE_CXX_COMPILER=cl -D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D CMAKE_C_COMPILER=cl -D CMAKE_C_COMPILER_LAUNCHER=ccache -D CMAKE_Fortran_COMPILER="" -D DOWNLOAD_POTENTIALS=off -D PKG_PYTHON=on -D WITH_PNG=off -D WITH_JPEG=off -S cmake -B build -D BUILD_SHARED_LIBS=on -D ENABLE_TESTING=on -D CMAKE_BUILD_TYPE=Release -G Ninja
-        cmake --build build
-        ccache -s
+        nuget install MSMPIsdk
+        nuget install MSMPIDIST
+        cmake -C cmake/presets/windows.cmake \
+              -D DOWNLOAD_POTENTIALS=off \
+              -D PKG_PYTHON=on \
+              -D WITH_PNG=off \
+              -D WITH_JPEG=off \
+              -S cmake -B build \
+              -D BUILD_SHARED_LIBS=on \
+              -D LAMMPS_EXCEPTIONS=on \
+              -D ENABLE_TESTING=on
+        cmake --build build --config Release --parallel 2
 
     - name: Run LAMMPS executable
+      shell: bash
       run: |
-        build\lmp.exe -h
-        build\lmp.exe -in bench\in.lj
+        ./build/Release/lmp.exe -h
+        ./build/Release/lmp.exe -in bench/in.lj
 
     - name: Run Unit Tests
       working-directory: build
-      run: ctest -V -E FixTimestep:python_move_nve
+      shell: bash
+      run: ctest -V -C Release -E FixTimestep:python_move_nve

.github/workflows/coverity.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
@@ -25,7 +25,7 @@ jobs:
 
     - name: Cache Coverity
       id: cache-coverity
-      uses: actions/cache@v4
+      uses: actions/cache@v3
       with:
         path: ./download/
         key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
@@ -59,20 +59,25 @@ jobs:
         -D BUILD_SHARED_LIBS=on \
         -D LAMMPS_SIZES=SMALLBIG \
         -D LAMMPS_EXCEPTIONS=off \
+        -D PKG_MESSAGE=on \
+        -D PKG_MPIIO=on \
         -D PKG_ATC=on \
         -D PKG_AWPMD=on \
+        -D PKG_BOCS=on \
+        -D PKG_EFF=on \
         -D PKG_H5MD=on \
         -D PKG_INTEL=on \
         -D PKG_LATBOLTZ=on \
         -D PKG_MANIFOLD=on \
-        -D PKG_MDI=on \
         -D PKG_MGPT=on \
+        -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
         -D PKG_MOLFILE=on \
         -D PKG_NETCDF=on \
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
+        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

.github/workflows/full-regression.yml

@@ -1,109 +0,0 @@
-# GitHub action to build LAMMPS on Linux and run regression tests
-name: "Full Regression Test"
-
-on:
-  push:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Build LAMMPS
-    # restrict to official LAMMPS repository
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-    strategy:
-      max-parallel: 8
-      matrix:
-        idx: [ 0, 1, 2, 3, 4, 5, 6, 7 ]
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-        show-progress: false
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache ninja-build libeigen3-dev \
-                     libcurl4-openssl-dev python3-dev \
-                     mpi-default-bin mpi-default-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-full-ccache-${{ github.sha }}
-        restore-keys: linux-full-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install --upgrade pip
-        python3 -m pip install numpy pyyaml junit_xml
-        cmake -S cmake -B build \
-              -C cmake/presets/gcc.cmake \
-              -C cmake/presets/most.cmake \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D BUILD_SHARED_LIBS=off \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D PKG_MANIFOLD=on \
-              -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=on \
-              -D PKG_RHEO=on \
-              -D PKG_PTM=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QTB=on \
-              -D PKG_SMTBQ=on \
-              -G Ninja
-        cmake --build build
-        ccache -s
-
-    - name: Run Full Regression Tests
-      shell: bash
-      run: |
-        source linuxenv/bin/activate
-        python3 tools/regression-tests/run_tests.py \
-               --lmp-bin=build/lmp \
-               --config-file=tools/regression-tests/config_serial.yaml \
-               --examples-top-level=examples --analyze --num-workers=8
-
-        python3 tools/regression-tests/run_tests.py \
-               --lmp-bin=build/lmp \
-               --config-file=tools/regression-tests/config_serial.yaml \
-               --list-input=input-list-${{ matrix.idx }}.txt \
-               --output-file=output-${{ matrix.idx }}.xml \
-               --progress-file=progress-${{ matrix.idx }}.yaml \
-               --log-file=run-${{ matrix.idx }}.log
-
-        tar -cvf full-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
-
-    - name: Upload artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: full-regression-test-artifact-${{ matrix.idx }}
-        path: full-regression-test-${{ matrix.idx }}.tar
-
-  merge:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: merged-full-regresssion-artifact
-          pattern: full-regression-test-artifact-*
-

.github/workflows/kokkos-regression.yaml

@@ -1,126 +0,0 @@
-# GitHub action to build LAMMPS on Linux and run selected regression tests
-name: "Kokkos OpenMP Regression Test"
-
-on:
-  push:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-jobs:
-  build:
-    name: Build LAMMPS with Kokkos OpenMP
-    # restrict to official LAMMPS repository
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-    strategy:
-      max-parallel: 6
-      matrix:
-        idx: [ 'pair-0', 'pair-1', 'fix-0', 'fix-1', 'compute', 'misc' ]
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-        show-progress: false
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache ninja-build libeigen3-dev \
-                     libcurl4-openssl-dev python3-dev \
-                     mpi-default-bin mpi-default-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-kokkos-ccache-${{ github.sha }}
-        restore-keys: linux-kokkos-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install --upgrade pip
-        python3 -m pip install numpy pyyaml junit_xml
-        cmake -S cmake -B build \
-              -C cmake/presets/gcc.cmake \
-              -C cmake/presets/basic.cmake \
-              -C cmake/presets/kokkos-openmp.cmake \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D BUILD_SHARED_LIBS=off \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D PKG_AMOEBA=on \
-              -D PKG_ASPHERE=on \
-              -D PKG_BROWNIAN=on \
-              -D PKG_CLASS2=on \
-              -D PKG_COLLOID=on \
-              -D PKG_CORESHELL=on \
-              -D PKG_DIPOLE=on \
-              -D PKG_DPD-BASIC=on \
-              -D PKG_EXTRA-COMPUTE=on \
-              -D PKG_EXTRA-FIX=on \
-              -D PKG_EXTRA-MOLECULE=on \
-              -D PKG_EXTRA-PAIR=on \
-              -D PKG_GRANULAR=on \
-              -D PKG_LEPTON=on \
-              -D PKG_MC=on \
-              -D PKG_MEAM=on \
-              -D PKG_POEMS=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QEQ=on \
-              -D PKG_REAXFF=on \
-              -D PKG_REPLICA=on \
-              -D PKG_SRD=on \
-              -D PKG_SPH=on \
-              -D PKG_VORONOI=on \
-              -G Ninja
-        cmake --build build
-        ccache -s
-
-    - name: Run Regression Tests for Selected Examples
-      shell: bash
-      run: |
-        source linuxenv/bin/activate
-        python3 tools/regression-tests/get_kokkos_input.py \
-               --examples-top-level=examples --batch-size=50 \
-               --filter-out="balance;fire;gcmc;granregion;hyper;mc;mdi;mliap;neb;pace;prd;pour;python;rigid;snap;streitz;shear;ttm"
-
-        export OMP_PROC_BIND=false
-        python3 tools/regression-tests/run_tests.py \
-               --lmp-bin=build/lmp \
-               --config-file=tools/regression-tests/config_kokkos_openmp.yaml \
-               --list-input=input-list-${{ matrix.idx }}-kk.txt \
-               --output-file=output-${{ matrix.idx }}.xml \
-               --progress-file=progress-${{ matrix.idx }}.yaml \
-               --log-file=run-${{ matrix.idx }}.log \
-               --quick-max=100
-
-        tar -cvf kokkos-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
-
-    - name: Upload artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: kokkos-regression-test-artifact-${{ matrix.idx }}
-        path: kokkos-regression-test-${{ matrix.idx }}.tar
-
-  merge:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: merged-kokkos-regresssion-artifact
-          pattern: kokkos-regression-test-artifact-*

.github/workflows/lammps-gui-flatpak.yml

@@ -1,53 +0,0 @@
-# GitHub action to build LAMMPS-GUI as a flatpak bundle
-name: "Build LAMMPS-GUI as flatpak bundle"
-
-on:
-  push:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
-jobs:
-  build:
-    name: LAMMPS-GUI flatpak build
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache \
-                                libeigen3-dev \
-                                libcurl4-openssl-dev \
-                                mold \
-                                ninja-build \
-                                python3-dev \
-                                flatpak \
-                                flatpak-builder
-
-    - name: Set up access to flatpak repo
-      run: flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
-
-    - name: Build flatpak
-      run: |
-        mkdir flatpack-state
-        sed -i -e 's/branch:.*/branch: develop/' tools/lammps-gui/org.lammps.lammps-gui.yml
-        flatpak-builder --force-clean --verbose --repo=flatpak-repo \
-                               --install-deps-from=flathub --state-dir=flatpak-state \
-                               --user --ccache --default-branch=${{ github.ref_name }} \
-                               flatpak-build tools/lammps-gui/org.lammps.lammps-gui.yml
-        flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo \
-                               --verbose  flatpak-repo LAMMPS-Linux-x86_64-GUI.flatpak \
-                               org.lammps.lammps-gui ${{ github.ref_name }}
-        flatpak install -y -v --user LAMMPS-Linux-x86_64-GUI.flatpak

.github/workflows/quick-regression.yml

@@ -1,118 +0,0 @@
-# GitHub action to build LAMMPS on Linux and run selected regression tests
-name: "Quick Regression Test"
-
-on:
-  pull_request:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
-jobs:
-  build:
-    name: Build LAMMPS
-    # restrict to official LAMMPS repository
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-    strategy:
-      max-parallel: 4
-      matrix:
-        idx: [ 0, 1, 2, 3 ]
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 0
-        show-progress: false
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache ninja-build libeigen3-dev \
-                     libcurl4-openssl-dev python3-dev \
-                     mpi-default-bin mpi-default-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-quick-ccache-${{ github.sha }}
-        restore-keys: linux-quick-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install --upgrade pip
-        python3 -m pip install numpy pyyaml junit_xml
-        cmake -S cmake -B build \
-              -C cmake/presets/gcc.cmake \
-              -C cmake/presets/most.cmake \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D BUILD_SHARED_LIBS=off \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D PKG_MANIFOLD=on \
-              -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=on \
-              -D PKG_RHEO=on \
-              -D PKG_PTM=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QTB=on \
-              -D PKG_SMTBQ=on \
-              -G Ninja
-        cmake --build build
-        ccache -s
-
-    - name: Run Regression Tests for Modified Styles
-      shell: bash
-      run: |
-        source linuxenv/bin/activate
-        python3 tools/regression-tests/run_tests.py \
-               --lmp-bin=build/lmp \
-               --config-file=tools/regression-tests/config_quick.yaml \
-               --examples-top-level=examples \
-               --quick-reference=tools/regression-tests/reference.yaml \
-               --quick --quick-branch=origin/develop --quick-max=100 --num-workers=4
-
-        if [ -f input-list-${{ matrix.idx }}.txt ]
-        then \
-           python3 tools/regression-tests/run_tests.py \
-               --lmp-bin=build/lmp \
-               --config-file=tools/regression-tests/config_quick.yaml \
-               --list-input=input-list-${{ matrix.idx }}.txt \
-               --output-file=output-${{ matrix.idx }}.xml \
-               --progress-file=progress-${{ matrix.idx }}.yaml \
-               --log-file=run-${{ matrix.idx }}.log
-        fi
-
-        tar -cvf quick-regression-test-${{ matrix.idx }}.tar run-${{ matrix.idx }}.log progress-${{ matrix.idx }}.yaml output-${{ matrix.idx }}.xml
-
-    - name: Upload artifacts
-      uses: actions/upload-artifact@v4
-      with:
-        name: quick-regression-test-artifact-${{ matrix.idx }}
-        path: quick-regression-test-${{ matrix.idx }}.tar
-
-  merge:
-    runs-on: ubuntu-latest
-    needs: build
-    steps:
-      - name: Merge Artifacts
-        uses: actions/upload-artifact/merge@v4
-        with:
-          name: merged-quick-regresssion-artifact
-          pattern: quick-regression-test-artifact-*
-

.github/workflows/style-check.yml

@@ -1,37 +0,0 @@
-# GitHub action to run checks from tools/coding_standard
-name: "Check for Programming Style Conformance"
-
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
-jobs:
-  build:
-    name: Programming Style Conformance
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 1
-
-    - name: Run Tests
-      working-directory: src
-      shell: bash
-      run: |
-         make check-whitespace
-         make check-permissions
-         make check-homepage
-         make check-errordocs

.github/workflows/unittest-linux.yml

@@ -1,86 +0,0 @@
-# GitHub action to build LAMMPS on Linux and run standard unit tests
-name: "Unittest for Linux /w LAMMPS_BIGBIG"
-
-on:
-  push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
-
-  workflow_dispatch:
-
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
-jobs:
-  build:
-    name: Linux Unit Test
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: ubuntu-latest
-    env:
-      CCACHE_DIR: ${{ github.workspace }}/.ccache
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v4
-      with:
-        fetch-depth: 2
-
-    - name: Install extra packages
-      run: |
-        sudo apt-get update
-        sudo apt-get install -y ccache \
-                                libeigen3-dev \
-                                libcurl4-openssl-dev \
-                                mold \
-                                ninja-build \
-                                python3-dev
-
-    - name: Create Build Environment
-      run: mkdir build
-
-    - name: Set up ccache
-      uses: actions/cache@v4
-      with:
-        path: ${{ env.CCACHE_DIR }}
-        key: linux-unit-ccache-${{ github.sha }}
-        restore-keys: linux-unit-ccache-
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        ccache -z
-        python3 -m venv linuxenv
-        source linuxenv/bin/activate
-        python3 -m pip install numpy
-        python3 -m pip install pyyaml
-        cmake -S cmake -B build \
-              -C cmake/presets/gcc.cmake \
-              -C cmake/presets/most.cmake \
-              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
-              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_SIZES=bigbig \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D ENABLE_TESTING=on \
-              -D MLIAP_ENABLE_ACE=on \
-              -D MLIAP_ENABLE_PYTHON=off \
-              -D PKG_MANIFOLD=on \
-              -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=on \
-              -D PKG_RHEO=on \
-              -D PKG_PTM=on \
-              -D PKG_PYTHON=on \
-              -D PKG_QTB=on \
-              -D PKG_SMTBQ=on \
-              -G Ninja
-        cmake --build build
-        ccache -s
-
-    - name: Run Tests
-      working-directory: build
-      shell: bash
-      run: ctest -V

.github/workflows/unittest-macos.yml

@@ -11,21 +11,17 @@ on:
 
   workflow_dispatch:
 
-concurrency:
-  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{github.event_name == 'pull_request'}}
-
 jobs:
   build:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: macos-13
+    runs-on: macos-latest
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v4
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
@@ -36,7 +32,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v4
+      uses: actions/cache@v3
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}
@@ -47,8 +43,6 @@ jobs:
       working-directory: build
       run: |
         ccache -z
-        python3 -m venv macosenv
-        source macosenv/bin/activate
         python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \

.gitignore

@@ -43,12 +43,12 @@ Thumbs.db
 
 #cmake
 /build*
-CMakeCache.txt
-CMakeFiles
+/CMakeCache.txt
+/CMakeFiles/
+/Testing
 /Makefile
-Testing
-Temporary
-cmake_install.cmake
+/Testing
+/cmake_install.cmake
 /lmp
 out/Debug
 out/RelWithDebInfo
@@ -60,4 +60,3 @@ src/Makefile.package.settings-e
 /cmake/build/x64-Debug-Clang
 /install/x64-GUI-MSVC
 /install
-.Rhistory

cmake/CMakeLists.txt

@@ -1,11 +1,8 @@
-# -*- CMake -*- master configuration file for building LAMMPS
 ########################################
 # CMake build system
 # This file is part of LAMMPS
-cmake_minimum_required(VERSION 3.16)
-if(CMAKE_VERSION VERSION_LESS 3.20)
-  message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
-endif()
+# Created by Christoph Junghans and Richard Berger
+cmake_minimum_required(VERSION 3.10)
 ########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
@@ -15,8 +12,8 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
-# set policy to silence warnings about requiring execute permission for find_program
-# we use OLD because the python-config script for the Fedora MinGW cross-compiler requires it currently
+# 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()
@@ -24,14 +21,19 @@ endif()
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
 endif()
-
+########################################
+# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
+if(CMAKE_VERSION VERSION_LESS 3.12)
+  unset(CONFIGURE_DEPENDS)
+else()
+  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
+endif()
 ########################################
 
 project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
-include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -98,27 +100,30 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 #####################################################################
 include(CheckIncludeFileCXX)
 
-# set required compiler flags, apply checks, and compiler/CPU arch specific optimizations
+# set required compiler flags and compiler/CPU arch specific optimizations
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-  # Intel classic compilers version 19 are broken and fail to compile the embedded fmtlib
-  if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 20.0)
-    message(ERROR "Intel classic compiler version ${CMAKE_CXX_COMPILER_VERSION} is too old")
-  endif()
-
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
     endif()
-    set(CMAKE_TUNE_DEFAULT "/QxHost")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
+    else()
+      set(CMAKE_TUNE_DEFAULT "/QxHost")
+    endif()
   else()
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
-    set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
+    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
+    else()
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+    endif()
   endif()
 endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
@@ -126,45 +131,20 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
-# this hack is required to compile fmt lib with CrayClang version 15.0.2
-# CrayClang is only directly recognized by version 3.28 and later
-if(CMAKE_VERSION VERSION_LESS 3.28)
-  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
-  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
-  endif()
-else()
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
-  endif()
-endif()
-
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
+  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
 endif()
 
-# we *require* C++11 without extensions but prefer C++17.
-# Kokkos requires at least C++17 (currently)
+# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
 if(NOT CMAKE_CXX_STANDARD)
-  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
-    set(CMAKE_CXX_STANDARD 17)
-  else()
-    set(CMAKE_CXX_STANDARD 11)
-  endif()
+  set(CMAKE_CXX_STANDARD 11)
 endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
-if(CMAKE_CXX_STANDARD LESS 17)
-  message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
-endif()
-if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
-  set(CMAKE_CXX_STANDARD 17)
-endif()
-# turn off C++17 check in lmptype.h
-if(LAMMPS_CXX11)
-  add_compile_definitions(LAMMPS_CXX11)
+if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
+  set(CMAKE_CXX_STANDARD 14)
 endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@@ -175,29 +155,11 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    add_compile_options(/wd4250)
     add_compile_options(/EHsc)
-    add_compile_options(/utf-8)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-# warn about potentially problematic GCC compiler versions
-if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-  if (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 9.0)
-      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
-        "with C++17 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 9.x or later")
-    endif()
-  endif()
-  if (CMAKE_CXX_STANDARD GREATER_EQUAL 11)
-    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 5.0)
-      message(WARNING "Using ${CMAKE_CXX_COMPILER_ID} compiler version ${CMAKE_CXX_COMPILER_VERSION} "
-        "with C++11 is not recommended. Please use ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
-    endif()
-  endif()
-endif()
-
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -206,20 +168,17 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# backward compatibility with CMake before 3.12 and older LAMMPS documentation
-if (PYTHON_EXECUTABLE)
-  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
-endif()
 # set path to python interpreter and thus enforcing python version when
-# in a virtual environment and Python_EXECUTABLE is not set on command line
-if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
+# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
   if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
-    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
   else()
-    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
   endif()
+  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
   message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
-    "   Setting Python interpreter to: ${Python_EXECUTABLE}")
+    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
 endif()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@@ -232,19 +191,20 @@ set(LAMMPS_BINARY lmp${LAMMPS_MACHINE})
 option(BUILD_SHARED_LIBS "Build shared library" OFF)
 option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared libraries" ON)
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
+option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 option(BUILD_LAMMPS_GUI "Build and install the LAMMPS GUI" OFF)
 
 # Support using clang-tidy for C++ files with selected options
 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=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
 else()
   unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
-
-file(GLOB ALL_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/main.cpp)
+include(GNUInstallDirs)
+file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
@@ -256,10 +216,6 @@ endif()
 add_executable(lmp ${MAIN_SOURCES})
 target_link_libraries(lmp PRIVATE lammps)
 set_target_properties(lmp PROPERTIES OUTPUT_NAME ${LAMMPS_BINARY})
-# re-export all symbols for plugins
-if(PKG_PLUGIN AND (NOT ((CMAKE_SYSTEM_NAME STREQUAL "Windows"))))
-  set_target_properties(lmp PROPERTIES ENABLE_EXPORTS TRUE)
-endif()
 install(TARGETS lmp EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
 
 option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
@@ -290,7 +246,6 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
-  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -316,14 +271,15 @@ set(STANDARD_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
-  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-UF3
+  ML-POD
   MOFFF
   MOLECULE
   MOLFILE
+  MPIIO
+  MSCG
   NETCDF
   ORIENT
   PERI
@@ -339,7 +295,6 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -359,17 +314,6 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
-set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
-foreach(PKG ${DEPRECATED_PACKAGES})
-  if(PKG_${PKG})
-    message(WARNING
-          "The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
-          "maintenance and use of code constructs that conflict with modern C++ compilers "
-          "and standards.  Please contact developers@lammps.org if you have any concerns "
-          "about this step.")
-  endif()
-endforeach()
-
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -441,9 +385,15 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
+option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
+if(LAMMPS_EXCEPTIONS)
+  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
+endif()
+
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
 pkg_depends(ML-IAP ML-SNAP)
+pkg_depends(MPIIO MPI)
 pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
 pkg_depends(SCAFACOS MPI)
@@ -454,8 +404,6 @@ pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
-pkg_depends(MESONT MOLECULE)
-pkg_depends(RHEO BPM)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -481,7 +429,6 @@ if(BUILD_OMP)
       (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 "CrayClang") 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.
     # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
@@ -492,43 +439,16 @@ if(BUILD_OMP)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
-
-  # this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
-  # CrayClang is only directly recognized by version 3.28 and later
-  if(CMAKE_VERSION VERSION_LESS 3.28)
-    get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
-    if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
-    endif()
-  else()
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
-    endif()
-  endif()
 endif()
 
-# lower C++ standard for fmtlib sources when using Intel classic compiler
-if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUAL 17)
-    AND (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 2021.10))
-  message(STATUS "Lowering C++ standard for compiling fmtlib sources with Intel Classic compiler")
-  get_filename_component(LMP_UTILS_SRC "${LAMMPS_SOURCE_DIR}/utils.cpp" ABSOLUTE)
-  get_filename_component(LMP_VARIABLE_SRC "${LAMMPS_SOURCE_DIR}/variable.cpp" ABSOLUTE)
-  get_filename_component(FMT_FORMAT_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_format.cpp" ABSOLUTE)
-  get_filename_component(FMT_OS_SRC "${LAMMPS_SOURCE_DIR}/fmtlib_os.cpp" ABSOLUTE)
-  set_source_files_properties("${FMT_FORMAT_SRC}" "${FMT_OS_SRC}" "${LMP_VARIABLE_SRC}" "${LMP_UTILS_SRC}"
-          PROPERTIES COMPILE_OPTIONS "-std=c++14")
-endif()
-
-if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
   endif()
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
+    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
     add_library(linalg STATIC ${LINALG_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
@@ -546,7 +466,12 @@ option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
   find_package(JPEG REQUIRED)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_JPEG)
-  target_link_libraries(lammps PRIVATE JPEG::JPEG)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(lammps PRIVATE ${JPEG_INCLUDE_DIRS})
+    target_link_libraries(lammps PRIVATE ${JPEG_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE JPEG::JPEG)
+  endif()
 endif()
 
 find_package(PNG QUIET)
@@ -596,22 +521,12 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM MSCG COMPRESS ML-PACE LEPTON)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
 endforeach()
 
-# settings for misc packages and styles
-if(PKG_MISC)
-  option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
-  mark_as_advanced(LAMMPS_ASYNC_IMD)
-  if(LAMMPS_ASYNC_IMD)
-    target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
-    message(STATUS "Using IMD in asynchronous mode")
-  endif()
-endif()
-
 # optionally enable building script wrappers using swig
 option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
 if(WITH_SWIG)
@@ -621,17 +536,22 @@ endif()
 
 set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
 separate_arguments(CMAKE_TUNE_FLAGS)
-target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
-target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
+foreach(_FLAG ${CMAKE_TUNE_FLAGS})
+  target_compile_options(lammps PRIVATE ${_FLAG})
+  # skip these flags when linking the main executable
+  if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
+    target_compile_options(lmp PRIVATE ${_FLAG})
+  endif()
+endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")))
-  check_include_file_cxx(cmath FOUND_CMATH)
-  if(NOT FOUND_CMATH)
-    message(FATAL_ERROR "Could not find the required 'cmath' header")
-  endif(NOT FOUND_CMATH)
-endif()
+foreach(HEADER cmath)
+  check_include_file_cxx(${HEADER} FOUND_${HEADER})
+  if(NOT FOUND_${HEADER})
+    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
+  endif(NOT FOUND_${HEADER})
+endforeach(HEADER)
 
 # make the standard math library overrideable and autodetected (for systems that don't have it)
 find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
@@ -663,8 +583,8 @@ endforeach()
 foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -680,12 +600,19 @@ foreach(PKG ${STANDARD_PACKAGES})
   RegisterPackages(${${PKG}_SOURCES_DIR})
 endforeach()
 
+# packages that need defines set
+foreach(PKG MPIIO)
+  if(PKG_${PKG})
+    target_compile_definitions(lammps PRIVATE -DLMP_${PKG})
+  endif()
+endforeach()
+
 # dedicated check for entire contents of accelerator packages
 foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS CONFIGURE_DEPENDS ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -699,7 +626,7 @@ endforeach()
 foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES CONFIGURE_DEPENDS
+    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
       ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
@@ -743,7 +670,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -851,15 +778,9 @@ foreach(_DEF ${LAMMPS_DEFINES})
   set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
 endforeach()
 if(BUILD_SHARED_LIBS)
-  install(TARGETS lammps EXPORT LAMMPS_Targets
-          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   if(NOT BUILD_MPI)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets
-            LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
   endif()
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
@@ -900,8 +821,20 @@ install(
 # This is primarily for people that only want to use the Python wrapper.
 ###############################################################################
 if(BUILD_SHARED_LIBS)
-  # backward compatibility
-  find_package(Python COMPONENTS Interpreter)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    find_package(PythonInterp) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+  else()
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
   if(BUILD_IS_MULTI_CONFIG)
     set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
   else()
@@ -927,7 +860,7 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 11.0)
+find_package(ClangFormat 8.0)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src
@@ -960,23 +893,13 @@ else()
 endif()
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
-if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
-  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
-    OUTPUT_VARIABLE GIT_DESCRIBE
-    ERROR_QUIET
-    WORKING_DIRECTORY ${LAMMPS_DIR}
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-endif()
 message(STATUS "<<< Build configuration >>>
-   LAMMPS Version:   ${PROJECT_VERSION} ${GIT_DESCRIBE}
+   LAMMPS Version:   ${PROJECT_VERSION}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
-if(CMAKE_CROSSCOMPILING)
-  message(STATUS "Cross compiling on ${CMAKE_HOST_SYSTEM}")
-endif()
 ###############################################################################
 # Print package summary
 ###############################################################################
@@ -997,12 +920,8 @@ message(STATUS "<<< Compilers and Flags: >>>
 -- C++ Compiler:     ${CMAKE_CXX_COMPILER}
       Type:          ${CMAKE_CXX_COMPILER_ID}
       Version:       ${CMAKE_CXX_COMPILER_VERSION}
-      C++ Standard:  ${CMAKE_CXX_STANDARD}
       C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
       Defines:       ${DEFINES}")
-if(CMAKE_CXX_COMPILER_LAUNCHER)
-  message(STATUS "      Launcher:      ${CMAKE_CXX_COMPILER_LAUNCHER}")
-endif()
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)
 if(OPTIONS)
   message("      Options:       ${OPTIONS}")
@@ -1021,15 +940,14 @@ if(_index GREATER -1)
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
       C Flags:      ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
-  if(CMAKE_C_COMPILER_LAUNCHER)
-    message(STATUS "      Launcher:      ${CMAKE_C_COMPILER_LAUNCHER}")
-  endif()
 endif()
 message(STATUS "<<< Linker flags: >>>")
 message(STATUS "Executable name:  ${LAMMPS_BINARY}")
-get_target_property(OPTIONS lammps LINK_OPTIONS)
-if(OPTIONS)
-  message(STATUS "Linker options:   ${OPTIONS}")
+if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  get_target_property(OPTIONS lammps LINK_OPTIONS)
+  if(OPTIONS)
+    message(STATUS "Linker options:   ${OPTIONS}")
+  endif()
 endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
@@ -1071,37 +989,34 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  if (FFT_USE_HEFFTE)
-    message(STATUS "<<< FFT settings >>>
--- Primary FFT lib:  heFFTe")
-    if (FFT_HEFFTE_BACKEND)
-      message(STATUS "heFFTe backend:  ${FFT_HEFFTE_BACKEND}")
-    else()
-      message(STATUS "heFFTe backend:  stock (builtin FFT implementation, tested for corrected but not optimized for production)")
-    endif()
-    message(STATUS "Using distributed FFT algorithms from heFTTe")
-    if(FFT_SINGLE)
-      message(STATUS "Using single precision FFTs")
-    else()
-      message(STATUS "Using double precision FFTs")
-    endif()
-  else()
-    message(STATUS "<<< FFT settings >>>
+  message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")
-    if(FFT_SINGLE)
-      message(STATUS "Using single precision FFTs")
-    else()
-      message(STATUS "Using double precision FFTs")
-    endif()
-    if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
-      message(STATUS "Using threaded FFTs")
-    else()
-      message(STATUS "Using non-threaded FFTs")
-    endif()
-    message(STATUS "Using builtin distributed FFT algorithms")
+  if(FFT_SINGLE)
+    message(STATUS "Using single precision FFTs")
+  else()
+    message(STATUS "Using double precision FFTs")
+  endif()
+  if(FFT_FFTW_THREADS OR FFT_MKL_THREADS)
+    message(STATUS "Using threaded FFTs")
+  else()
+    message(STATUS "Using non-threaded FFTs")
   endif()
   if(PKG_KOKKOS)
-    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
+    if(Kokkos_ENABLE_CUDA)
+      if(FFT STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: cuFFT")
+      endif()
+    elseif(Kokkos_ENABLE_HIP)
+      if(FFT STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: hipFFT")
+      endif()
+    else()
+      message(STATUS "Kokkos FFT: ${FFT}")
+    endif()
   endif()
 endif()
 if(BUILD_DOC)
@@ -1110,16 +1025,8 @@ endif()
 if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
-if(BUILD_LAMMPS_GUI)
-  message(STATUS "<<< Building LAMMPS-GUI >>>")
-  if(LAMMPS_GUI_USE_PLUGIN)
-    message(STATUS "Loading LAMMPS library as plugin at run time")
-  else()
-    message(STATUS "Linking LAMMPS library at compile time")
-  endif()
-  if(BUILD_WHAM)
-    message(STATUS "<<< Building WHAM >>>")
-  endif()
+if(BUILD_LAMMPS_SHELL)
+  message(STATUS "<<< Building LAMMPS Shell >>>")
 endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")

cmake/Modules/CodingStandard.cmake

@@ -1,11 +1,19 @@
-# use default (or custom) Python executable, if version is sufficient
-if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
-  set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.5 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+        set(Python3_VERSION ${PYTHON_VERSION_STRING})
+    endif()
+else()
+    # use default (or custom) Python executable, if version is sufficient
+    if(Python_VERSION VERSION_GREATER_EQUAL 3.5)
+      set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+    endif()
+    find_package(Python3 COMPONENTS Interpreter QUIET)
 endif()
-find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
+    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
         add_custom_target(
           check-whitespace
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

cmake/Modules/DetectHIPInstallation.cmake

@@ -1,3 +1,11 @@
+if(NOT DEFINED HIP_PATH)
+    if(NOT DEFINED ENV{HIP_PATH})
+        message(FATAL_ERROR "HIP support requires HIP_PATH to be defined.\n"
+        "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
+    else()
+        set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
+    endif()
+endif()
 if(NOT DEFINED ROCM_PATH)
     if(NOT DEFINED ENV{ROCM_PATH})
         set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
@@ -5,4 +13,4 @@ if(NOT DEFINED ROCM_PATH)
         set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
     endif()
 endif()
-list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})
+list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})

cmake/Modules/Documentation.cmake

@@ -4,21 +4,33 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
-  option(BUILD_DOC_VENV "Build LAMMPS documentation virtual environment" ON)
-  mark_as_advanced(BUILD_DOC_VENV)
   # Current Sphinx versions require at least Python 3.8
-  # use default (or custom) Python executable, if version is sufficient
-  if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
-    set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.8 REQUIRED)
+    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
+  else()
+    # use default (or custom) Python executable, if version is sufficient
+    if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
+      set(Python3_EXECUTABLE ${Python_EXECUTABLE})
+    endif()
+    find_package(Python3 REQUIRED COMPONENTS Interpreter)
+    if(Python3_VERSION VERSION_LESS 3.8)
+      message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
+    endif()
+    set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
   endif()
-  find_package(Python3 REQUIRED COMPONENTS Interpreter)
-  if(Python3_VERSION VERSION_LESS 3.8)
-    message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
-  endif()
-  set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
-
   find_package(Doxygen 1.8.10 REQUIRED)
-  file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+
+  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+
+
+  add_custom_command(
+    OUTPUT docenv
+    COMMAND ${VIRTUALENV} docenv
+  )
+
+  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
 
   set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
   set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
@@ -38,32 +50,14 @@ if(BUILD_DOC)
   # configure paths in conf.py, since relative paths change when file is copied
   configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
-  if(BUILD_DOC_VENV)
-    add_custom_command(
-      OUTPUT docenv
-      COMMAND ${VIRTUALENV} docenv
-    )
-
-    set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
-    set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
-
-    add_custom_command(
-      OUTPUT ${DOC_BUILD_DIR}/requirements.txt
-      DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
-      COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
-      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
-    )
-
-    set(DOCENV_DEPS docenv ${DOC_BUILD_DIR}/requirements.txt)
-    if(NOT TARGET Sphinx::sphinx-build)
-      add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
-      set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${DOCENV_BINARY_DIR}/sphinx-build")
-    endif()
-  else()
-    find_package(Sphinx)
-  endif()
+  add_custom_command(
+    OUTPUT ${DOC_BUILD_DIR}/requirements.txt
+    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
+    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+  )
 
   set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
   set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
@@ -86,7 +80,7 @@ if(BUILD_DOC)
       message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
     endif()
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    file(GLOB MATHJAX_VERSION_DIR CONFIGURE_DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
 
@@ -109,9 +103,8 @@ if(BUILD_DOC)
   endif()
   add_custom_command(
     OUTPUT html
-    DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
-    COMMAND ${Python3_EXECUTABLE} ${LAMMPS_DOC_DIR}/utils/make-globbed-tocs.py -d ${LAMMPS_DOC_DIR}/src
-    COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
+    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
+    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
     COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
     COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF
     COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

cmake/Modules/ExternalCMakeProject.cmake

@@ -43,5 +43,5 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
       "${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}/CMakeLists.txt")
   endif()
   add_subdirectory("${CMAKE_BINARY_DIR}/_deps/${target}-src/${cmakedir}"
-    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build")
 endfunction(ExternalCMakeProject)

cmake/Modules/FindClangFormat.cmake

@@ -1,10 +1,5 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
-                                          clang-format-20.0
-                                          clang-format-19.0
-                                          clang-format-18.0
-                                          clang-format-17.0
-                                          clang-format-16.0
                                           clang-format-15.0
                                           clang-format-14.0
                                           clang-format-13.0
@@ -24,7 +19,7 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
+  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
     # Arch Linux output:
     # clang-format version 10.0.0
     #
@@ -37,15 +32,9 @@ if(ClangFormat_EXECUTABLE)
     # Ubuntu 22.04 LTS output:
     # Ubuntu clang-format version 14.0.0-1ubuntu1
     #
-    # Debian 11 output:
-    # Debian clang-format version 11.0.1-2
-    #
-    # Debian 12 output:
-    # Debian clang-format version 14.0.6
-    #
     # Fedora 36 output:
     # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
-    string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
+    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
                          "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")

cmake/Modules/FindCythonize.cmake

@@ -7,7 +7,15 @@
 # adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
 #=============================================================================
 
-find_package(Python 3.6 COMPONENTS Interpreter QUIET)
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+else()
+    find_package(Python 3.6 COMPONENTS Interpreter QUIET)
+endif()
 
 # Use the Cython executable that lives next to the Python executable
 # if it is a local installation.

cmake/Modules/FindSphinx.cmake

@@ -1,29 +0,0 @@
-# Find sphinx-build
-find_program(Sphinx_EXECUTABLE NAMES sphinx-build
-	                       PATH_SUFFIXES bin
-			       DOC "Sphinx documenation build executable")
-mark_as_advanced(Sphinx_EXECUTABLE)
-
-if(Sphinx_EXECUTABLE)
-  execute_process(COMMAND ${Sphinx_EXECUTABLE} --version
-                  OUTPUT_VARIABLE sphinx_version
-                  OUTPUT_STRIP_TRAILING_WHITESPACE
-                  RESULT_VARIABLE _sphinx_version_result)
-
-  if(_sphinx_version_result)
-    message(WARNING "Unable to determine sphinx-build verison: ${_sphinx_version_result}")
-  else()
-    string(REGEX REPLACE "sphinx-build ([0-9.]+).*"
-                         "\\1"
-                         Sphinx_VERSION
-                         "${sphinx_version}")
-  endif()
-
-  if(NOT TARGET Sphinx::sphinx-build)
-    add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
-    set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${Sphinx_EXECUTABLE}")
-  endif()
-endif()
-
-include(FindPackageHandleStandardArgs)
-find_package_handle_standard_args(Sphinx REQUIRED_VARS Sphinx_EXECUTABLE VERSION_VAR Sphinx_VERSION)

cmake/Modules/FindVORO.cmake

@@ -21,9 +21,9 @@ if(VORO_FOUND)
   set(VORO_LIBRARIES ${VORO_LIBRARY})
   set(VORO_INCLUDE_DIRS ${VORO_INCLUDE_DIR})
 
-  if(NOT TARGET VORO::voro++)
-    add_library(VORO::voro++ UNKNOWN IMPORTED)
-    set_target_properties(VORO::voro++ PROPERTIES
+  if(NOT TARGET VORO::VORO)
+    add_library(VORO::VORO UNKNOWN IMPORTED)
+    set_target_properties(VORO::VORO PROPERTIES
       IMPORTED_LOCATION "${VORO_LIBRARY}"
       INTERFACE_INCLUDE_DIRECTORIES "${VORO_INCLUDE_DIR}")
   endif()

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -28,8 +28,9 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    add_compile_options(/wd4250)
-    add_compile_options(/EHsc)
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -64,7 +65,7 @@ endfunction(validate_option)
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs CONFIGURE_DEPENDS ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})

cmake/Modules/LAMMPSUtils.cmake

@@ -32,13 +32,7 @@ function(check_omp_h_include)
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
     set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-    # there are all kinds of problems with finding omp.h
-    # for Clang and derived compilers so we pretend it is there.
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
-      set(_have_omp_h TRUE)
-    else()
-      check_include_file_cxx(omp.h _have_omp_h)
-    endif()
+    check_include_file_cxx(omp.h _have_omp_h)
   else()
     set(_have_omp_h FALSE)
   endif()
@@ -47,7 +41,7 @@ endfunction()
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs CONFIGURE_DEPENDS ${path})
+  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -86,20 +80,20 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
-    list(APPEND SRC_AUTOGEN_FILES ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})
         message(FATAL_ERROR "\n########################################################################\n"
-                            "Found header file ${source_dir}/${FILENAME} generated by the make-based build system\n"
-                            "\n"
-                            "Please run\n"
-                            "make -C ${source_dir} purge\n"
-                            "to remove\n"
-                            "########################################################################")
+                              "Found header file(s) generated by the make-based build system\n"
+                              "\n"
+                              "Please run\n"
+                              "make -C ${source_dir} purge\n"
+                              "to remove\n"
+                              "########################################################################")
       endif()
     endforeach()
 endfunction()

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2024.05.09.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "e7796826b21c059224fabe997e0f2075" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 
@@ -8,3 +8,4 @@ set(INSTALL_LIBOPENCL OFF CACHE BOOL "" FORCE)
 include(ExternalCMakeProject)
 ExternalCMakeProject(opencl_loader ${OPENCL_LOADER_URL} ${OPENCL_LOADER_MD5} opencl-loader . "")
 
+add_library(OpenCL::OpenCL ALIAS OpenCL)

cmake/Modules/Packages/COLVARS.cmake

@@ -1,6 +1,6 @@
 set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-file(GLOB COLVARS_SOURCES CONFIGURE_DEPENDS ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
 option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
 
@@ -24,12 +24,6 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
-if(BUILD_OMP)
-  # Enable OpenMP for Colvars as well
-  target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
-  target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
-endif()
-
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

cmake/Modules/Packages/DPD-BASIC.cmake

@@ -1,9 +0,0 @@
-# pair style dpd/coul/slater/long may only be installed if also KSPACE is installed
-if(NOT PKG_KSPACE)
-  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
-  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.h)
-  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
-  get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/DPD-BASIC/pair_dpd_coul_slater_long.cpp)
-  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
-endif()

cmake/Modules/Packages/EXTRA-COMMAND.cmake

@@ -1,10 +0,0 @@
-# the geturl command needs libcurl
-
-find_package(CURL QUIET COMPONENTS HTTP HTTPS)
-option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
-if(WITH_CURL)
-  find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
-  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
-  target_link_libraries(lammps PRIVATE CURL::libcurl)
-endif()
-

cmake/Modules/Packages/GPU.cmake

@@ -1,10 +1,3 @@
-
-# Silence CMake warnings about FindCUDA being obsolete.
-# We may need to eventually rewrite this section to use enable_language(CUDA)
-if(POLICY CMP0146)
-  cmake_policy(SET CMP0146 OLD)
-endif()
-
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
@@ -46,7 +39,7 @@ if (PKG_AMOEBA)
               ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
 endif()
 
-file(GLOB GPU_LIB_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
 if(GPU_API STREQUAL "CUDA")
@@ -77,7 +70,7 @@ if(GPU_API STREQUAL "CUDA")
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
-  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
   if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
@@ -87,15 +80,15 @@ if(GPU_API STREQUAL "CUDA")
       "########################################################################")
   endif()
 
-  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
   if(CUDPP_OPT)
     cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-    file(GLOB GPU_LIB_CUDPP_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-    file(GLOB GPU_LIB_CUDPP_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+    file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
   endif()
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
@@ -158,10 +151,10 @@ 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 -allow-unsupported-compiler -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -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 -allow-unsupported-compiler -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -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)
@@ -212,7 +205,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -342,7 +335,7 @@ elseif(GPU_API STREQUAL "HIP")
     endif()
   endif()
 
-  file(GLOB GPU_LIB_CU CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   set(GPU_LIB_CU_HIP "")

cmake/Modules/Packages/H5MD.cmake

@@ -3,7 +3,7 @@ enable_language(C)
 # we don't use the parallel i/o interface.
 set(HDF5_PREFER_PARALLEL FALSE)
 
-find_package(HDF5 COMPONENTS C REQUIRED)
+find_package(HDF5 REQUIRED)
 
 # parallel HDF5 will import incompatible MPI headers with a serial build
 if((NOT BUILD_MPI) AND HDF5_IS_PARALLEL)

cmake/Modules/Packages/INTEL.cmake

@@ -111,9 +111,6 @@ if(PKG_KSPACE)
   list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/verlet_lrt_intel.cpp)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
-if(PKG_ML-SNAP)
-  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/sna_intel.cpp)
-endif()
 
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KIM.cmake

@@ -1,7 +1,12 @@
 set(KIM-API_MIN_VERSION 2.1.3)
 find_package(CURL)
 if(CURL_FOUND)
-  target_link_libraries(lammps PRIVATE CURL::libcurl)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    target_include_directories(lammps PRIVATE ${CURL_INCLUDE_DIRS})
+    target_link_libraries(lammps PRIVATE ${CURL_LIBRARIES})
+  else()
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
+  endif()
   target_compile_definitions(lammps PRIVATE -DLMP_KIM_CURL)
   set(LMP_DEBUG_CURL OFF CACHE STRING "Set libcurl verbose mode on/off. If on, it displays a lot of verbose information about its operations.")
   mark_as_advanced(LMP_DEBUG_CURL)

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,33 +1,25 @@
 ########################################################################
-# As of version 4.0.0 Kokkos requires C++17
-if(CMAKE_CXX_STANDARD LESS 17)
-  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to
-be set to at least C++17")
+# As of version 3.3.0 Kokkos requires C++14
+if(CMAKE_CXX_STANDARD LESS 14)
+  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
 endif()
 
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
-if(Kokkos_ENABLE_HIP)
-  option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
-  mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
-  option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
-  mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
+if(Kokkos_ENABLE_CUDA)
+  message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
+  set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
 endif()
-
 # Adding OpenMP compiler flags without the checks done for
 # BUILD_OMP can result in compile failures. Enforce consistency.
 if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
-  endif()
-endif()
-
-if(Kokkos_ENABLE_SERIAL)
-  if(NOT (Kokkos_ENABLE_OPENMP OR Kokkos_ENABLE_THREADS OR
-    Kokkos_ENABLE_CUDA OR Kokkos_ENABLE_HIP OR Kokkos_ENABLE_SYCL
-    OR Kokkos_ENABLE_OPENMPTARGET))
-  option(Kokkos_ENABLE_ATOMICS_BYPASS "Disable atomics for Kokkos Serial Backend" ON)
-  mark_as_advanced(Kokkos_ENABLE_ATOMICS_BYPASS)
+  else()
+    # NVHPC/(AMD)Clang does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
+    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
+      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
+    endif()
   endif()
 endif()
 ########################################################################
@@ -57,8 +49,8 @@ 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/4.5.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "4d832aa0284169d9e3fbae3165286bc6" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -83,7 +75,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.5.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.02 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -117,7 +109,6 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
-                       ${KOKKOS_PKG_SOURCES_DIR}/group_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp
@@ -139,45 +130,19 @@ if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
-  set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
-  set(FFT_KOKKOS_VALUES KISS FFTW3 MKL NVPL HIPFFT CUFFT MKL_GPU)
-  set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
-  validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
-  string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
-
   if(Kokkos_ENABLE_CUDA)
-    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
-      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
-    elseif(FFT_KOKKOS STREQUAL "KISS")
-      message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
-    elseif(FFT_KOKKOS STREQUAL "CUFFT")
-      find_package(CUDAToolkit REQUIRED)
-      target_link_libraries(lammps PRIVATE CUDA::cufft)
+    if(NOT (FFT STREQUAL "KISS"))
+      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
+      target_link_libraries(lammps PRIVATE cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
-    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
-      message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
-    elseif(FFT_KOKKOS STREQUAL "KISS")
-      message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
-      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
-    elseif(FFT_KOKKOS STREQUAL "HIPFFT")
+    if(NOT (FFT STREQUAL "KISS"))
       include(DetectHIPInstallation)
       find_package(hipfft REQUIRED)
+      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
       target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
-  elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
-    if(NOT Kokkos_ENABLE_SYCL)
-      message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
-    endif()
-    find_package(MKL REQUIRED)
-    target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
-  elseif(FFT_KOKKOS STREQUAL "MKL")
-    find_package(MKL REQUIRED)
-  elseif(FFT_KOKKOS STREQUAL "NVPL")
-      find_package(nvpl_fft REQUIRED)
-      target_link_libraries(lammps PRIVATE nvpl::fftw)
   endif()
-  target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS})
 endif()
 
 if(PKG_ML-IAP)
@@ -190,7 +155,7 @@ if(PKG_ML-IAP)
 
   # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
   if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
-    file(GLOB MLIAP_KOKKOS_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
+    file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
     foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
       get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
       add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h

cmake/Modules/Packages/KSPACE.cmake

@@ -10,7 +10,7 @@ if(${FFTW}_FOUND)
 else()
   set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
 endif()
-set(FFT_VALUES KISS FFTW3 MKL NVPL)
+set(FFT_VALUES KISS FFTW3 MKL)
 set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
 validate_option(FFT FFT_VALUES)
 string(TOUPPER ${FFT} FFT)
@@ -41,70 +41,11 @@ elseif(FFT STREQUAL "MKL")
     target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS)
   endif()
   target_link_libraries(lammps PRIVATE MKL::MKL)
-elseif(FFT STREQUAL "NVPL")
-  find_package(nvpl_fft REQUIRED)
-  target_compile_definitions(lammps PRIVATE -DFFT_NVPL)
-  target_link_libraries(lammps PRIVATE nvpl::fftw)
 else()
   # last option is KISSFFT
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)
 endif()
 
-option(FFT_USE_HEFFTE  "Use heFFTe as the distributed FFT engine, overrides the FFT option."  OFF)
-if(FFT_USE_HEFFTE)
-  # if FFT_HEFFTE is enabled, use the heFFTe parallel engine instead of the builtin fftMPI engine
-
-  # map standard FFT choices to available heFFTe backends: FFTW3 -> FFTW, KISS -> BUILTIN
-  set(FFT_HEFFTE_BACKEND_VALUES FFTW MKL BUILTIN)
-  string(REPLACE FFTW3 FFTW FFT_HEFFTE_BACKEND_DEFAULT ${FFT})
-  string(REPLACE KISS BUILTIN FFT_HEFFTE_BACKEND_DEFAULT ${FFT_HEFFTE_BACKEND_DEFAULT})
-  set(FFT_HEFFTE_BACKEND "${FFT_HEFFTE_BACKEND_DEFAULT}" CACHE STRING "Select heFFTe backend, e.g., FFTW or MKL")
-  set_property(CACHE FFT_HEFFTE_BACKEND PROPERTY STRINGS ${FFT_HEFFTE_BACKEND_VALUES})
-  validate_option(FFT_HEFFTE_BACKEND FFT_HEFFTE_BACKEND_VALUES)
-
-  if(FFT_HEFFTE_BACKEND STREQUAL "FFTW") # respect the backend choice, FFTW or MKL
-    set(HEFFTE_COMPONENTS "FFTW")
-    set(Heffte_ENABLE_FFTW "ON" CACHE BOOL "Enables FFTW backend for heFFTe")
-  elseif(FFT_HEFFTE_BACKEND STREQUAL "MKL")
-    set(HEFFTE_COMPONENTS "MKL")
-    set(Heffte_ENABLE_MKL "ON" CACHE BOOL "Enables MKL backend for heFFTe")
-  else()
-    set(HEFFTE_COMPONENTS "BUILTIN")
-    message(WARNING "FFT_HEFFTE_BACKEND not selected, defaulting to the builtin 'stock' backend, which is intended for testing and is not optimized for production runs")
-  endif()
-
-  find_package(Heffte 2.4.0 QUIET COMPONENTS ${HEFFTE_COMPONENTS})
-  if (NOT Heffte_FOUND) # download and build
-    if(BUILD_SHARED_LIBS)
-      set(BUILD_SHARED_LIBS_WAS_ON YES)
-      set(BUILD_SHARED_LIBS OFF)
-    endif()
-    if(CMAKE_REQUEST_PIC)
-      set(CMAKE_POSITION_INDEPENDENT_CODE ON)
-    endif()
-    set(Heffte_ENABLE_${FFT_HEFFTE_BACKEND} ON)
-    include(FetchContent)
-    FetchContent_Declare(HEFFTE_PROJECT # using v2.4.0
-      URL  "https://github.com/icl-utk-edu/heffte/archive/refs/tags/v2.4.0.tar.gz"
-      URL_HASH SHA256=02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d
-      )
-    FetchContent_Populate(HEFFTE_PROJECT)
-
-    # fixup git hash to show "(unknown)" to avoid compilation failures.
-    file(READ ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h HEFFTE_CFG_FILE_TEXT)
-    string(REPLACE "@Heffte_GIT_HASH@" "(unknown)" HEFFTE_CFG_FILE_TEXT "${HEFFTE_CFG_FILE_TEXT}")
-    file(WRITE ${heffte_project_SOURCE_DIR}/include/heffte_config.cmake.h "${HEFFTE_CFG_FILE_TEXT}")
-
-    add_subdirectory(${heffte_project_SOURCE_DIR} ${heffte_project_BINARY_DIR} EXCLUDE_FROM_ALL)
-    add_library(Heffte::Heffte ALIAS Heffte)
-    if(BUILD_SHARED_LIBS_WAS_ON)
-      set(BUILD_SHARED_LIBS ON)
-    endif()
-  endif()
-  target_compile_definitions(lammps PRIVATE -DFFT_HEFFTE "-DFFT_HEFFTE_${FFT_HEFFTE_BACKEND}")
-  target_link_libraries(lammps PRIVATE Heffte::Heffte)
-endif()
-
 set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
 set(FFT_PACK_VALUES array pointer memcpy)
 set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})

cmake/Modules/Packages/LEPTON.cmake

@@ -4,7 +4,7 @@ if(LEPTON_SOURCE_DIR)
 endif()
 set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
 
-file(GLOB LEPTON_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
+file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
 
 if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
    (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
@@ -15,7 +15,7 @@ else()
 endif()
 
 if(LEPTON_ENABLE_JIT)
-  file(GLOB ASMJIT_SOURCES CONFIGURE_DEPENDS ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
+  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
 endif()
 
 add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)
@@ -26,9 +26,29 @@ if(DOWNLOAD_MDI)
 
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
-  find_package(Python QUIET COMPONENTS Development)
-  if(Python_Development_FOUND)
-    set(MDI_USE_PYTHON_PLUGINS ON)
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(NOT PYTHON_VERSION_STRING)
+      set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+      # search for interpreter first, so we have a consistent library
+      find_package(PythonInterp) # Deprecated since version 3.12
+      if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      endif()
+    endif()
+    # search for the library matching the selected interpreter
+    set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
+    find_package(PythonLibs QUIET) # Deprecated since version 3.12
+    if(PYTHONLIBS_FOUND)
+      if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+        message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+      endif()
+      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()
   # python plugins are not supported and thus must be always off on Windows
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@@ -82,9 +102,13 @@ if(DOWNLOAD_MDI)
   # if compiling with python plugins we need
   # to add python libraries as dependency.
   if(MDI_USE_PYTHON_PLUGINS)
-    list(APPEND MDI_DEP_LIBS Python::Python)
-  endif()
+    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}")

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,7 +2,12 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  find_package(Python COMPONENTS NumPy QUIET)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy QUIET)
+  else()
+    # assume we have NumPy
+    set(Python_NumPy_FOUND ON)
+  endif()
   if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
@@ -10,26 +15,26 @@ endif()
 
 option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
-# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
-set(MLIAP_ENABLE_ACE_DEFAULT OFF)
-if(PKG_ML-PACE)
-  set(MLIAP_ENABLE_ACE_DEFAULT ON)
-endif()
-
-option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
-
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
-  find_package(Python COMPONENTS NumPy REQUIRED)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy REQUIRED)
+  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
-  if(Python_VERSION VERSION_LESS 3.6)
-    message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
+      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 ML-IAP requires Python 3.6 or later")
+    endif()
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
     get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
@@ -44,10 +49,3 @@ if(MLIAP_ENABLE_PYTHON)
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()
-
-if(MLIAP_ENABLE_ACE)
-  if(NOT PKG_ML-PACE)
-    message(FATAL_ERROR "Must enable ML-PACE package for including ACE support in ML-IAP")
-  endif()
-  target_compile_definitions(lammps PRIVATE -DMLIAP_ACE)
-endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,62 +1,37 @@
-# PACE library support for ML-PACE package
-find_package(pace QUIET)
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-if(pace_FOUND)
-    find_package(pace)
-    target_link_libraries(lammps PRIVATE pace::pace)
-else()
-    # set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
-    if(POLICY CMP0135)
-      cmake_policy(SET CMP0135 OLD)
-    endif()
+set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
-    set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
-    set(PACELIB_MD5 "a53bd87cfee8b07d9f44bc17aad69c3f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
-    mark_as_advanced(PACELIB_URL)
-    mark_as_advanced(PACELIB_MD5)
-    GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
-
-    # LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
-    # to make it easier to check local build without going through the public github releases
-    if(LOCAL_ML-PACE)
-     set(lib-pace "${LOCAL_ML-PACE}")
-    else()
-      # download library sources to build folder
-      if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-        file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-      endif()
-      if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-        message(STATUS "Downloading ${PACELIB_URL}")
-        file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-        file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-        if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-          message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-          file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-        endif()
-      else()
-        message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-      endif()
-
-
-      # 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 ${CMAKE_BINARY_DIR}
-      )
-      get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
-    endif()
-
-    # some preinstalled yaml-cpp versions don't provide a namespaced target
-    find_package(yaml-cpp QUIET)
-    if(TARGET yaml-cpp AND NOT TARGET yaml-cpp::yaml-cpp)
-      add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
-    endif()
-
-    add_subdirectory(${lib-pace} build-pace)
-    set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-
-    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
-      target_link_libraries(lammps PRIVATE pace)
-    endif()
+# download library sources to build folder
+if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+endif()
+if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+  message(STATUS "Downloading ${PACELIB_URL}")
+  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+  endif()
+else()
+  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+endif()
+
+# 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 ${CMAKE_BINARY_DIR}
+)
+get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+
+add_subdirectory(${lib-pace} build-pace)
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+
+if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+  target_link_libraries(lammps PRIVATE pace)
 endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,16 +18,14 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
     set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
-    # quip library uses GNU fortran extensions. If any more restrictive standards are set, reset them
-    string(REGEX REPLACE -std=f[0-9]+ -std=gnu _fopt "${CMAKE_Fortran_FLAGS_${BTYPE}}")
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${_fopt} -fmax-stack-var-size=6553600\n")
+    set(temp "${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 -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")
@@ -58,7 +56,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

cmake/Modules/Packages/MSCG.cmake

@@ -0,0 +1,28 @@
+find_package(GSL REQUIRED)
+find_package(MSCG QUIET)
+if(MSGC_FOUND)
+  set(DOWNLOAD_MSCG_DEFAULT OFF)
+else()
+  set(DOWNLOAD_MSCG_DEFAULT ON)
+endif()
+option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
+if(DOWNLOAD_MSCG)
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/491270a73539e3f6951e76f7dbe84e258b3ebb45.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "7ea50748fba5c3a372e0266bd31d2f11" CACHE STRING "MD5 checksum of MSCG tarball")
+  mark_as_advanced(MSCG_URL)
+  mark_as_advanced(MSCG_MD5)
+
+  include(ExternalCMakeProject)
+  ExternalCMakeProject(mscg ${MSCG_URL} ${MSCG_MD5} MSCG-release src/CMake "")
+
+  # set include and link library
+  target_include_directories(lammps PRIVATE "${CMAKE_BINARY_DIR}/_deps/mscg-src/src")
+  target_link_libraries(lammps PRIVATE mscg)
+else()
+  find_package(MSCG)
+  if(NOT MSCG_FOUND)
+    message(FATAL_ERROR "MSCG not found, help CMake to find it by setting MSCG_LIBRARY and MSCG_INCLUDE_DIR, or set DOWNLOAD_MSCG=ON to download it")
+  endif()
+  target_link_libraries(lammps PRIVATE MSCG::MSCG)
+endif()
+target_link_libraries(lammps PRIVATE GSL::gsl ${LAPACK_LIBRARIES})

cmake/Modules/Packages/PLUMED.cmake

@@ -1,14 +1,5 @@
 # Plumed2 support for PLUMED package
 
-# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
-if(POLICY CMP0135)
-  cmake_policy(SET CMP0135 OLD)
-endif()
-
-# for supporting multiple concurrent plumed2 installations for debugging and testing
-set(PLUMED_SUFFIX "" CACHE STRING "Suffix for Plumed2 library")
-mark_as_advanced(PLUMED_SUFFIX)
-
 if(BUILD_MPI)
   set(PLUMED_CONFIG_MPI "--enable-mpi")
   set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
@@ -30,11 +21,9 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-# Note: must also adjust check for supported API versions in
-# fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
@@ -86,9 +75,6 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
     DEPENDS plumed_build
     COMMENT "Copying Plumed files"
   )
-  if(CMAKE_PROJECT_NAME STREQUAL "lammps")
-    target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
-  endif()
 
 else()
 
@@ -163,26 +149,21 @@ else()
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
-      target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
-    endif()
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
+    pkg_check_modules(PLUMED REQUIRED plumed)
     add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
     if(PLUMED_MODE STREQUAL "STATIC")
-      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.shared)
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
     elseif(PLUMED_MODE STREQUAL "RUNTIME")
-      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${PLUMED_SUFFIX}Kernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.runtime)
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
-    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
-      target_link_libraries(lammps PUBLIC LAMMPS::PLUMED)
-    endif()
   endif()
 endif()
 
+target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)

cmake/Modules/Packages/PYTHON.cmake

@@ -1,11 +1,29 @@
-
-if(NOT Python_INTERPRETER)
-  # backward compatibility with CMake before 3.12 and older LAMMPS documentation
-  if(PYTHON_EXECUTABLE)
-    set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+if(CMAKE_VERSION VERSION_LESS 3.12)
+  if(NOT PYTHON_VERSION_STRING)
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    # search for interpreter first, so we have a consistent library
+    find_package(PythonInterp) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
   endif()
-  find_package(Python COMPONENTS Interpreter)
+  # search for the library matching the selected interpreter
+  set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
+  find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
+  if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+    message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+  endif()
+  target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
+  target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
+else()
+  if(NOT Python_INTERPRETER)
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
+  find_package(Python REQUIRED COMPONENTS Interpreter Development)
+  target_link_libraries(lammps PRIVATE Python::Python)
 endif()
-find_package(Python REQUIRED COMPONENTS Interpreter Development)
-target_link_libraries(lammps PRIVATE Python::Python)
 target_compile_definitions(lammps PRIVATE -DLMP_PYTHON)

cmake/Modules/Packages/VORONOI.cmake

@@ -54,5 +54,5 @@ else()
   if(NOT VORO_FOUND)
     message(FATAL_ERROR "Voro++ library not found. Help CMake to find it by setting VORO_LIBRARY and VORO_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
   endif()
-  target_link_libraries(lammps PRIVATE VORO::voro++)
+  target_link_libraries(lammps PRIVATE VORO::VORO)
 endif()

cmake/Modules/Packages/VTK.cmake

@@ -1,5 +1,3 @@
-# FindVTK requires that C support is enabled when looking for MPI support
-enable_language(C)
 find_package(VTK REQUIRED NO_MODULE)
 target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
 if (VTK_MAJOR_VERSION VERSION_LESS 9.0)

cmake/Modules/StyleHeaderUtils.cmake

@@ -1,5 +1,5 @@
 function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(hlist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})
@@ -187,7 +187,7 @@ endfunction(DetectBuildSystemConflict)
 
 
 function(FindPackagesHeaders path style_class file_pattern headers)
-    file(GLOB files CONFIGURE_DEPENDS "${path}/${file_pattern}*.h")
+    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
     get_property(plist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})

cmake/Modules/Testing.cmake

@@ -6,7 +6,7 @@ if(ENABLE_TESTING)
   find_program(VALGRIND_BINARY NAMES valgrind)
   # generate custom suppression file
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
-  file(GLOB VALGRIND_SUPPRESSION_FILES CONFIGURE_DEPENDS ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
   foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")
@@ -19,7 +19,7 @@ if(ENABLE_TESTING)
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
   # also only verified with Fedora Linux > 30 and Ubuntu 18.04 or 22.04+(Ubuntu 20.04 fails)
-  if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
+  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_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04)))
@@ -66,8 +66,16 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
   mark_as_advanced(ENABLE_COVERAGE)
   if(ENABLE_COVERAGE)
-    target_compile_options(lammps PUBLIC --coverage)
-    target_link_options(lammps PUBLIC --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()
 
@@ -102,16 +110,24 @@ endif()
 #######################################
 # select code sanitizer options
 #######################################
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
+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 hwaddress leak thread undefined)
+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 (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-    target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${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")

cmake/Modules/Tools.cmake

@@ -26,7 +26,7 @@ if(BUILD_TOOLS)
 
   enable_language(C)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
-  file(GLOB MSI2LMP_SOURCES CONFIGURE_DEPENDS ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
   if(STANDARD_MATH_LIB)
     target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
@@ -37,6 +37,40 @@ if(BUILD_TOOLS)
   add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
+find_package(PkgConfig QUIET)
+if(BUILD_LAMMPS_SHELL)
+  if(NOT PkgConfig_FOUND)
+    message(FATAL_ERROR "Must have pkg-config installed for building LAMMPS shell")
+  endif()
+  find_package(PkgConfig REQUIRED)
+  pkg_check_modules(READLINE IMPORTED_TARGET REQUIRED readline)
+  if(NOT LAMMPS_EXCEPTIONS)
+    message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
+  endif()
+
+  # include resource compiler to embed icons into the executable on Windows
+  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    enable_language(RC)
+    set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
+  endif()
+
+  add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
+  target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
+  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
+
+  # workaround for broken readline pkg-config file on FreeBSD
+  if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
+    target_include_directories(lammps-shell PRIVATE /usr/local/include)
+  endif()
+  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
+    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
+    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
+  endif()
+  install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
+  install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
+endif()
+
 if(BUILD_LAMMPS_GUI)
   get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
   get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)

cmake/packaging/MacOSXBundleInfo.plist.in

@@ -17,7 +17,7 @@
 	<key>CFBundleLongVersionString</key>
 	<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
 	<key>CFBundleName</key>
-	<string>LAMMPS_GUI</string>
+	<string>LAMMPS</string>
 	<key>CFBundlePackageType</key>
 	<string>APPL</string>
 	<key>CFBundleShortVersionString</key>

cmake/packaging/README.macos

@@ -9,7 +9,7 @@ of the available packages.
 The following individual commands are included:
 binary2txt lammps-gui lmp msi2lmp phana stl_bin2txt
 
-After copying the LAMMPS_GUI folder into your Applications folder, please follow
+After copying the lammps-gui folder into your Applications folder, please follow
 these steps:
 
 1. Open the Terminal app
@@ -23,7 +23,7 @@ these steps:
 
 3. Add the following lines to the end of the file, save it, and close the editor
 
-   LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.app/Contents
+   LAMMPS_INSTALL_DIR=/Applications/LAMMPS.app/Contents
    LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
    LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
    MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
@@ -38,9 +38,9 @@ these steps:
    the changes from .zprofile automatically.
 
    Note: the above assumes you use the default shell (zsh) that comes with
-   MacOS. If you customized MacOS to use a different shell, you'll need to
-   modify that shell's init file (.cshrc, .bashrc, etc.) instead with
-   appropiate commands to modify the same environment variables.
+   MacOS. If you customized MacOS to use a different shell, you'll need to modify
+   that shell's init file (.cshrc, .bashrc, etc.) instead with appropiate commands
+   to modify the same environment variables.
 
 5. Try running LAMMPS (which might fail, see step 7)
 
@@ -50,10 +50,10 @@ these steps:
 
    lammps-gui ${LAMMPS_BENCH_DIR}/in.rhodo
 
-   Depending on the size and resolution of your screen, the fonts may be too
-   small to read. This can be adjusted by setting the environment variable
-   QT_FONT_DPI. The default value would be 72, so to increase the fonts by a
-   third, one can add to the .zprofile file the line
+   Depending on the size and resolution of your screen, the fonts may
+   be too small to read. This can be adjusted by setting the environment
+   variable QT_FONT_DPI. The default value would be 72, so to increase
+   the fonts by a third one can add to the .zprofile file the line
 
    export QT_FONT_DPI=96
 
@@ -61,9 +61,9 @@ these steps:
 
 7. Give permission to execute the commands (lmp, lammps-gui, msi2lmp, binary2txt, phana, stl_bin2txt)
 
-   MacOS will likely block the initial run of the executables, since they were
-   downloaded from the internet and are missing a known signature from an
-   identified developer. Go to "Settings" and search for "Security settings".
-   It should display a message that an executable like "lmp" was blocked. Press
+   MacOS will likely block the initial run of the executables, since they
+   were downloaded from the internet and are missing a known signature from an
+   identified developer. Go to "Settings" and search for "Security settings". It
+   should display a message that an executable like "lmp" was blocked. Press
    "Open anyway", which might prompt you for your admin credentials. Afterwards
    "lmp" and the other executables should work as expected.

cmake/packaging/build_linux_tgz.sh

@@ -2,10 +2,9 @@
 
 APP_NAME=lammps-gui
 DESTDIR=${PWD}/../LAMMPS_GUI
-VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
+rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
@@ -60,19 +59,17 @@ done
 
 echo "Set up wrapper script"
 MYDIR=$(dirname "$0")
-cp ${MYDIR}/xdg-open ${DESTDIR}/bin
 cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
 for s in ${DESTDIR}/bin/*
 do \
         EXE=$(basename $s)
         test ${EXE} = linux_wrapper.sh && continue
         test ${EXE} = qt.conf && continue
-        test ${EXE} = xdg-open && continue
         ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
 done
 
 pushd ..
-tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
+tar -czvvf LAMMPS-Linux-amd64.tar.gz LAMMPS_GUI
 popd
 
 echo "Cleanup dir"

cmake/packaging/build_macos_dmg.sh

@@ -1,10 +1,9 @@
 #!/bin/bash
 
 APP_NAME=lammps-gui
-VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
+rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS-macOS-multiarch.dmg
 
 echo "Create initial dmg file with macdeployqt"
 macdeployqt  lammps-gui.app -dmg
@@ -23,8 +22,8 @@ ln -s /Applications .
 mv  ${APP_NAME}.app/Contents/Resources/README.txt .
 mkdir  .background
 mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
-mv ${APP_NAME}.app LAMMPS_GUI.app
-cd LAMMPS_GUI.app/Contents
+mv ${APP_NAME}.app LAMMPS.app
+cd LAMMPS.app/Contents
 
 echo "Attach icons to LAMMPS console and GUI executables"
 echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
@@ -76,7 +75,7 @@ echo '
           set statusbar visible to false
           set toolbar visible to false
           set the bounds to { 100, 40, 868, 640 }
-          set position of item "'LAMMPS_GUI'.app" to { 190, 216 }
+          set position of item "'LAMMPS'.app" to { 190, 216 }
           set position of item "Applications" to { 576, 216 }
           set position of item "README.txt" to { 190, 400 }
         end tell
@@ -97,12 +96,12 @@ sync
 
 echo "Unmount modified disk image and convert to compressed read-only image"
 hdiutil detach "${DEVICE}"
-hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
+hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS-macOS-multiarch.dmg"
 
 echo "Attach icon to .dmg file"
 echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
-Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
-SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
+Rez -a icon.rsrc -o LAMMPS-macOS-multiarch.dmg
+SetFile -a C LAMMPS-macOS-multiarch.dmg
 rm icon.rsrc
 
 echo "Delete temporary disk images"

cmake/packaging/build_windows_cross_zip.sh

@@ -1,65 +1,26 @@
-#!/bin/bash
+#!/bin/bash -vx
 
 APP_NAME=lammps-gui
-DESTDIR=${PWD}/LAMMPS_GUI
-SYSROOT="$1"
-VERSION="$2"
+DESTDIR=${PWD}/../LAMMPS_GUI
 
 echo "Delete old files, if they exist"
-rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
+rm -rvf ${DESTDIR} LAMMPS-Win10-amd64.zip
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
 
-# no static libs needed
-rm -rvf ${DESTDIR}/lib
-# but the LAMMPS lib
-
-echo "Copying required DLL files"
-for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+echo "Add required dependencies for Qt"
+for dll in Qt5Core.dll Qt5Gui.dll Qt5Widgets.dll
 do \
-    doskip=0
-    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
-    do \
-        test ${dll} = ${skip}.dll && doskip=1
-    done
-    test ${doskip} -eq 1 && continue
-    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
+    cp /usr/x86_64-w64-mingw32/sys-root/mingw/bin/${dll} ${DESTDIR}/bin/
+done
+for dir in styles platforms imageformats
+do \
+    mkdir -p ${DESTDIR}/${dir}
+    cp -r /usr/x86_64-w64-mingw32/sys-root/mingw/lib/qt5/plugins/${dir}/*.dll ${DESTDIR}/${dir}
 done
 
-echo "Copy required Qt plugins"
-mkdir -p ${DESTDIR}/qt5plugins
-for plugin in imageformats platforms styles
-do \
-    cp -r ${SYSROOT}/lib/qt5/plugins/${plugin} ${DESTDIR}/qt5plugins/
-done
-
-echo "Check dependencies of DLL files"
-for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
-do \
-    doskip=0
-    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
-    do \
-        test ${dll} = ${skip}.dll && doskip=1
-    done
-    test ${doskip} -eq 1 && continue
-    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
-done
-
-for dll in $(objdump -p ${DESTDIR}/bin/*.dll ${DESTDIR}/qt5plugins/*/*.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
-do \
-    doskip=0
-    for skip in ADVAPI32 CFGMGR32 GDI32 KERNEL32 MPR NETAPI32 PSAPI SHELL32 USER32 USERENV UxTheme VERSION WS2_32 WSOCK32 d3d11 dwmapi liblammps msvcrt_ole32
-    do \
-        test ${dll} = ${skip}.dll && doskip=1
-    done
-    test ${doskip} -eq 1 && continue
-    test -f ${DESTDIR}/bin/${dll} || cp -v ${SYSROOT}/bin/${dll} ${DESTDIR}/bin
-done
-
-cat > ${DESTDIR}/bin/qt.conf <<EOF
-[Paths]
-Plugins = ../qt5plugins
-EOF
-zip -9rvD LAMMPS-Win10-amd64-${VERSION}.zip LAMMPS_GUI
-
+pushd ..
+zip -9rv LAMMPS-Win10-amd64.zip LAMMPS_GUI
+popd
+exit 0

cmake/packaging/build_windows_vs.cmake

@@ -1,7 +1,7 @@
 # CMake script to be run post installation to build zipped package
 
 # clean up old zipfile and deployment tree
-file(REMOVE LAMMPS_GUI-Win10-amd64.zip)
+file(REMOVE LAMMPS-Win10-amd64.zip)
 file(REMOVE_RECURSE LAMMPS_GUI)
 file(RENAME ${INSTNAME} LAMMPS_GUI)
 
@@ -21,15 +21,8 @@ file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r
 execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
 file(REMOVE qtdeploy.bat)
 
-# download and uncompress static FFMpeg and gzip binaries
-file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip)
-file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI")
-execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1)
-file(REMOVE unpackzip.ps1)
-file(REMOVE ffmpeg-gzip.zip)
-
 # create zip archive
-file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip")
+file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS-Win10-amd64.zip")
 execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
 file(REMOVE makearchive.ps1)
 file(REMOVE_RECURSE LAMMPS_GUI)

cmake/packaging/linux_wrapper.sh

@@ -1,20 +1,15 @@
 #!/bin/sh
 # wrapper for bundled executables
 
-# reset locale to avoid problems with decimal numbers
-export LC_ALL=C
-
-BASEDIR="$(dirname "$0")"
-EXENAME="$(basename "$0")"
-
-PATH="${BASEDIR}/bin:${PATH}"
+BASEDIR=$(dirname "$0")
+EXENAME=$(basename "$0")
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
-LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
+LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:${BASEDIR}/lib
 
 # set some environment variables for LAMMPS etc.
-LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
-MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
+LAMMPS_POTENTIALS=${BASEDIR}/share/lammps/potentials
+MSI2LMP_LIBRARY=${BASEDIR}/share/lammps/frc_files
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/presets/all_off.cmake

@@ -26,9 +26,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  EFF
   ELECTRODE
-  EXTRA-COMMAND
+  EFF
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -61,10 +60,11 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
+  MPIIO
+  MSCG
   NETCDF
   OPENMP
   OPT
@@ -82,7 +82,6 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -28,9 +28,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  EFF
   ELECTRODE
-  EXTRA-COMMAND
+  EFF
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -63,10 +62,11 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
+  MPIIO
+  MSCG
   NETCDF
   OPENMP
   OPT
@@ -84,7 +84,6 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/clang.cmake

@@ -1,10 +1,10 @@
 # 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-new flang gfortran f95)
+find_program(CLANG_FORTRAN NAMES flang gfortran f95)
 set(ENV{OMPI_FC} ${CLANG_FORTRAN})
 get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
-if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
+if (_tmp_fc STREQUAL "flang")
   set(FC_STD_VERSION "-std=f2018")
   set(BUILD_MPI OFF)
 else()

cmake/presets/download.cmake

@@ -9,6 +9,7 @@ endforeach()
 
 set(DOWNLOAD_KIM 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)

cmake/presets/gpu-cuda.cmake

@@ -1,11 +0,0 @@
-# preset that enables GPU and selects CUDA API
-
-set(PKG_GPU ON CACHE BOOL "Build GPU package" FORCE)
-set(GPU_API "cuda" CACHE STRING "APU used by GPU package" FORCE)
-set(GPU_PREC "mixed" CACHE STRING "" FORCE)
-
-set(CUDA_NVCC_FLAGS "-allow-unsupported-compiler" CACHE STRING "" FORCE)
-set(CUDA_NVCC_FLAGS_DEBUG "-allow-unsupported-compiler" CACHE STRING "" FORCE)
-set(CUDA_NVCC_FLAGS_MINSIZEREL "-allow-unsupported-compiler" CACHE STRING "" FORCE)
-set(CUDA_NVCC_FLAGS_RELWITHDEBINFO "-allow-unsupported-compiler" CACHE STRING "" FORCE)
-set(CUDA_NVCC_FLAGS_RELEASE "-allow-unsupported-compiler" CACHE STRING "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -6,11 +6,6 @@ set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
-get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
-set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)
-
-# If KSPACE is also enabled, use CUFFT for FFTs
-set(FFT_KOKKOS "CUFFT" CACHE STRING "" FORCE)
 
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -12,9 +12,6 @@ set(BUILD_OMP ON CACHE BOOL "" FORCE)
 set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
 set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
 
-# If KSPACE is also enabled, use CUFFT for FFTs
-set(FFT_KOKKOS "HIPFFT" CACHE STRING "" FORCE)
-
 # hide deprecation warnings temporarily for stable release
 set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 

cmake/presets/kokkos-sycl-intel.cmake

@@ -1,29 +0,0 @@
-# preset that enables KOKKOS and selects SYCL compilation with OpenMP
-# enabled as well. Also sets some performance related compiler flags.
-set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_SYCL   ON CACHE BOOL "" FORCE)
-
-set(FFT "MKL" CACHE STRING "" FORCE)
-set(FFT_KOKKOS "MKL_GPU" CACHE STRING "" FORCE)
-
-unset(USE_INTERNAL_LINALG)
-unset(USE_INTERNAL_LINALG CACHE)
-set(BLAS_VENDOR "Intel10_64_dyn")
-
-# hide deprecation warnings temporarily for stable release
-set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
-
-set(CMAKE_CXX_COMPILER icpx CACHE STRING "" FORCE)
-set(CMAKE_C_COMPILER icx CACHE STRING "" FORCE)
-set(CMAKE_Fortran_COMPILER "" CACHE STRING "" FORCE)
-set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-# Silence everything
-set(CMAKE_CXX_FLAGS "-w" CACHE STRING "" FORCE)
-#set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
-#set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen" CACHE STRING "" FORCE)
-set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code " CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-O3 -fsycl -fsycl-device-code-split=per_kernel " CACHE STRING "" FORCE)

cmake/presets/macos-multiarch.cmake

@@ -10,3 +10,5 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
 set(BUILD_MPI FALSE CACHE BOOL "" FORCE)
+set(BUILD_SHARED_LIBS FALSE CACHE BOOL "" FORCE)
+set(LAMMPS_EXCEPTIONS TRUE CACHE BOOL "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -22,9 +22,8 @@ set(WIN_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  EFF
   ELECTRODE
-  EXTRA-COMMAND
+  EFF
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -33,6 +32,7 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
+  INTEL
   INTERLAYER
   KSPACE
   LEPTON
@@ -50,7 +50,6 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
-  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -67,7 +66,6 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SHOCK
   SMTBQ
@@ -85,6 +83,7 @@ endforeach()
 
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
+  set(PKG_MPIIO ON CACHE BOOL "" FORCE)
   set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 

cmake/presets/most.cmake

@@ -24,9 +24,8 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  EFF
   ELECTRODE
-  EXTRA-COMMAND
+  EFF
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -46,7 +45,6 @@ set(ALL_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
-  ML-UF3
   MOFFF
   MOLECULE
   OPENMP
@@ -60,7 +58,6 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SHOCK
   SPH

cmake/presets/nolib.cmake

@@ -19,6 +19,8 @@ set(PACKAGES_WITH_LIB
   ML-PACE
   ML-QUIP
   MOLFILE
+  MPIIO
+  MSCG
   NETCDF
   PLUMED
   PYTHON

cmake/presets/oneapi.cmake

@@ -3,9 +3,26 @@
 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)
 
-# force using internal BLAS/LAPCK since external ones may not be ABI compatible
-set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(OpenMP_C "icx" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

cmake/presets/windows.cmake

@@ -22,7 +22,6 @@ set(WIN_PACKAGES
   DRUDE
   EFF
   ELECTRODE
-  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -33,7 +32,6 @@ set(WIN_PACKAGES
   INTERLAYER
   KSPACE
   LEPTON
-  MACHDYN
   MANIFOLD
   MANYBODY
   MC
@@ -43,24 +41,21 @@ set(WIN_PACKAGES
   ML-IAP
   ML-POD
   ML-SNAP
-  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
   OPENMP
-  OPT
   ORIENT
   PERI
   PHONON
-  PLUGIN
   POEMS
+  PLUGIN
   PTM
   QEQ
   QTB
   REACTION
   REAXFF
   REPLICA
-  RHEO
   RIGID
   SHOCK
   SMTBQ

doc/.gitignore

@@ -17,10 +17,3 @@
 *.el
 /utils/sphinx-config/_static/mathjax
 /utils/sphinx-config/_static/polyfill.js
-/src/pairs.rst
-/src/bonds.rst
-/src/angles.rst
-/src/dihedrals.rst
-/src/impropers.rst
-/src/computes.rst
-/src/fixes.rst

doc/Makefile

@@ -63,7 +63,6 @@ help:
 	@echo "  anchor_check  scan for duplicate anchor labels"
 	@echo "  style_check   check for complete and consistent style lists"
 	@echo "  package_check check for complete and consistent package lists"
-	@echo "  role_check    check for misformatted role keywords"
 	@echo "  spelling      spell-check the manual"
 
 # ------------------------------------------
@@ -83,10 +82,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-globbed-tocs:
-	$(PYTHON) $(BUILDDIR)/utils/make-globbed-tocs.py -d $(RSTDIR)
-
-html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -102,8 +98,6 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -116,7 +110,7 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
@@ -135,7 +129,7 @@ fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(M
 	@rm -rf fasthtml/PDF/.[sg]*
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
-spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; \
@@ -146,7 +140,7 @@ spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/fa
 	)
 	@echo "Spell check finished."
 
-epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
@@ -169,7 +163,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
@@ -185,8 +179,6 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -235,8 +227,6 @@ char_check :
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
-	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
-	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/documentation_conventions.md

@@ -10,7 +10,7 @@ Last change: 2022-12-30
 
 In fall 2019, the LAMMPS documentation file format has changed from a
 home grown markup designed to generate HTML format files only, to
-[reStructuredText](https://docutils.sourceforge.io/rst.html>).  For a
+[reStructuredText](https://docutils.sourceforge.io/rst.html>.  For a
 transition period all files in the old .txt format were transparently
 converted to .rst and then processed.  The `txt2rst tool` is still
 included in the distribution to obtain an initial .rst file for legacy
@@ -45,7 +45,8 @@ what kind of information and sections are needed.
 
 ## Formatting conventions
 
-For headlines we try to follow the conventions posted [here](https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings).
+For headlines we try to follow the conventions posted here:
+https://documentation-style-guide-sphinx.readthedocs.io/en/latest/style-guide.html#headings
 It seems to be sufficient to have this consistent only within
 any single file and it is not (yet) enforced strictly, but making
 this globally consistent makes it easier to move sections around.
@@ -63,7 +64,7 @@ Groups of shell commands or LAMMPS input script or C/C++/Python source
 code should be typeset into a `.. code-block::` section. A syntax
 highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
 can be used to indicate the language in the code block in addition to
-`bash`, `c`, `c++`, `console`, `csh`, `diff`, `fortran`, `json`, `make`,
+`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
 `perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`.  When
 no syntax style is indicated, no syntax highlighting is performed.  When
 typesetting commands executed on the shell, please do not prefix
@@ -83,7 +84,7 @@ block can be used, followed by multiple `.. tab::` blocks, one
 for each alternative. This is only used for HTML output. For other
 outputs, the `.. tabs::` directive is transparently removed and
 the individual `.. tab::` blocks will be replaced with an
-`.. admonition::` block. Thus in PDF and ePUB output those will
+`.. admonition::`` block. Thus in PDF and ePUB output those will
 be realized as sequential and plain notes.
 
 Special remarks can be highlighted with a `.. note::` block and

doc/doxygen/Doxyfile.in

@@ -2,7 +2,7 @@
 
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "LAMMPS Programmer's Guide"
-PROJECT_NUMBER         = "19 November 2024"
+PROJECT_NUMBER         = "4 May 2022"
 PROJECT_BRIEF          = "Documentation of the LAMMPS library interface and Python wrapper"
 PROJECT_LOGO           = lammps-logo.png
 CREATE_SUBDIRS         = NO

doc/github-development-workflow.md

@@ -6,9 +6,7 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change, and we try to
-adapt it accordingly.
-
-Last change: 2023-02-10
+adapt it accordingly. Last change 2023-02-10.
 
 ## Table of Contents
 
@@ -38,10 +36,10 @@ requests.
 MUST be submitted as a pull request to GitHub.  All changes to the
 "develop" branch must be made exclusively through merging pull requests.
 The "release" and "stable" branches, respectively, are only to be
-updated upon "feature releases" or "stable releases" based on the
-associated tags.  Updates to the stable release in between stable releases
+updated upon feature or stable releases based on the associated
+tags.  Updates to the stable release in between stable releases
 (for example, back-ported bug fixes) are first merged into the "maintenance"
-branch and then into the "stable" branch as "stable update releases".
+branch and then into the "stable" branch as update releases.
 
 Pull requests may also be submitted to (long-running) feature branches
 created by LAMMPS developers inside the LAMMPS project, if needed. Those
@@ -74,7 +72,7 @@ be assigned to signal urgency to merge this pull request quickly.
 People can be assigned to review a pull request in two ways:
 
   * They can be assigned manually to review a pull request
-    by the submitter or a LAMMPS developer.
+    by the submitter or a LAMMPS developer
   * They can be automatically assigned, because a developer's GitHub
     handle matches a file pattern in the `.github/CODEOWNERS` file,
     which associates developers with the code they contributed and
@@ -88,9 +86,9 @@ required before merging, in addition to passing all automated
 compilation and unit tests.  Merging counts as implicit approval, so
 does submission of a pull request (by a LAMMPS developer). So the person
 doing the merge may not also submit an approving review.  The GitHub
-feature that reviews from code owners are "hard" reviews (i.e. they
-must all approve before merging is allowed) is currently disabled.
-It is at the discretion of the merge maintainer to assess when a
+feature, that reviews from code owners are "hard" reviews (i.e. they
+must all approve before merging is allowed), is currently disabled.
+It is in the discretion of the merge maintainer to assess when a
 sufficient degree of approval has been reached, especially from external
 collaborators.  Reviews may be (automatically) dismissed, when the
 reviewed code has been changed. Review may be requested a second time.
@@ -133,7 +131,7 @@ testing -- that the code in the branch "develop" does not get easily
 broken.  These tests are run after every update to a pull request.  More
 extensive and time-consuming tests (including regression testing) are
 performed after code is merged to the "develop" branch.  There are feature
-releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-6 weeks at a point, when the LAMMPS
 developers feel, that a sufficient number of changes have been included
 and all post-merge testing has been successful.  These feature releases are
 marked with a `patch_<version date>` tag and the "release" branch
@@ -149,8 +147,7 @@ only contain bug fixes, feature additions to peripheral functionality,
 and documentation updates.  In between stable releases, bug fixes and
 infrastructure updates are back-ported from the "develop" branch to the
 "maintenance" branch and occasionally merged into "stable" and published
-as update releases. Further explanation of LAMMPS versions can be found
-[in the documentation](https://docs.lammps.org/Manual_version.html).
+as update releases.
 
 ## Project Management
 

doc/graphviz/Makefile

@@ -16,11 +16,8 @@ clean:
 	rm -f $(IMGSVG) $(IMGPDF) $(IMGPNG) *~
 
 ifeq ($(HAS_DOT),YES)
-$(IMGDIR)/lammps-classes.png : lammps-classes.dot
-	dot -Tpng -Kneato -o $@ $<
-
 $(IMGDIR)/%.png: %.dot
-	dot -Tpng -Kdot -o $@ $<
+	dot -Tpng -Kneato -o $@ $<
 endif
 
 ifeq ($(HAS_DOT),NO)

doc/graphviz/lammps-releases.dot

@@ -1,34 +0,0 @@
-// LAMMPS branches and releases
-digraph releases {
-    rankdir="LR";
-    github [shape="box" label="Pull Requests\non GitHub" height=0.75];
-    github -> develop [label="Merge commits"];
-    {
-        rank = "same";
-        work [shape="none" label="Development branches:"]
-        develop [label="'develop' branch" height=0.75];
-        maintenance [label="'maintenance' branch" height=0.75];
-    };
-    {
-        rank = "same";
-        upload [shape="none" label="Release branches:"]
-        release [label="'release' branch" height=0.75];
-        stable [label="'stable' branch" height=0.75];
-    };
-    develop -> release [label="Feature release\n(every 4-8 weeks)"];
-    release -> stable [label="Stable release\n(once per year)"];
-    stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
-    develop -> maintenance [label="Backports of bugfixes" style="dashed"];
-    maintenance -> stable [label="Updates to stable release"];
-    {
-        rank = "same";
-        tag [shape="none" label="Applied tags:"];
-        patchtag [shape="box" label="patch_<date>"];
-        stabletag [shape="box" label="stable_<date>"];
-        updatetag [shape="box" label="stable_<date>_update<num>"];
-    };
-    release -> patchtag [label="feature release" style="dotted"];
-    stable -> stabletag [label="stable release" style="dotted"];
-    stable -> updatetag [label="update release" style="dotted"];
-}
-

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "19 November 2024" "2024-11-19"
+.TH LAMMPS "1" "2 August 2023" "2023-08-2"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 19 November 2024
+\- Molecular Dynamics Simulator.  Version 2 August 2023
 
 .SH SYNOPSIS
 .B lmp
@@ -226,20 +226,6 @@ arguments of the "dump" command. See the
 .B LAMMPS
 manual for details on either of the two commands.
 .TP
-\fB\-r2info <restart file> <keyword> ...\fR or
-\fB\-restart2info <restart file> <keyword> ...\fR
-Write information about the <restart file> previously written by
-.B LAMMPS
-to the screen and immediately exit.  Following <restart file>
-argument, additional keywords for the
-.B LAMMPS
-"info" command may be added to increase the amount of information
-written. By default "system" "group" "fix" "compute" are already
-set. See the
-.B LAMMPS
-manual for details on the "info" command.
-.TP
-.TP
 \fB\-sc <file name>\fR or \fB\-screen <file name>\fR
 Specify a file for
 .B LAMMPS
@@ -311,7 +297,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2024 Sandia Corporation
+© 2003--2022 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/msi2lmp.1

@@ -1,4 +1,4 @@
-.TH MSI2LMP "1" "v3.9.11" "2024-09-06"
+.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
@@ -101,7 +101,7 @@ msi2lmp decane -c 0 -f oplsaa
 
 
 .SH COPYRIGHT
-© 2003--2024 Sandia Corporation
+© 2003--2022 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/src/Bibliography.rst

@@ -1,12 +1,6 @@
 Bibliography
 ************
 
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-
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-
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@@ -28,24 +22,21 @@ Bibliography
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-**(Albe1)**
+**(Albe)**
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+**(Allen)**
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+**(Babadi)**
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+**(Banna)**
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+**(Bartok_2010)**
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 **(Bartok_PhD)**
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+**(Berendsen)**
+   Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
+
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 **(Beutler)**
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+**(Bialke)**
+   J.\  Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
+
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 **(Bitzek)**
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@@ -161,7 +134,7 @@ Bibliography
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 **(BoreschKarplus)**
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+   Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
 
 **(Botu1)**
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-
 **(Bussi)**
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+   G.\  Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
 
 **(Bussi1)**
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@@ -208,20 +178,20 @@ Bibliography
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-**(COMB_1)**
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-
-**(COMB_2)**
+**(COMB)**
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 **(COMB3)**
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+**(COMB_1)**
+   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+
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 **(Campana)**
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 **(Ceriotti)**
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-
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-
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-
 **(Cusentino)**
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+   Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
 
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-**(Ellis)**
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-
-**(Emmrich)**
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@@ -415,18 +328,9 @@ Bibliography
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@@ -463,36 +367,18 @@ Bibliography
 **(Frenkel)**
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-**(Fu)**
-   Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
+**(GLE4MD)**
+   `https://gle4md.org/ <https://gle4md.org/>`_
 
 **(Gao)**
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    P.\  Steinhardt, D. Nelson, and M. Ronchetti, Phys. Rev. B 28, 784 (1983).
 
-**(Steward)**
-   Stewart, Spearot, Modelling Simul. Mater. Sci. Eng. 21, 045003, (2013).
-
-**(Stewart2018)**
-   J.A. Stewart, et al. (2018) Journal of Applied Physics, 123(16), 165902.
-
 **(Stiles)**
    Stiles , Hubbard, and Kayser, J Chem Phys, 77, 6189 (1982).
 
@@ -1443,21 +1147,12 @@ Bibliography
 **(Tainter 2015)**
    Tainter, Shi, and Skinner, 11, 2268 (2015)
 
-**(Tang and Toennies)**
-   J Chem Phys, 80, 3726 (1984).
-
-**(Tee)**
-   Tee and Searles, J. Chem. Phys. 156, 184101 (2022).
-
 **(Templeton2010)**
    Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
 
 **(Templeton2011)**
    Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
 
-**(tenWolde)**
-   P.\  R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
-
 **(Tersoff_1)**
    J.\  Tersoff, Phys Rev B, 37, 6991 (1988).
 
@@ -1500,9 +1195,6 @@ Bibliography
 **(Tranchida)**
    Tranchida, Plimpton, Thibaudeau and Thompson, Journal of Computational Physics, 372, 406-425, (2018).
 
-**(Tribello)**
-   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
-
 **(Tsuji et al, 1992)**
    Tsuji, Y., Tanaka, T., & Ishida, T. (1992). Lagrangian numerical simulation of plug flow of cohesionless particles in a horizontal pipe. Powder technology, 71(3),
 
@@ -1521,9 +1213,6 @@ Bibliography
 **(Tuckerman4)**
    Tuckerman, Mundy, Balasubramanian, Klein, J Chem Phys, 106, 5615 (1997).
 
-**(Tyagi)**
-   Tyagi, Suzen, Sega, Barbosa, Kantorovich, Holm, J Chem Phys, 132, 154112 (2010)
-
 **(Ulomek)**
    Ulomek, Brien, Foiles, Mohles, Modelling Simul. Mater. Sci. Eng. 23 (2015) 025007
 
@@ -1533,15 +1222,6 @@ Bibliography
 **(Valone)**
    Valone, Baskes, Martin, Phys. Rev. B, 73, 214209 (2006).
 
-**(vanWijk)**
-   M. M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)
-
-**(Van Workum)**
-   K. Van Workum et al., J. Chem. Phys. 125 144506 (2006)
-
-**(Vargas and McCarthy 2001)**
-   Vargas, W.L. and McCarthy, J.J. (2001).
-
 **(Varshalovich)**
    Varshalovich, Moskalev, Khersonskii, Quantum Theory of Angular Momentum, World Scientific, Singapore (1987).
 
@@ -1554,9 +1234,6 @@ Bibliography
 **(Veld)**
    In 't Veld, Ismail, Grest, J Chem Phys, 127, 144711 (2007).
 
-**(Verstraelen)**
-   Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).
-
 **(Volkov1)**
    Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
 
@@ -1581,9 +1258,6 @@ Bibliography
 **(Wang et al, 2015)**
    Wang, Y., Alonso-Marroquin, F., & Guo, W. W. (2015).  Rolling and sliding in 3-D discrete element models. Particuology, 23, 49-55.
 
-**(Wang2020)**
-   X. Wang, S. Ramirez-Hinestrosa, J. Dobnikar, and D. Frenkel, Phys. Chem. Chem. Phys. 22, 10624 (2020).
-
 **(Wang1)**
    J.\  Wang, H. S. Yu, P. A. Langston, F. Y. Fraige, Granular Matter, 13, 1 (2011).
 
@@ -1623,9 +1297,6 @@ Bibliography
 **(Wicaksono2)**
    Wicaksono, figshare, https://doi.org/10.6084/m9.figshare.1488628.v1 (2015).
 
-**(Winkler)**
-   Winkler, Wysocki, and Gompper, Soft Matter, 11, 6680 (2015).
-
 **(Wirnsberger)**
    Wirnsberger, Frenkel, and Dellago, J Chem Phys, 143, 124104 (2015).
 
@@ -1638,27 +1309,9 @@ Bibliography
 **(Wood)**
    Wood and Thompson, J Chem Phys, 148, 241721, (2018)
 
-**(Xie23)**
-   Xie, S.R., Rupp, M. & Hennig, R.G. Ultra-fast interpretable machine-learning potentials. npj Comput Mater 9, 162 (2023). https://doi.org/10.1038/s41524-023-01092-7
-
-**(Yade-DEM)**
-   V. Smilauer et al. (2021), Yade Documentation 3rd ed.
-
-**(Yanxon2020)**
-   Yanxon, Zagaceta, Tang, Matteson, Zhu, Mach. Learn.: Sci. Technol. 2, 027001 (2020).
-
 **(Yeh)**
    Yeh and Berkowitz, J Chem Phys, 111, 3155 (1999).
 
-**(Yuan2010a)**
-   Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
-
-**(Yuan2010b)**
-   Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
-
-**(Zagaceta2020)**
-   Zagaceta, Yanxon, Zhu, J Appl Phys, 128, 045113 (2020).
-
 **(ZBL)**
    J.F. Ziegler, J.P. Biersack, U. Littmark, 'Stopping and Ranges of Ions in Matter' Vol 1, 1985, Pergamon Press.
 
@@ -1728,6 +1381,17 @@ Bibliography
 **(Zimmerman2010)**
    Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
 
+**(de Buyl)**
+   de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
+
+**(de Koning)**
+   de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
+
 **(electronic stopping)**
    Wikipedia - Electronic Stopping Power: https://en.wikipedia.org/wiki/Stopping_power_%28particle_radiation%29
 
+**(tenWolde)**
+   P.\  R. ten Wolde, M. J. Ruiz-Montero, D. Frenkel, J. Chem. Phys. 104, 9932 (1996).
+
+**(vanWijk)**
+   M.\  M. van Wijk, A. Schuring, M. I. Katsnelson, and A. Fasolino, Physical Review Letters, 113, 135504 (2014)

doc/src/Build.rst

@@ -1,14 +1,10 @@
 Build LAMMPS
 ============
 
-LAMMPS is built as a library and an executable from source code using a
-build environment generated by CMake (Unix Makefiles, Ninja, Xcode,
-Visual Studio, KDevelop, CodeBlocks and more depending on the platform).
-Using CMake is the preferred way to build LAMMPS.  In addition, LAMMPS
-can be compiled using the legacy build system based on traditional
-makefiles for use with GNU make (which may require manual editing).
-Support for the legacy build system is slowly being phased out and may
-not be available for all optional features.
+LAMMPS is built as a library and an executable from source code using
+either traditional makefiles for use with GNU make (which may require
+manual editing), or using a build environment generated by CMake (Unix
+Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
 
 As an alternative, you can download a package with pre-built executables
 or automated build trees, as described in the :doc:`Install <Install>`

doc/src/Build_basics.rst

@@ -37,9 +37,8 @@ standard. A more detailed discussion of that is below.
 
       .. code-block:: bash
 
-         -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI
-         -D BUILD_OMP=value        # yes or no, default is yes if a compatible
-                                   # compiler is detected
+         -D BUILD_MPI=value        # yes or no, default is yes if CMake finds MPI, else no
+         -D BUILD_OMP=value        # yes or no, default is yes if a compatible compiler is detected
          -D LAMMPS_MACHINE=name    # name = mpi, serial, mybox, titan, laptop, etc
                                    # no default value
 
@@ -55,9 +54,9 @@ standard. A more detailed discussion of that is below.
 
       .. code-block:: bash
 
-         make mpi      # parallel build, produces lmp_mpi using Makefile.mpi
-         make serial   # serial build, produces lmp_serial using Makefile/serial
-         make mybox    # uses Makefile.mybox to produce lmp_mybox
+         make mpi                # parallel build, produces lmp_mpi using Makefile.mpi
+         make serial             # serial build, produces lmp_serial using Makefile/serial
+         make mybox              # uses Makefile.mybox to produce lmp_mybox
 
       Any ``make machine`` command will look up the make settings from a
       file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
@@ -75,15 +74,15 @@ standard. A more detailed discussion of that is below.
       this is ``-fopenmp``\ , which can be added to the ``CC`` and
       ``LINK`` makefile variables.
 
-      For the serial build the following make variables are set (see ``src/MAKE/Makefile.serial``):
+      For the serial build the following make variables are set (see src/MAKE/Makefile.serial):
 
       .. code-block:: make
 
-         CC =       g++
-         LINK =     g++
-         MPI_INC =  -I../STUBS
-         MPI_PATH = -L../STUBS
-         MPI_LIB =  -lmpi_stubs
+         CC =            g++
+         LINK =          g++
+         MPI_INC =       -I../STUBS
+         MPI_PATH =      -L../STUBS
+         MPI_LIB =       -lmpi_stubs
 
       You also need to build the STUBS library for your platform before
       making LAMMPS itself.  A ``make serial`` build does this for you
@@ -91,7 +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. ``LATBOLTZ``,
+      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -129,13 +128,14 @@ 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 ``ML-SNAP``,
-``DIFFRACTION``, and ``DPD-REACT`` packages.  Furthermore, some packages
-support OpenMP threading indirectly through the libraries they interface
-to: e.g. ``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.
+In addition, there are a few commands in LAMMPS that have native
+OpenMP support included as well.  These are commands in the ``MPIIO``,
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.
+Furthermore, some packages support OpenMP threading indirectly through
+the libraries they interface to: e.g. ``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.
 
 For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
 and turn on their native OpenMP support and turn on their native OpenMP
@@ -160,7 +160,7 @@ with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
 with compiler versions in use.  If compilation with OpenMP enabled fails
 because of your compiler requiring strict OpenMP 4.0 semantics, you can
 change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the
-``LMP_INC`` variable in your makefile, or add it to the command-line flags
+``LMP_INC`` variable in your makefile, or add it to the command line
 while configuring with CMake.  LAMMPS will auto-detect a suitable setting
 for most GNU, Clang, and Intel compilers.
 
@@ -232,32 +232,24 @@ LAMMPS.
       .. code-block:: bash
 
          # Building with GNU Compilers:
-         cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ \
-               -DCMAKE_Fortran_COMPILER=gfortran ../cmake
-         # Building with Intel Classic Compilers:
-         cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc \
-               -DCMAKE_Fortran_COMPILER=ifort ../cmake
+         cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
+         # Building with Intel Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
          # Building with Intel oneAPI Compilers:
-         cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
-               -DCMAKE_Fortran_COMPILER=ifx ../cmake
+         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
          # Building with LLVM/Clang Compilers:
-         cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
-               -DCMAKE_Fortran_COMPILER=flang ../cmake
+         cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
          # Building with PGI/Nvidia Compilers:
-         cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ \
-               -DCMAKE_Fortran_COMPILER=pgfortran ../cmake
-         # Building with the NVHPC Compilers:
-         cmake -DCMAKE_C_COMPILER=nvc -DCMAKE_CXX_COMPILER=nvc++ \
-               -DCMAKE_Fortran_COMPILER=nvfortran ../cmake
+         cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
 
       For compiling with the Clang/LLVM compilers a CMake preset is
       provided that can be loaded with
-      ``-C ../cmake/presets/clang.cmake``.  Similarly,
-      ``-C ../cmake/presets/intel.cmake`` should switch the compiler
-      toolchain to the legacy Intel compilers, ``-C ../cmake/presets/oneapi.cmake``
+      `-C ../cmake/presets/clang.cmake`.  Similarly,
+      `-C ../cmake/presets/intel.cmake` should switch the compiler
+      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
       will switch to the LLVM based oneAPI Intel compilers,
-      ``-C ../cmake/presets/pgi.cmake`` will switch the compiler to the PGI compilers,
-      and ``-C ../cmake/presets/nvhpc.cmake`` will switch to the NVHPC compilers.
+      and `-C ../cmake/presets/pgi.cmake`
+      will switch the compiler to the PGI compilers.
 
       Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts.
@@ -268,7 +260,7 @@ LAMMPS.
          When the cmake command completes, it prints a summary to the
          screen which compilers it is using and what flags and settings
          will be used for the compilation.  Note that if the top-level
-         compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
+         compiler is mpicxx, it is simply a wrapper on a real compiler.
          The underlying compiler info is what CMake will try to
          determine and report.  You should check to confirm you are
          using the compiler and optimization flags you want.
@@ -287,19 +279,19 @@ LAMMPS.
 
       .. code-block:: make
 
-         CC =        mpicxx
-         CCFLAGS =   -g -O3
-         LINK =      mpicxx
-         LINKFLAGS = -g -O
+         CC =            mpicxx
+         CCFLAGS =       -g -O3
+         LINK =          mpicxx
+         LINKFLAGS =     -g -O
 
       Serial build with GNU gcc (see ``src/MAKE/Makefile.serial``):
 
       .. code-block:: make
 
-         CC =        g++
-         CCFLAGS =   -g -O3
-         LINK =      g++
-         LINKFLAGS = -g -O
+         CC =            g++
+         CCFLAGS =       -g -O3
+         LINK =          g++
+         LINKFLAGS =     -g -O
 
       .. note::
 
@@ -325,10 +317,10 @@ LAMMPS.
          there may be specific compiler or linker flags that are either
          required or recommended to enable required features and to
          achieve optimal performance.  You need to include these in the
-         ``CCFLAGS`` and ``LINKFLAGS`` settings above.  For details, see the
+         CCFLAGS and LINKFLAGS settings above.  For details, see the
          documentation for the individual packages listed on the
          :doc:`Speed_packages` page.  Or examine these files in the
-         ``src/MAKE/OPTIONS`` directory.  They correspond to each of the 5
+         src/MAKE/OPTIONS directory.  They correspond to each of the 5
          accelerator packages and their hardware variants:
 
          .. code-block:: bash
@@ -397,8 +389,7 @@ running LAMMPS from Python via its library interface.
 
          make machine               # build LAMMPS executable lmp_machine
          make mode=static machine   # same as "make machine"
-         make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so
-                                    # instead
+         make mode=shared machine   # build LAMMPS shared lib liblammps_machine.so instead
 
       The "static" build will generate a static library called
       ``liblammps_machine.a`` and an executable named ``lmp_machine``\ ,
@@ -460,7 +451,7 @@ installation.
 Including or removing debug support
 -----------------------------------
 
-By default the compilation settings will include the ``-g`` flag which
+By default the compilation settings will include the *-g* flag which
 instructs the compiler to include debug information (e.g. which line of
 source code a particular instruction correspond to).  This can be
 extremely useful in case LAMMPS crashes and can help to provide crucial
@@ -473,7 +464,7 @@ If this is a concern, you can change the compilation settings or remove
 the debug information from the LAMMPS executable:
 
 - **Traditional make**: edit your ``Makefile.<machine>`` to remove the
-  ``-g`` flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
+  *-g* flag from the ``CCFLAGS`` and ``LINKFLAGS`` definitions
 - **CMake**: use ``-D CMAKE_BUILD_TYPE=Release`` or explicitly reset
   the applicable compiler flags (best done using the text mode or
   graphical user interface).
@@ -498,12 +489,8 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default). Build binary2txt,
-                                      # chain.x, micelle2d.x, msi2lmp, phana,
-                                      # stl_bin2txt
-         -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build LAMMPS-GUI
-         -D BUILD_WHAM=value          # yes (default). Download and build WHAM;
-                                      # only available for BUILD_LAMMPS_GUI=yes
+         -D BUILD_TOOLS=value         # yes or no (default)
+         -D BUILD_LAMMPS_SHELL=value  # yes or no (default)
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -517,10 +504,10 @@ using CMake or Make.
          make binary2txt       # build only binary2txt tool
          make chain            # build only chain tool
          make micelle2d        # build only micelle2d tool
+         make thermo_extract   # build only thermo_extract tool
 
-      .. note::
-
-         Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
+         cd lammps/tools/lammps-shell
+         make                  # build LAMMPS shell
 
 ----------
 

doc/src/Build_cmake.rst

@@ -8,7 +8,7 @@ packages.  Links to those pages on the :doc:`Build overview <Build>`
 page.
 
 The following text assumes some familiarity with CMake and focuses on
-using the command-line tool ``cmake`` and what settings are supported
+using the command line tool ``cmake`` and what settings are supported
 for building LAMMPS.  A more detailed tutorial on how to use CMake
 itself, the text mode or graphical user interface, to change the
 generated output files for different build tools and development
@@ -16,7 +16,8 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
-   LAMMPS currently requires that CMake version 3.20 or later is available.
+   LAMMPS currently requires that CMake version 3.10 or later is available;
+   version 3.12 or later is preferred.
 
 .. warning::
 
@@ -32,22 +33,23 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 Advantages of using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-CMake is the preferred way of compiling LAMMPS in contrast to the legacy
-build system based on GNU make and through :doc:`(manually customized)
-makefiles <Build_make>`.  Using CMake has multiple advantages that are
-specifically helpful for people with limited experience in compiling
+CMake is an alternative to compiling LAMMPS in the traditional way
+through :doc:`(manually customized) makefiles <Build_make>` and a recent
+addition to LAMMPS thanks to the efforts of Christoph Junghans (LANL)
+and Richard Berger (Temple U).  Using CMake has multiple advantages that
+are specifically helpful for people with limited experience in compiling
 software or for people that want to modify or extend LAMMPS.
 
 - CMake can detect available hardware, tools, features, and libraries
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
-- CMake supports customization of settings with a command-line, text
-  mode, or graphical user interface.  No manual editing of files,
-  knowledge of file formats or complex command-line syntax is required.
+- CMake supports customization of settings with a command line, text
+  mode, or graphical user interface.  No knowledge of file formats or
+  complex command line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
-- Support for true out-of-source compilation.  Multiple configurations
+- Support for true out-of-source compilation. Multiple configurations
   and settings with different choices of LAMMPS packages, settings, or
   compilers can be configured and built concurrently from the same
   source tree.
@@ -68,7 +70,7 @@ that purpose you can use either the command-line utility ``cmake`` (or
 graphical utility ``cmake-gui``, or use them interchangeably.  The
 second step is then the compilation and linking of all objects,
 libraries, and executables using the selected build tool.  Here is a
-minimal example using the command-line version of CMake to build LAMMPS
+minimal example using the command line version of CMake to build LAMMPS
 with no add-on packages enabled and no customization:
 
 .. code-block:: bash
@@ -131,21 +133,21 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
 configuration step.  The cache file contains all current CMake settings.
 
 To modify settings, enable or disable features, you need to set
-*variables* with either the ``-D`` command-line flag (``-D
+*variables* with either the *-D* command line flag (``-D
 VARIABLE1_NAME=value``) or change them in the text mode of the graphical
-user interface.  The ``-D`` flag can be used several times in one command.
+user interface.  The *-D* flag 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
+a different compiler tool chain.  Those are loaded with the *-C* flag
 (``-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.
+by adding one or more *-D* flags to the CMake command line.
 
 Generating files for alternate build tools (e.g. Ninja) and project files
-for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
-command-line flag.  A list of available generator settings for your
+for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
+command line flag.  A list of available generator settings for your
 specific CMake version is given when running ``cmake --help``.
 
 .. _cmake_multiconfig:
@@ -171,19 +173,19 @@ files. E.g.  with:
 In that case the resulting binaries are not in the build folder directly
 but in subdirectories corresponding to the build type (i.e. Release in
 the example from above).  Similarly, for running unit tests the
-configuration is selected with the ``-C`` flag:
+configuration is selected with the *-C* flag:
 
 .. code-block:: bash
 
    ctest -C Debug
 
-The CMake scripts in LAMMPS have basic support for being compiled using
-a multi-config build system, but not all of it has been ported.  This is
-in particular applicable to compiling packages that require additional
-libraries that would be downloaded and compiled by CMake.  The
-``windows.cmake`` preset file tries to keep track of which packages can
-be compiled natively with the MSVC compilers out-of-the box.  Not all of
-the external libraries are portable to Windows, either.
+The CMake scripts in LAMMPS have basic support for being compiled using a
+multi-config build system, but not all of it has been ported.  This is in
+particular applicable to compiling packages that require additional libraries
+that would be downloaded and compiled by CMake.  The "windows" preset file
+tries to keep track of which packages can be compiled natively with the
+MSVC compilers out-of-the box.  Not all of those external libraries are
+portable to Windows, either.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -88,8 +88,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Leak, Undefined Behavior, and Thread Sanitizer Support (CMake only)
-----------------------------------------------------------------------------
+Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
+----------------------------------------------------------------------
 
 Compilers such as GCC and Clang support generating instrumented binaries
 which use different sanitizer libraries to detect problems in the code
@@ -110,7 +110,6 @@ compilation and linking stages.  This is done through setting the
 
    -D ENABLE_SANITIZER=none       # no sanitizer active (default)
    -D ENABLE_SANITIZER=address    # enable address sanitizer / memory leak checker
-   -D ENABLE_SANITIZER=hwaddress  # enable hardware assisted address sanitizer / memory leak checker
    -D ENABLE_SANITIZER=leak       # enable memory leak checker (only)
    -D ENABLE_SANITIZER=undefined  # enable undefined behavior sanitizer
    -D ENABLE_SANITIZER=thread     # enable thread sanitizer
@@ -123,59 +122,32 @@ Code Coverage and Unit Testing (CMake only)
 -------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
-during development:
+during development: integration testing (i.e. whether the code compiles
+on various platforms and with a variety of settings), unit testing
+(i.e. whether certain individual parts of the code produce the expected
+results for given inputs), run testing (whether selected complete input
+decks run without crashing for multiple configurations), and regression
+testing (i.e. whether selected input examples reproduce the same
+results over a given number of steps and operations within a given
+error margin).  The status of this automated testing can be viewed on
+`https://ci.lammps.org <https://ci.lammps.org>`_.
 
-- Integration testing (i.e. whether the code compiles
-  on various platforms and with a variety of compilers and settings),
-- Unit testing (i.e. whether certain functions or classes of the code
-  produce the expected results for given inputs),
-- Run testing (i.e. whether selected input decks can run to completion
-  without crashing for multiple configurations),
-- Regression testing (i.e. whether selected input examples reproduce the
-  same results over a given number of steps and operations within a
-  given error margin).
+The scripts and inputs for integration, run, and regression testing
+are maintained in a
+`separate repository <https://github.com/lammps/lammps-testing>`_
+of the LAMMPS project on GitHub.
 
-The status of this automated testing can be viewed on `https://ci.lammps.org
-<https://ci.lammps.org>`_.
-
-The scripts and inputs for integration, run, and legacy regression
-testing are maintained in a `separate repository
-<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
-GitHub.  A few tests are also run as GitHub Actions and their
-configuration files are in the ``.github/workflows/`` folder of the
-LAMMPS git tree.
-
-Regression tests can also be performed locally with the :ref:`regression
-tester tool <regression>`.  The tool checks if a given LAMMPS binary run
-with selected input examples produces thermo output that is consistent
-with the provided log files.  The script can be run in one pass over all
-available input files, but it can also first create multiple lists of
-inputs or folders that can then be run with multiple workers
-concurrently to speed things up.  Another mode allows to do a quick
-check of inputs that contain commands that have changes in the current
-checkout branch relative to a git branch.  This works similar to the two
-pass mode, but will select only shorter runs and no more than 100 inputs
-that are chosen randomly.  This ensures that this test runs
-significantly faster compared to the full test run.  These test runs can
-also be performed with instrumented LAMMPS binaries (see previous
-section).
-
-The unit testing facility is integrated into the CMake build process of
-the LAMMPS source code distribution itself.  It can be enabled by
+The unit testing facility is integrated into the CMake build process
+of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <https://pyyaml.org/>`_ library and matching
-development headers to compile (if those are not found locally a recent
-version of that library will be downloaded and compiled along with
-LAMMPS and the test programs) and will download and compile a specific
-version of the `GoogleTest <https://github.com/google/googletest/>`_ C++
-test framework that is used to implement the tests.  Those unit tests
-may be combined with memory access and leak checking with valgrind
-(see below for how to enable it).  In that case, running so-called
-death tests will create a lot of false positives and thus they can be
-disabled by configuring compilation with the additional setting
-``-D SKIP_DEATH_TESTS=on``.
+It requires the `YAML <https://pyyaml.org/>`_ library and development
+headers (if those are not found locally a recent version will be
+downloaded and compiled along with LAMMPS and the test program) to
+compile and will download and compile a specific recent version of the
+`Googletest <https://github.com/google/googletest/>`_ C++ test framework
+for implementing the tests.
 
-.. admonition:: Software version and LAMMPS configuration requirements
+.. admonition:: Software version requirements for testing
    :class: note
 
    The compiler and library version requirements for the testing
@@ -183,7 +155,7 @@ disabled by configuring compilation with the additional setting
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
    to detect incompatible versions and either skip incompatible tests or
-   stop with an error.  Also the number of available tests will depend on
+   stop with an error.  Also the number of tests will depend on
    installed LAMMPS packages, development environment, operating system,
    and configuration settings.
 
@@ -196,24 +168,24 @@ The output of this command will be looking something like this:
     $ ctest
     Test project /home/akohlmey/compile/lammps/build-testing
          Start   1: RunLammps
-   1/563 Test   #1: RunLammps ..................................   Passed    0.28 sec
+   1/563 Test   #1: RunLammps ..........................................   Passed    0.28 sec
          Start   2: HelpMessage
-   2/563 Test   #2: HelpMessage ................................   Passed    0.06 sec
+   2/563 Test   #2: HelpMessage ........................................   Passed    0.06 sec
          Start   3: InvalidFlag
-   3/563 Test   #3: InvalidFlag ................................   Passed    0.06 sec
+   3/563 Test   #3: InvalidFlag ........................................   Passed    0.06 sec
          Start   4: Tokenizer
-   4/563 Test   #4: Tokenizer ..................................   Passed    0.05 sec
+   4/563 Test   #4: Tokenizer ..........................................   Passed    0.05 sec
          Start   5: MemPool
-   5/563 Test   #5: MemPool ....................................   Passed    0.05 sec
+   5/563 Test   #5: MemPool ............................................   Passed    0.05 sec
          Start   6: ArgUtils
-   6/563 Test   #6: ArgUtils ...................................   Passed    0.05 sec
+   6/563 Test   #6: ArgUtils ...........................................   Passed    0.05 sec
        [...]
          Start 561: ImproperStyle:zero
- 561/563 Test #561: ImproperStyle:zero .........................   Passed    0.07 sec
+ 561/563 Test #561: ImproperStyle:zero .................................   Passed    0.07 sec
          Start 562: TestMliapPyUnified
- 562/563 Test #562: TestMliapPyUnified .........................   Passed    0.16 sec
+ 562/563 Test #562: TestMliapPyUnified .................................   Passed    0.16 sec
          Start 563: TestPairList
- 563/563 Test #563: TestPairList ...............................   Passed    0.06 sec
+ 563/563 Test #563: TestPairList .......................................   Passed    0.06 sec
 
  100% tests passed, 0 tests failed out of 563
 
@@ -228,25 +200,24 @@ The output of this command will be looking something like this:
 The ``ctest`` command has many options, the most important ones are:
 
 .. list-table::
-   :widths: 20 80
 
    * - Option
      - Function
-   * - ``-V``
+   * - -V
      - verbose output: display output of individual test runs
-   * - ``-j <num>``
+   * - -j <num>
      - parallel run: run <num> tests in parallel
-   * - ``-R <regex>``
+   * - -R <regex>
      - run subset of tests matching the regular expression <regex>
-   * - ``-E <regex>``
+   * - -E <regex>
      - exclude subset of tests matching the regular expression <regex>
-   * - ``-L <regex>``
+   * - -L <regex>
      - run subset of tests with a label matching the regular expression <regex>
-   * - ``-LE <regex>``
+   * - -LE <regex>
      - exclude subset of tests with a label matching the regular expression <regex>
-   * - ``-N``
+   * - -N
      - dry-run: display list of tests without running them
-   * - ``-T memcheck``
+   * - -T memcheck
      - run tests with valgrind memory checker (if available)
 
 In its full implementation, the unit test framework will consist of multiple
@@ -263,31 +234,12 @@ will be skipped if prerequisite features are not available in LAMMPS.
    time.  Preference is given to parts of the code base that are easy to
    test or commonly used.
 
-Tests as shown by the ``ctest`` program are commands defined in the
-``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
-tests simply execute LAMMPS with specific command-line flags and check
-the output to the screen for expected content.  A large number of unit
-tests are special tests programs using the `GoogleTest framework
-<https://github.com/google/googletest/>`_ and linked to the LAMMPS
-library that test individual functions or create a LAMMPS class
-instance, execute one or more commands and check data inside the LAMMPS
-class hierarchy.  There are also tests for the C-library, Fortran, and
-Python module interfaces to LAMMPS.  The Python tests use the Python
-"unittest" module in a similar fashion than the others use `GoogleTest`.
-These special test programs are structured to perform multiple
-individual tests internally and each of those contains several checks
-(aka assertions) for internal data being changed as expected.
-
-Tests for force computing or modifying styles (e.g. styles for non-bonded
-and bonded interactions and selected fixes) are run by using a more generic
-test program that reads its input from files in YAML format. The YAML file
-provides the information on how to customized the test program to test
-a specific style and - if needed - with specific settings.
-To add a test for another, similar style (e.g. a new pair style) it is
-usually sufficient to add a suitable YAML file.  :doc:`Detailed
-instructions for adding tests <Developer_unittest>` are provided in the
-Programmer Guide part of the manual.  A description of what happens
-during the tests is given below.
+Tests for styles of the same kind of style (e.g. pair styles or bond
+styles) are performed with the same test executable using different
+input files in YAML format.  So to add a test for another style of the
+same kind it may be sufficient to add a suitable YAML file.
+:doc:`Detailed instructions for adding tests <Developer_unittest>` are
+provided in the Programmer Guide part of the manual.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -303,18 +255,16 @@ A test run is then a a collection multiple individual test runs each
 with many comparisons to reference results based on template input
 files, individual command settings, relative error margins, and
 reference data stored in a YAML format file with ``.yaml``
-suffix. Currently the programs ``test_pair_style``, ``test_bond_style``,
-``test_angle_style``, ``test_dihedral_style``, and
-``test_improper_style`` are implemented.  They will compare forces,
-energies and (global) stress for all atoms after a ``run 0`` calculation
-and after a few steps of MD with :doc:`fix nve <fix_nve>`, each in
-multiple variants with different settings and also for multiple
-accelerated styles. If a prerequisite style or package is missing, the
-individual tests are skipped.  All force style tests will be executed on
-a single MPI process, so using the CMake option ``-D BUILD_MPI=off`` can
-significantly speed up testing, since this will skip the MPI
-initialization for each test run.  Below is an example command and
-output:
+suffix. Currently the programs ``test_pair_style``, ``test_bond_style``, and
+``test_angle_style`` are implemented.  They will compare forces, energies and
+(global) stress for all atoms after a ``run 0`` calculation and after a
+few steps of MD with :doc:`fix nve <fix_nve>`, each in multiple variants
+with different settings and also for multiple accelerated styles. If a
+prerequisite style or package is missing, the individual tests are
+skipped.  All tests will be executed on a single MPI process, so using
+the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
+since this will skip the MPI initialization for each test run.
+Below is an example command and output:
 
 .. code-block:: console
 
@@ -352,17 +302,16 @@ paths in the individual source files.
 The force style test programs have a common set of options:
 
 .. list-table::
-   :widths: 25 75
 
    * - Option
      - Function
-   * - ``-g <newfile>``
+   * - -g <newfile>
      - regenerate reference data in new YAML file
-   * - ``-u``
+   * - -u
      - update reference data in the original YAML file
-   * - ``-s``
+   * - -s
      - print error statistics for each group of comparisons
-   * - ``-v``
+   * - -v
      - verbose output: also print the executed LAMMPS commands
 
 The ``ctest`` tool has no mechanism to directly pass flags to the individual
@@ -376,10 +325,10 @@ set in an environment variable ``TEST_ARGS``. Example:
 To add a test for a style that is not yet covered, it is usually best
 to copy a YAML file for a similar style to a new file, edit the details
 of the style (how to call it, how to set its coefficients) and then
-run test command with either the ``-g`` and the replace the initial
-test file with the regenerated one or the ``-u`` option.  The ``-u`` option
+run test command with either the *-g* and the replace the initial
+test file with the regenerated one or the *-u* option.  The *-u* option
 will destroy the original file, if the generation run does not complete,
-so using ``-g`` is recommended unless the YAML file is fully tested
+so using *-g* is recommended unless the YAML file is fully tested
 and working.
 
 Some of the force style tests are rather slow to run and some are very
@@ -420,7 +369,7 @@ during MD timestepping and manipulate per-atom properties like
 positions, velocities, and forces.  For those fix styles, testing can be
 done in a very similar fashion as for force fields and thus there is a
 test program `test_fix_timestep` that shares a lot of code, properties,
-and command-line flags with the force field style testers described in
+and command line flags with the force field style testers described in
 the previous section.
 
 This tester will set up a small molecular system run with verlet run
@@ -467,16 +416,15 @@ When compiling LAMMPS with enabled tests, most test executables will
 need to be linked against the LAMMPS library.  Since this can be a very
 large library with many C++ objects when many packages are enabled, link
 times can become very long on machines that use the GNU BFD linker (e.g.
-Linux systems).  Alternatives like the ``mold`` linker, the ``lld``
-linker of the LLVM project, or the ``gold`` linker available with GNU
-binutils can speed up this step substantially (in this order).  CMake
-will by default test if any of the three can be enabled and use it when
-``ENABLE_TESTING`` is active.  It can also be selected manually through
-the ``CMAKE_CUSTOM_LINKER`` CMake variable.  Allowed values are
-``mold``, ``lld``, ``gold``, ``bfd``, or ``default``.  The ``default``
-option will use the system default linker otherwise, the linker is
-chosen explicitly.  This option is only available for the GNU or Clang
-C++ compilers.
+Linux systems).  Alternatives like the ``lld`` linker of the LLVM project
+or the ``gold`` linker available with GNU binutils can speed up this step
+substantially. CMake will by default test if any of the two can be
+enabled and use it when ``ENABLE_TESTING`` is active.  It can also be
+selected manually through the ``CMAKE_CUSTOM_LINKER`` CMake variable.
+Allowed values are ``lld``, ``gold``, ``bfd``, or ``default``.  The
+``default`` option will use the system default linker otherwise, the
+linker is chosen explicitly.  This option is only available for the
+GNU or Clang C++ compiler.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -529,51 +477,27 @@ After post-processing with ``gen_coverage_html`` the results are in
 a folder ``coverage_html`` and can be viewed with a web browser.
 The images below illustrate how the data is presented.
 
-.. only:: not latex
+.. list-table::
 
-   .. list-table::
+      * - .. figure:: JPG/coverage-overview-top.png
+             :scale: 25%
 
-         * - .. figure:: JPG/coverage-overview-top.png
-                :scale: 25%
+          Top of the overview page
 
-             Top of the overview page
+        - .. figure:: JPG/coverage-overview-manybody.png
+             :scale: 25%
 
-           - .. figure:: JPG/coverage-overview-manybody.png
-                :scale: 25%
+          Styles with good coverage
 
-             Styles with good coverage
+        - .. figure:: JPG/coverage-file-top.png
+             :scale: 25%
 
-           - .. figure:: JPG/coverage-file-top.png
-                :scale: 25%
+          Top of individual source page
 
-             Top of individual source page
+        - .. figure:: JPG/coverage-file-branches.png
+             :scale: 25%
 
-           - .. figure:: JPG/coverage-file-branches.png
-                :scale: 25%
-
-             Source page with branches
-
-.. only:: latex
-
-   .. figure:: JPG/coverage-overview-top.png
-      :width: 60%
-
-      Top of the overview page
-
-   .. figure:: JPG/coverage-overview-manybody.png
-      :width: 60%
-
-      Styles with good coverage
-
-   .. figure:: JPG/coverage-file-top.png
-      :width: 60%
-
-      Top of individual source page
-
-   .. figure:: JPG/coverage-file-branches.png
-      :width: 60%
-
-      Source page with branches
+          Source page with branches
 
 Coding style utilities
 ----------------------
@@ -594,8 +518,6 @@ The following options are available.
    make fix-errordocs       # remove error docs in header files
    make check-permissions   # search for files with permissions issues
    make fix-permissions     # correct permissions issues in files
-   make check-docs          # search for several issues in the manual
-   make check-version       # list files with pending release version tags
    make check               # run all check targets from above
 
 These should help to make source and documentation files conforming
@@ -642,38 +564,14 @@ The following target are available for both, GNU make and CMake:
 
 .. _gh-cli:
 
-GitHub command-line interface
+GitHub command line interface
 -----------------------------
 
-GitHub has developed a `command-line tool <https://cli.github.com>`_
-to interact with the GitHub website via a command called ``gh``.
-This is extremely convenient when working with a Git repository hosted
-on GitHub (like LAMMPS).  It is thus highly recommended to install it
-when doing LAMMPS development.  To use ``gh`` you must be within a git
-checkout of a repository and you must obtain an authentication token
-to connect your checkout with a GitHub user.  This is done with the
-command: ``gh auth login`` where you then have to follow the prompts.
-Here are some examples:
+GitHub is developing a `tool for the command line
+<https://cli.github.com>`_ that interacts with the GitHub website via a
+command called ``gh``.  This can be extremely convenient when working
+with a Git repository hosted on GitHub (like LAMMPS).  It is thus highly
+recommended to install it when doing LAMMPS development.
 
-.. list-table::
-   :header-rows: 1
-   :widths: 34 66
-
-   * - Command
-     - Description
-   * - ``gh pr list``
-     - List currently open pull requests
-   * - ``gh pr checks 404``
-     - Shows the status of all checks for pull request #404
-   * - ``gh pr view 404``
-     - Shows the description and recent comments for pull request #404
-   * - ``gh co 404``
-     - Check out the branch from pull request #404; set up for pushing changes
-   * - ``gh issue list``
-     - List currently open issues
-   * - ``gh issue view 430 --comments``
-     - Shows the description and all comments for issue #430
-
-The capabilities of the ``gh`` command are continually expanding, so
-for more details please see the documentation at https://cli.github.com/manual/
-or use ``gh --help`` or ``gh <command> --help`` for embedded help.
+The capabilities of the ``gh`` command is continually expanding, so
+please see the documentation at https://cli.github.com/manual/

doc/src/Build_link.rst

@@ -37,7 +37,7 @@ executable code from the library is copied into the calling executable.
    .. tab:: CMake build
 
       This assumes that LAMMPS has been configured without setting a
-      ``LAMMPS_MACHINE`` name, installed with ``make install``, and the
+      ``LAMMPS_MACHINE`` name, installed with "make install", and the
       ``PKG_CONFIG_PATH`` environment variable has been updated to
       include the ``liblammps.pc`` file installed into the configured
       destination folder.  The commands to compile and link a coupled
@@ -45,8 +45,8 @@ executable code from the library is copied into the calling executable.
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
+         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicxx -o caller caller.o -$(pkgconf liblammps --libs)
 
    .. tab:: Traditional make
 
@@ -59,10 +59,10 @@ executable code from the library is copied into the calling executable.
          mpicc -c -O -I${HOME}/lammps/src caller.c
          mpicxx -o caller caller.o -L${HOME}/lammps/src -llammps_mpi
 
-      The ``-I`` argument is the path to the location of the ``library.h``
+      The *-I* argument is the path to the location of the ``library.h``
       header file containing the interface to the LAMMPS C-style library
-      interface.  The ``-L`` argument is the path to where the
-      ``liblammps_mpi.a`` file is located.  The ``-llammps_mpi`` argument
+      interface.  The *-L* argument is the path to where the
+      ``liblammps_mpi.a`` file is located.  The *-llammps_mpi* argument
       is shorthand for telling the compiler to link the file
       ``liblammps_mpi.a``.  If LAMMPS has been built as a shared
       library, then the linker will use ``liblammps_mpi.so`` instead.
@@ -142,7 +142,7 @@ When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
 in the shared library or registered as a dependent library in the shared
 library file.  Thus, those libraries need not be specified when linking
-the calling executable.  Only the ``-I`` flags are needed.  So the example
+the calling executable.  Only the *-I* flags are needed.  So the example
 case from above of the serial version static LAMMPS library with the
 POEMS package installed becomes:
 
@@ -155,8 +155,8 @@ POEMS package installed becomes:
 
       .. code-block:: bash
 
-         mpicc -c -O $(pkg-config --cflags liblammps) caller.c
-         mpicxx -o caller caller.o -$(pkg-config --libs liblammps)
+         mpicc -c -O $(pkgconf liblammps --cflags) caller.c
+         mpicxx -o caller caller.o -$(pkgconf --libs)
 
    .. tab:: Traditional make
 

doc/src/Build_make.rst

@@ -8,10 +8,6 @@ Building LAMMPS with traditional makefiles requires that you have a
 for customizing your LAMMPS build with a number of global compilation
 options and features.
 
-This build system is slowly being phased out and may not support all
-optional features and packages in LAMMPS.  It is recommended to switch
-to the :doc:`CMake based build system <Build_cmake>`.
-
 Requirements
 ^^^^^^^^^^^^
 
@@ -29,7 +25,7 @@ additional tools to be available and functioning.
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
   * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
   * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * Python (optional, required for ``make lib-<pkg>`` in the ``src``
+  * Python (optional, required for ``make lib-<pkg>`` in the src
     folder).  Python scripts are currently tested with python 2.7 and
     3.6 to 3.11. The procedure for :doc:`building the documentation
     <Build_manual>` *requires* Python 3.5 or later.

doc/src/Build_package.rst

@@ -49,13 +49,13 @@ packages:
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
-   * :ref:`MISC <misc>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
    * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
+   * :ref:`MSCG <mscg>`
    * :ref:`NETCDF <netcdf>`
    * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
@@ -63,7 +63,6 @@ packages:
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
-   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -101,10 +100,10 @@ versus make.
       .. code-block:: bash
 
          cd lammps/src
-         make ps        # check which packages are currently installed
-         make yes-name  # install a package with name
-         make no-name   # uninstall a package with name
-         make mpi       # build LAMMPS with whatever packages are now installed
+         make ps                    # check which packages are currently installed
+         make yes-name              # install a package with name
+         make no-name               # uninstall a package with name
+         make mpi                   # build LAMMPS with whatever packages are now installed
 
       Examples:
 
@@ -173,41 +172,17 @@ make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
-    # enable just a few core packages
-    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake
-
-    # enable most packages
-    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake
-
-    # enable packages which download sources or potential files
-    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
-
-    # disable packages that do require extra libraries or tools
-    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake
-
-    # change settings to use the Clang compilers by default
-    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake
-
-    # change settings to use the GNU compilers by default
-    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake
-
-    # change settings to use the Intel compilers by default
-    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake
-
-    # change settings to use the PGI compilers by default
-    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake
-
-    # enable all packages
-    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake
-
-    # disable all packages
-    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake
-
-    #  compile with MinGW cross-compilers
-    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
-
-    # compile serial multi-arch binaries on macOS
-    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
+    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
+    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake  # change settings to use the GNU compilers by default
+    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@@ -233,8 +208,7 @@ Example
    # GPU package and configure it for using CUDA. You can run.
    mkdir build
    cd build
-   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
-         -D PKG_GPU=on -D GPU_API=cuda ../cmake
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
 
    # to add another package, say BODY to the previous configuration you can run:
    cmake -D PKG_BODY=on .

doc/src/Build_settings.rst

@@ -1,7 +1,3 @@
-.. raw:: latex
-
-    \clearpage
-
 Optional build settings
 =======================
 
@@ -12,8 +8,7 @@ explains how to do this for building both with CMake and make.
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
 * `Size of LAMMPS integer types and size limits`_
 * `Read or write compressed files`_
-* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
-* `Support for downloading files`_
+* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
@@ -24,7 +19,7 @@ explains how to do this for building both with CMake and make.
 .. _cxx11:
 
 C++11 standard compliance
--------------------------
+------------------------------------------
 
 A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
 LAMMPS version 3 March 2020 is the last version compatible with the previous
@@ -36,16 +31,12 @@ flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
 
    CCFLAGS = -g -O3 -std=c++11
 
-Individual packages may require compliance with a later C++ standard
-like C++14 or C++17.  These requirements will be documented with the
-:doc:`individual packages <Packages_details>`.
-
 ----------
 
 .. _fft:
 
 FFT library
------------
+---------------------
 
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@@ -53,36 +44,21 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
-.. versionadded:: 7Feb2024
-
-Alternatively, LAMMPS can use the `heFFTe
-<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
-communication algorithms, which comes with many optimizations for
-special cases, e.g. leveraging available 2D and 3D FFTs in the back end
-libraries and better pipelining for packing and communication.
-
 .. tabs::
 
    .. tab:: CMake build
 
       .. code-block:: bash
 
-         -D FFT=value              # FFTW3 or MKL or NVPL or KISS,
-                                   # default is FFTW3 if found, else KISS
-         -D FFT_KOKKOS=value       # FFTW3 or MKL or NVPL or KISS or CUFFT
-                                   # or HIPFFT or MKL_GPU, default is KISS
+         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
-         -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
 
       .. note::
 
-         When the Kokkos variant of a package is compiled and selected at run time,
-         the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
-         the FFT library selected by the FFT variable applies.
-         The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
-         Kokkos back end - for example, when using the CUDA back end of Kokkos,
-         you must use either ``CUFFT`` or ``KISS``.
+         The values for the FFT variable must be in upper-case.  This is
+         an exception to the rule that all CMake variables can be specified
+         with lower-case values.
 
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
@@ -100,19 +76,6 @@ libraries and better pipelining for packing and communication.
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
-         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
-                                     # heFFTe back end
-         -D Heffte_ROOT=path         # path to an existing heFFTe installation
-         -D nvpl_fft_INCLUDE_DIR=path # path to NVPL FFT include files
-         -D nvpl_fft_LIBRARY_DIR=path # path to NVPL FFT libraries
-
-      .. note::
-
-         heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
-         default internal FFT implementation; however, this stock back
-         end is intended for testing purposes only and is not optimized
-         for production runs.
-
 
    .. tab:: Traditional make
 
@@ -122,82 +85,32 @@ libraries and better pipelining for packing and communication.
 
       .. code-block:: make
 
-         FFT_INC = -DFFT_<NAME>        # where <NAME> is KISS (default), FFTW3,
-                                       # FFTW (same as FFTW3), NVPL, or MKL
-         FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
-                                       # FFTW (same as FFTW3), NVPL, MKL, CUFFT,
-                                       # HIPFFT, or MKL_GPU
-         FFT_INC = -DFFT_SINGLE       # do not specify for double precision
-         FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
-         FFT_INC = -DFFT_MKL_THREADS  # enable using threaded FFTs with MKL libraries
-         FFT_INC = -DFFT_PACK_ARRAY   # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
-                                      # default is FFT_PACK_ARRAY if not specified
+         FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
+                                       # default is KISS if not specified
+         FFT_INC = -DFFT_SINGLE        # do not specify for double precision
+         FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
+         FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
+         FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+                                       # default is FFT_PACK_ARRAY if not specified
 
       .. code-block:: make
 
-         FFT_INC =  -I/usr/local/include
-         FFT_PATH = -L/usr/local/lib
-
-         # hipFFT either precision
-         FFT_LIB =  -lhipfft
-
-         # cuFFT either precision
-         FFT_LIB =  -lcufft
-
-         # MKL_GPU either precision
-         FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb
-
-         # FFTW3 double precision
-         FFT_LIB =  -lfftw3
-
-         # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
-         FFT_LIB =  -lfftw3 -lfftw3_omp
-
-         # FFTW3 single precision
-         FFT_LIB =  -lfftw3 -lfftw3f
-
-         # serial MKL with Intel compiler
-         FFT_LIB =  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
-
-         # serial MKL with GNU compiler
-         FFT_LIB =  -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
-
-         # threaded MKL with Intel compiler
-         FFT_LIB =  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
-
-         # threaded MKL with GNU compiler
-         FFT_LIB =  -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
-
-         # MKL with automatic runtime selection of interface libs
-         FFT_LIB =  -lmkl_rt
-
-         # threaded NVPL FFT
-         FFT_LIB =  -lnvpl_fftw
-
+         FFT_INC =       -I/usr/local/include
+         FFT_PATH =      -L/usr/local/lib
+         FFT_LIB =       -lfftw3             # FFTW3 double precision
+         FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
+         FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
+         FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
+         FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
+         FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
+         FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
+         FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
 
       As with CMake, you do not need to set paths in ``FFT_INC`` or
       ``FFT_PATH``, if the compiler can find the FFT header and library
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
-      Traditional make can also link to heFFTe using an existing installation
-
-      .. code-block:: make
-
-         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
-         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
-         FFT_PATH =
-         FFT_LIB = $(heffte_link) $(heffte_libs)
-
-      The heFFTe install path will contain ``HeffteMakefile.in``.
-      which will define the ``heffte_`` include variables needed to link to heFFTe from
-      an external project using traditional make.
-      The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
-      selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
-      omitting the variable will default to the `stock` back end.
-      The heFFTe `stock` back end is intended to be used for testing and debugging,
-      but is not performance optimized for large scale production runs.
-
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -221,23 +134,13 @@ it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
-the ``--prefix`` option of configure.  Type ``./configure --help`` to see
+the "--prefix" option of configure.  Type ``./configure --help`` to see
 various options.
 
 The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
-The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA
-Grace Armv9.0 architecture. You can download it from https://docs.nvidia.com/nvpl/
-
-The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
-AMD's HIP installations, respectively. These FFT libraries require the
-Kokkos acceleration package to be enabled and the Kokkos back end to be
-GPU-resident (i.e., HIP or CUDA). Similarly, GPU offload of FFTs on
-Intel GPUs with oneMKL currently requires the Kokkos acceleration
-package to be enabled with the SYCL back end.
-
 Performing 3d FFTs in parallel can be time-consuming due to data access
 and required communication.  This cost can be reduced by performing
 single-precision FFTs instead of double precision.  Single precision
@@ -249,11 +152,11 @@ generally less than the difference in precision. Using the
 ``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
 use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
-the FFTW3 installation includes support for single-precision.
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
+library a second time with support for single-precision.
 
-When compiler FFTW3 from source, you can do the following, which should
-produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
+For FFTW3, do the following, which should produce the additional
+library ``libfftw3f.a`` or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 
@@ -262,27 +165,13 @@ produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 Performing 3d FFTs requires communication to transpose the 3d FFT
 grid.  The data packing/unpacking for this can be done in one of 3
-modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
+modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
 Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
-When using ``-DFFT_HEFFTE`` CMake will first look for an existing
-install with hints provided by ``-DHeffte_ROOT``, as recommended by the
-CMake standard and note that the name is case sensitive. If CMake cannot
-find a heFFTe installation with the correct back end (e.g., FFTW or
-MKL), it will attempt to download and build the library automatically.
-In this case, LAMMPS CMake will also accept all heFFTe specific
-variables listed in the `heFFTe documentation
-<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
-and those variables will be passed into the heFFTe build.
-
 ----------
 
-.. raw:: latex
-
-    \clearpage
-
 .. _size:
 
 Size of LAMMPS integer types and size limits
@@ -323,7 +212,7 @@ LAMMPS system size restrictions
 
 .. list-table::
    :header-rows: 1
-   :widths: 18 27 28 27
+   :widths: auto
    :align: center
 
    * -
@@ -392,8 +281,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
 
 .. _graphics:
 
-Output of JPEG, PNG, and movie files
-------------------------------------
+Output of JPG, PNG, and movie files
+--------------------------------------------------
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
 PNG image files.  Likewise, the :doc:`dump movie <dump_image>` command
@@ -406,13 +295,12 @@ requires the following settings:
 
       .. code-block:: bash
 
-         -D WITH_JPEG=value    # yes or no
-                               # default = yes if CMake finds JPEG development files, else no
-         -D WITH_PNG=value     # yes or no
-                               # default = yes if CMake finds PNG and ZLIB development files,
-                               # else no
-         -D WITH_FFMPEG=value  # yes or no
-                               # default = yes if CMake can find ffmpeg, else no
+         -D WITH_JPEG=value      # yes or no
+                                 # default = yes if CMake finds JPEG files, else no
+         -D WITH_PNG=value       # yes or no
+                                 # default = yes if CMake finds PNG and ZLIB files, else no
+         -D WITH_FFMPEG=value    # yes or no
+                                 # default = yes if CMake can find ffmpeg, else no
 
       Usually these settings are all that is needed.  If CMake cannot
       find the graphics header, library, executable files, you can set
@@ -434,10 +322,8 @@ requires the following settings:
 
          LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG  <other LMP_INC settings>
 
-         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h headers
-                                          # if make cannot find them
-         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so)
-                                          # files if make cannot find them
+         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
+         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
          JPG_LIB = -ljpeg -lpng -lz       # library names
 
       As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@@ -468,8 +354,8 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Supported compression tools and algorithms are currently
-``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
+:doc:`dump <dump>`.  Supported compression tools are currently
+``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
 
 .. tabs::
 
@@ -477,8 +363,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
 
       .. code-block:: bash
 
-         -D WITH_GZIP=value  # yes or no
-                             # default is yes if CMake can find the gzip program
+         -D WITH_GZIP=value       # yes or no
+                                  # default is yes if CMake can find the gzip program, else no
 
    .. tab:: Traditional make
 
@@ -500,64 +386,18 @@ during a run.
    available using a compression library instead, which is what the
    :ref:`COMPRESS package <PKG-COMPRESS>` enables.
 
---------------------------------------------------
-
-.. _libcurl:
-
-Support for downloading files
------------------------------
-
-.. versionadded:: 29Aug2024
-
-The :doc:`geturl command <geturl>` command uses the `the libcurl library
-<https://curl.se/libcurl/>`_ to download files.  This requires that
-LAMMPS is compiled accordingly which needs the following settings:
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D WITH_CURL=value      # yes or no
-                                 # default = yes if CMake finds CURL development files, else no
-
-      Usually these settings are all that is needed.  If CMake cannot
-      find the graphics header, library, executable files, you can set
-      these variables:
-
-      .. code-block:: bash
-
-         -D CURL_INCLUDE_DIR=path    # path to folder which contains curl.h header file
-         -D CURL_LIBRARY=path        # path to libcurls.a (.so) file
-
-   .. tab:: Traditional make
-
-      .. code-block:: make
-
-         LMP_INC = -DLAMMPS_CURL  <other LMP_INC settings>
-
-         CURL_INC = -I/usr/local/include   # path to curl folder with curl.h
-         CURL_PATH = -L/usr/lib            # paths to libcurl.a(.so) if make cannot find it
-         CURL_LIB = -lcurl                 # library names
-
-      As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
-      if make can find the libcurl header and library files in their
-      default system locations.  You must specify ``CURL_LIB`` with a
-      paths or linker flags to link to libcurl.
-
 ----------
 
 .. _align:
 
 Memory allocation alignment
----------------------------
+---------------------------------------
 
-This setting enables the use of the ``posix_memalign()`` call instead of
-``malloc()`` when LAMMPS allocates large chunks of memory.  Vector
+This setting enables the use of the "posix_memalign()" call instead of
+"malloc()" when LAMMPS allocates large chunks of memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
-current operating systems, the ``malloc()`` implementation returns
+current operating systems, the "malloc()" implementation returns
 pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being aligned
 on 64-byte boundaries.
@@ -571,9 +411,9 @@ on 64-byte boundaries.
          -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
       Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
-      ``posix_memalign()`` and revert to using the ``malloc()`` C-library
+      "posix_memalign()" and revert to using the "malloc()" C-library
       function instead.  When compiling LAMMPS for Windows systems,
-      ``malloc()`` will always be used and this setting is ignored.
+      "malloc()" will always be used and this setting is ignored.
 
    .. tab:: Traditional make
 
@@ -582,7 +422,7 @@ on 64-byte boundaries.
          LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
 
       Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
-      allocated with the ``malloc()`` function call
+      allocated with the "malloc()" function call
       instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
       Windows different function calls with different semantics for
       allocating aligned memory, that are not compatible with how LAMMPS
@@ -619,13 +459,27 @@ those systems:
 .. _exceptions:
 
 Exception handling when using LAMMPS as a library
--------------------------------------------------
+------------------------------------------------------------------
 
-LAMMPS errors do not kill the calling code, but throw an exception.  In
-the C-library interface, the call stack is unwound and control returns
-to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
-error status can then be queried.  When using C++ directly, the calling
-code has to be set up to *catch* exceptions thrown from within LAMMPS.
+This setting is useful when external codes drive LAMMPS as a library.
+With this option enabled, LAMMPS errors do not kill the calling code.
+Instead, the call stack is unwound and control returns to the caller,
+e.g. to Python. Of course, the calling code has to be set up to
+*catch* exceptions thrown from within LAMMPS.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
+
+   .. tab:: Traditional make
+
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_EXCEPTIONS   <other LMP_INC settings>
 
 .. note::
 

doc/src/Build_windows.rst

@@ -100,9 +100,9 @@ procedure.
 
 It is possible to use both the integrated CMake support of the Visual
 Studio IDE or use an external CMake installation (e.g. downloaded from
-cmake.org) to create build files and compile LAMMPS from the command-line.
+cmake.org) to create build files and compile LAMMPS from the command line.
 
-Compilation via command-line and unit tests are checked automatically
+Compilation via command line and unit tests are checked automatically
 for the LAMMPS development branch through
 `GitHub Actions <https://github.com/lammps/lammps/actions/workflows/compile-msvc.yml>`_.
 
@@ -115,7 +115,7 @@ for the LAMMPS development branch through
 
 Please note, that for either approach CMake will create a so-called
 :ref:`"multi-configuration" build environment <cmake_multiconfig>`, and
-the commands for building and testing LAMMPS must be adjusted
+the command lines for building and testing LAMMPS must be adjusted
 accordingly.
 
 The LAMMPS cmake folder contains a ``CMakeSettings.json`` file with

doc/src/Classes_lammps.rst

@@ -4,7 +4,7 @@ LAMMPS Class
 The LAMMPS class is encapsulating an MD simulation state and thus it is
 the class that needs to be created when starting a new simulation system
 state.  The LAMMPS executable essentially creates one instance of this
-class and passes the command-line flags and tells it to process the
+class and passes the command line flags and tells it to process the
 provided input (a file or ``stdin``).  It shuts the class down when
 control is returned to it and then exits.  When using LAMMPS as a
 library from another code it is required to create an instance of this

doc/src/Commands_all.rst

@@ -1,30 +1,26 @@
-.. only:: html
+.. table_from_list::
+   :columns: 3
 
-   .. table_from_list::
-      :columns: 5
-
-      * :doc:`General commands <Commands_all>`
-      * :doc:`Fix styles <Commands_fix>`
-      * :doc:`Compute styles <Commands_compute>`
-      * :doc:`Pair styles <Commands_pair>`
-      * :ref:`Bond styles <bond>`
-      * :ref:`Angle styles <angle>`
-      * :ref:`Dihedral styles <dihedral>`
-      * :ref:`Improper styles <improper>`
-      * :doc:`KSpace styles <Commands_kspace>`
-      * :doc:`Dump styles <Commands_dump>`
-
-.. raw:: latex
-
-   \clearpage
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.
+An alphabetic list of general LAMMPS commands.  Note that style
+commands with many variants, can be more easily accessed via the small
+table above.
 
 .. table_from_list::
-   :columns: 6
+   :columns: 5
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
@@ -58,7 +54,6 @@ An alphabetic list of general LAMMPS commands.
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
    * :doc:`fix_modify <fix_modify>`
-   * :doc:`geturl <geturl>`
    * :doc:`group <group>`
    * :doc:`if <if>`
    * :doc:`improper_coeff <improper_coeff>`
@@ -126,7 +121,7 @@ commands have accelerated versions.  This is indicated by an
 additional letter in parenthesis: k = KOKKOS.
 
 .. table_from_list::
-   :columns: 6
+   :columns: 5
 
    * :doc:`dynamical_matrix (k) <dynamical_matrix>`
    * :doc:`group2ndx <group2ndx>`

doc/src/Commands_bond.rst

@@ -1,7 +1,21 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
+
 .. _bond:
 
-Bond styles
-===========
+Bond_style potentials
+=====================
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -9,13 +23,11 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`none <bond_none>`
    * :doc:`zero <bond_zero>`
-   * :doc:`hybrid (k) <bond_hybrid>`
-   *
-   *
+   * :doc:`hybrid <bond_hybrid>`
    *
    *
    *
@@ -42,14 +54,13 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
-   * :doc:`rheo/shell <bond_rheo_shell>`
    * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 
 .. _angle:
 
-Angle styles
-============
+Angle_style potentials
+======================
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -57,13 +68,11 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`none <angle_none>`
    * :doc:`zero <angle_zero>`
-   * :doc:`hybrid (k) <angle_hybrid>`
-   *
-   *
+   * :doc:`hybrid <angle_hybrid>`
    *
    *
    *
@@ -80,7 +89,6 @@ OPT.
    * :doc:`cosine/shift (o) <angle_cosine_shift>`
    * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
    * :doc:`cosine/squared (o) <angle_cosine_squared>`
-   * :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
    * :doc:`cross <angle_cross>`
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
@@ -90,15 +98,14 @@ OPT.
    * :doc:`lepton (o) <angle_lepton>`
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
-   * :doc:`mwlc <angle_mwlc>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`spica (ko) <angle_spica>`
+   * :doc:`spica (o) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
 
-Dihedral styles
-===============
+Dihedral_style potentials
+=========================
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -106,23 +113,20 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`none <dihedral_none>`
    * :doc:`zero <dihedral_zero>`
-   * :doc:`hybrid (k) <dihedral_hybrid>`
-   *
-   *
+   * :doc:`hybrid <dihedral_hybrid>`
    *
    *
    *
    *
    *
    * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw (k) <dihedral_charmm>`
+   * :doc:`charmmfsw <dihedral_charmm>`
    * :doc:`class2 (ko) <dihedral_class2>`
    * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
-   * :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
@@ -137,8 +141,8 @@ OPT.
 
 .. _improper:
 
-Improper styles
-===============
+Improper_style potentials
+=========================
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -146,13 +150,11 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`none <improper_none>`
    * :doc:`zero <improper_zero>`
-   * :doc:`hybrid (k) <improper_hybrid>`
-   *
-   *
+   * :doc:`hybrid <improper_hybrid>`
    *
    *
    *

doc/src/Commands_category.rst

@@ -1,7 +1,3 @@
-.. raw:: latex
-
-   \clearpage
-
 Commands by category
 ====================
 
@@ -10,8 +6,8 @@ This page lists most of the LAMMPS commands, grouped by category.  The
 alphabetically.  Style options for entries like fix, compute, pair etc.
 have their own pages where they are listed alphabetically.
 
-Initialization
---------------
+Initialization:
+------------------------------
 
 .. table_from_list::
    :columns: 5
@@ -22,8 +18,8 @@ Initialization
    * :doc:`suffix <suffix>`
    * :doc:`units <units>`
 
-Setup simulation box
---------------------
+Setup simulation box:
+------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -35,8 +31,8 @@ Setup simulation box
    * :doc:`lattice <lattice>`
    * :doc:`region <region>`
 
-Setup atoms
------------
+Setup atoms:
+------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -59,8 +55,8 @@ Setup atoms
    * :doc:`set <set>`
    * :doc:`velocity <velocity>`
 
-Force fields
-------------
+Force fields:
+------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -83,8 +79,8 @@ Force fields
    * :doc:`pair_write <pair_write>`
    * :doc:`special_bonds <special_bonds>`
 
-Settings
---------
+Settings:
+------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -102,8 +98,8 @@ Settings
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
 
-Operations within timestepping (fixes) and diagnostics (computes)
------------------------------------------------------------------
+Operations within timestepping (fixes) and diagnostics (computes):
+------------------------------------------------------------------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -115,8 +111,8 @@ Operations within timestepping (fixes) and diagnostics (computes)
    * :doc:`uncompute <uncompute>`
    * :doc:`unfix <unfix>`
 
-Output
-------
+Output:
+------------------------------
 
 .. table_from_list::
    :columns: 4
@@ -135,8 +131,8 @@ Output
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
 
-Actions
--------
+Actions:
+------------------------------
 
 .. table_from_list::
    :columns: 6
@@ -150,8 +146,8 @@ Actions
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
 
-Input script control
---------------------
+Input script control:
+------------------------------
 
 .. table_from_list::
    :columns: 7

doc/src/Commands_compute.rst

@@ -1,5 +1,19 @@
-Compute styles
-==============
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
+
+Compute commands
+================
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
@@ -7,7 +21,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
 KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`ackland/atom <compute_ackland_atom>`
    * :doc:`adf <compute_adf>`
@@ -77,7 +91,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
-   * :doc:`composition/atom (k) <compute_composition_atom>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -86,7 +99,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
-   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -94,10 +106,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/mol/tally <compute_tally>`
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
-   * :doc:`pod/atom <compute_pod_atom>`
-   * :doc:`podd/atom <compute_pod_atom>`
-   * :doc:`pod/local <compute_pod_atom>`
-   * :doc:`pod/global <compute_pod_atom>`
    * :doc:`pressure <compute_pressure>`
    * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
@@ -106,16 +114,12 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
-   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
-   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
-   * :doc:`rheo/property/atom <compute_rheo_property_atom>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
-   * :doc:`slcsa/atom <compute_slcsa_atom>`
    * :doc:`slice <compute_slice>`
    * :doc:`smd/contact/radius <compute_smd_contact_radius>`
    * :doc:`smd/damage <compute_smd_damage>`