Merge pull request #4645 from akohlmey/improve-tests-for-set

Add or improve unit test programs to improve test coverage and specifically check recent additions

.github/CODEOWNERS

@@ -37,7 +37,8 @@ src/MESONT/*          @iafoss
 src/ML-HDNNP/*        @singraber
 src/ML-IAP/*          @athomps
 src/ML-PACE/*         @yury-lysogorskiy
-src/ML-POD/*          @exapde @rohskopf
+src/ML-POD/*          @exapde
+src/ML-UF3/*          @monk-04
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
@@ -49,6 +50,7 @@ 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
@@ -58,16 +60,29 @@ src/VTK/*             @rbberger
 
 # individual files in packages
 src/GPU/pair_vashishta_gpu.*        @andeplane
-src/KOKKOS/pair_vashishta_kokkos.*  @andeplane
+src/KOKKOS/pair_vashishta_kokkos.*  @andeplane @stanmoore1
+src/KOSSOS/pair_pod_kokkos.*        @exapde @stanmoore1
 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-DUMP/dump_extxyz.*          @fxcoudert
+src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
+src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
+src/EXTRA-PAIR/d3_parameters.h      @soniasolomoni @arthurfl
 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
@@ -79,7 +94,7 @@ src/bond.*                @sjplimp
 src/comm*.*               @sjplimp
 src/compute.*             @sjplimp
 src/dihedral.*            @sjplimp
-src/domain.*              @sjplimp
+src/domain.*              @sjplimp @stanmoore1
 src/dump*.*               @sjplimp
 src/error.*               @sjplimp
 src/finish.*              @sjplimp
@@ -87,9 +102,11 @@ src/fix.*                 @sjplimp
 src/force.*               @sjplimp
 src/group.*               @sjplimp
 src/improper.*            @sjplimp
+src/info.*                @akohlmey
 src/kspace.*              @sjplimp
-src/lmptyp.h              @sjplimp
-src/library.*             @sjplimp
+src/lmptype.h             @sjplimp
+src/label_map.*           @jrgissing @akohlmey
+src/library.*             @sjplimp @akohlmey
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
@@ -97,12 +114,12 @@ src/modify.*              @sjplimp @stanmoore1
 src/molecule.*            @sjplimp
 src/my_page.h             @sjplimp
 src/my_pool_chunk.h       @sjplimp
-src/npair*.*              @sjplimp
-src/ntopo*.*              @sjplimp
-src/nstencil*.*           @sjplimp
-src/neighbor.*            @sjplimp
-src/nbin*.*               @sjplimp
-src/neigh_*.*             @sjplimp
+src/npair*.*              @sjplimp @jtclemm
+src/ntopo*.*              @sjplimp @jtclemm
+src/nstencil*.*           @sjplimp @jtclemm
+src/neighbor.*            @sjplimp @jtclemm
+src/nbin*.*               @sjplimp @jtclemm
+src/neigh_*.*             @sjplimp @jtclemm
 src/output.*              @sjplimp
 src/pair.*                @sjplimp
 src/rcb.*                 @sjplimp
@@ -135,6 +152,7 @@ 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
@@ -151,12 +169,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @rbberger
+cmake/*               @akohlmey
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @rbberger @ellio167
+cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @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://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)
+* [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)
 
 ## 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 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.
+> **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.
 
 ## 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://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
+to one of the [LAMMPS core developers](https://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.
 
 ### 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://lammps.sandia.gov/guidelines.html) to maximize your chances to receive a helpful response.
+You can post to list by sending your email to lammps-users at lists.sourceforge.net (no subscription required), but before posting, please read the [mailing list guidelines](https://www.lammps.org/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://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.
+While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://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.
 
 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://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)
+* [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)
 
 
 ## 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 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 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.
 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

@@ -0,0 +1,370 @@
+# LAMMPS Release Steps
+
+The following notes chronicle the current steps for preparing and
+publishing LAMMPS releases.  For definitions of LAMMPS versions and
+releases, 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.  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.  We currently use a mix of automated tests running on
+either Temple's Jenkins cluster or GitHub workflows.  Those include time
+consuming tests not run on pull requests.  If needed, a bug-fix 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 or update the 'develop' branch locally, pull the latest
+changes, merge them into 'release' with a fast forward(!) merge, and
+apply a suitable release tag (for historical reasons the tag starts with
+"patch_" followed by the date, and finally push everything back to
+GitHub.  There should be no commits made to 'release' but only
+fast forward merges.  Example:
+
+```
+git checkout develop
+git pull
+git checkout release
+git pull
+git merge --ff-only develop
+git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
+git push git@github.com:lammps/lammps.git --tags develop release
+```
+
+Applying this tag will trigger two actions on the Temple Jenkins cluster:
+- The online manual at https://docs.lammps.org/ will be updated to the
+  state of the 'release' branch.  Merges to the 'develop' branch will
+  trigger updating https://docs.lammps.org/latest/ so by reviewing the
+  version of the manual under the "latest" URL, it is possible to preview
+  what the updated release documentation will look like.
+- A downloadable tar archive of the LAMMPS distribution that includes the
+  html format documentation and a PDF of the manual will be created and
+  uploaded to the download server at https://download.lammps.org/tars
+  Note that the file is added, but the `index.html` file is not updated,
+  so it is not yet publicly visible.
+
+Go to https://github.com/lammps/lammps/releases and create a new (draft)
+release page with a summary of all the changes included and references
+to the pull requests they were merged from 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" drop-down 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.
+
+### Prepare pre-compiled packages, update packages to GitHub
+
+A suitable build environment is provided with the
+https://download.lammps.org/static/fedora41_musl_mingw.sif container
+image.  The corresponding container build definition file is maintained
+in the tools/singularity folder of the LAMMPS source distribution.
+
+#### Fully portable static Linux x86_64 non-MPI binaries
+
+The following commands use the Fedora container to build a fully static
+LAMMPS installation using a musl-libc cross-compiler, install it into a
+`lammps-static` folder, and create a tarball called
+`lammps-linux-x86_64-4Feb2025.tar.gz` (or using a corresponding date
+with a future release) from the `lammps-static` folder.
+
+``` sh
+rm -rf release-packages
+mkdir release-packages
+cd release-packages
+wget https://download.lammps.org/static/fedora41_musl_mingw.sif
+apptainer shell fedora41_musl_mingw.sif
+git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
+cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
+cmake --build build-release --target all
+cmake --build build-release --target install
+/usr/musl/bin/x86_64-linux-musl-strip -g lammps-static/bin/*
+tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
+exit # fedora 41 container
+cd ..
+```
+
+The resulting tar archive can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
+```
+
+#### Linux x86_64 Flatpak bundle with GUI included
+
+Make sure you have the `flatpak` and `flatpak-builder` packages
+installed locally (they require binaries that run with elevated
+privileges and thus cannot be used from the container) and build a
+LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
+with:
+
+``` sh
+cd release-packages
+flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+flatpak-builder  --force-clean --verbose --repo=$PWD/flatpak-repo --install-deps-from=flathub --state-dir=$PWD --user --ccache --default-branch=release flatpak-build lammps-release/tools/lammps-gui/org.lammps.lammps-gui.yml
+flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo ../LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak org.lammps.lammps-gui release
+cd ..
+```
+
+The resulting flatpak bundle file can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak
+```
+
+#### LAMMPS Source tarball
+
+The container for the static binary can also be used to prepare the source
+tarball including the HTML and PDF manual (this is currently done automatically
+when the releases is created and the tarball uploaded to https://download.lammps.org/tars/).
+The steps are as follows:
+
+``` sh
+cd release-packages
+apptainer shell fedora41_musl_mingw.sif
+cd lammps-release
+rm -f ../release.tar*
+git archive --output=../release.tar --prefix=lammps-4Feb2025/ HEAD
+cd doc
+make clean-all
+make html pdf
+tar -rf ../../release.tar --transform 's,^,lammps-4Feb2025/doc/,' html Manual.pdf
+gzip -9v ../../release.tar
+mv ../../release.tar.gz ../../lammps-src-4Feb2025.tar.gz
+exit # fedora41 container
+cd ..
+```
+
+The resulting source tarball can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 lammps-src-4Feb2025.tar.gz
+```
+
+#### Build Windows Installer Packages with MinGW Linux-to-Windows Cross-compiler
+
+The various Windows installer packages can also be built with
+apptainer container image.
+
+``` sh
+cd release-packages
+apptainer shell fedora41_musl_mingw.sif
+git clone --depth 10 https://github.com/lammps/lammps-packages.git lammps-packages
+cd lammps-packages/mingw-cross
+ln -sf ../../lammps-release lammps
+./buildall.sh release >& mk.log & less +F mk.log
+```
+
+The installer with the GUI included can be uploaded to the GitHub release page with:
+
+``` sh
+ln -sf LAMMPS-64bit-GUI-4Feb2025.exe LAMMPS-Win10-64bit-GUI-4Feb2025.exe
+gh release upload patch_4Feb2025 LAMMPS-Win10-64bit-GUI-4Feb2025.exe
+```
+
+The symbolic link is used to have a consistent naming scheme for the packages
+attached to the GitHub release page.
+
+#### Clean up:
+
+``` sh
+cd ..
+rm -r release-packages
+```
+
+#### Build Multi-arch App-bundle with GUI for macOS
+
+Building app-bundles for macOS is not as easily automated and portable
+as some of the other steps.  It requires a machine actually running
+macOS.  In that machine the Xcode compiler package needs to be
+installed. This also includes tools for building and manipulating disk
+images.  This compiler supports building executables for both, the
+x86_64 and the arm64 architectures.  This requires building with CMake
+and using the CMake settings:
+
+``` sh
+-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
+-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
+```
+
+This will add the compiler flags `-arch arm64 -arch x86_64
+-mmacosx-version-min=11.0` and thus produce object for both
+architectures and support for macOS versions back to version 11 (aka Big
+Sur).  With these settings the following libraries should be compiled
+and installed (e.g. to `$HOME/.local`) as static libraries only:
+- libomp taken from the LLVM/Clang source distribution (to support OpenMP)
+- jpeg
+- zlib
+- png
+- Qt (for LAMMPS-GUI)
+
+When configuring LAMMPS the `cmake/presets/clang.cmake` should be used
+and as many packages as possible enabled. For LAMMPS-GUI, MPI should be
+disabled with `-D BUILD_MPI=OFF` and LAMMPS-GUI enabled with 
+`-D BUILD_LAMMPS_GUI=ON`.  If the CMake configuration is successful,
+settings for building a macOS app-bundle are enabled and with `cmake
+--build build --target dmg` extra steps will be executed that will build
+a macOS application installer image under the name
+`LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg`
+
+The application image can be uploaded to the GitHub release page with:
+
+``` sh
+ln -sf LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
+gh release upload patch_4Feb2025 LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
+```
+
+The symbolic link is used to have a consistent naming scheme for the packages
+attached to the GitHub release page.
+
+We are currently building the application images on macOS 12 (aka Monterey).
+
+#### Build Linux x86_64 binary tarball with GUI on Ubuntu 20.04LTS
+
+While the flatpak Linux version uses portable runtime libraries provided
+by the flatpak environment, we also build regular Linux executables that
+use a wrapper script and matching shared libraries in a tarball.  To be
+compatible with many Linux distributions, one has to build this on a
+very old Linux distribution, since most Linux system libraries are
+usually backward compatible but not forward compatible.  This is
+currently done on an Ubuntu 20.04LTS system. Once LAMMPS moves to
+require CMake 3.20 and C++17, we will have to move to Ubuntu 22.04LTS.
+This installation (either on a real or a virtual machine) should have
+the packages installed that are indicated in
+`tools/singularity/ubuntu20.04.def` plus Qt version 5.x with development
+headers, so that LAMMPS-GUI can be compiled.
+
+Also the building of the binary tarball and setup of the bundled
+libraries and wrapper scripts is automated and can executed with `cmake
+--build build --target tgz`.  This should produce a file
+`LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz` which can be uploaded to the
+GitHub release page with:
+
+``` sh
+ln -sf LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
+gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
+```
+
+### Update download page on LAMMPS website
+
+Check out the LAMMPS website repo
+https://github.com/lammps/lammps-website.git and edit the file
+`src/download.txt` for the new release.  Test translation with `make
+html` and review `html/download.html` Then add and commit to git and
+push the changes to GitHub.  The Temple Jenkis cluster will
+automatically update https://www.lammps.org/download.html accordingly.
+
+Also notify Steve of the release so he can update `src/bug.txt` on the
+website from the available release notes.
+
+## 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
+
+After making a stable release, bugfixes from the 'develop' branch
+are selectively backported to the 'maintenance' branch.  This is
+done with "git cherry-pick \<commit hash\>' wherever possible.
+The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
+
+### Prerequesites
+
+When a sufficient number of bugfixes has accumulated or an urgent
+or important bugfix needs to be distributed a new stable update
+release is made.  To make this publicly visible a pull request
+is submitted that will merge 'maintenance' into 'stable'.  Before
+merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
+"#" indicating the update count (1, 2, and so on).
+Also draft suitable release notes under https://github.com/lammps/lammps/releases
+
+### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
+
+Do a fast-forward merge of 'maintenance' to 'stable' and then
+apply the stable\_DMmmYYYY\_update# tag and push branch and tag
+to GitHub. The corresponding pull request will be automatically
+closed.   Example:
+
+```
+git checkout maintenance
+git pull
+git checkout stable
+git pull
+git merge --ff-only maintenance
+git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
+git push git@github.com:lammps/lammps.git --tags maintenance stable
+```
+
+Associate draft release notes with new tag and publish as "latest release".
+
+On https://ci.lammps.org/ go to "dev", "stable" and manually execute
+the "update\_release" task. This will update https://docs.lammps.org/stable
+and prepare a stable tarball.
+
+### Build and upload binary packages and source tarball to GitHub
+
+The build procedure is the same as for the feature releases, only
+that packages are built from the 'stable' branch.

.github/workflows/check-cpp23.yml

@@ -0,0 +1,103 @@
+# GitHub action to build LAMMPS on Linux with gcc or clang and C++23
+name: "Check for C++23 Compatibility"
+
+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: Build with C++23 support enabled
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+    strategy:
+      max-parallel: 2
+      matrix:
+        idx: [ gcc, clang ]
+    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 \
+                                clang \
+                                libcurl4-openssl-dev \
+                                libeigen3-dev \
+                                libfftw3-dev \
+                                libomp-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: ${{ env.CCACHE_DIR }}
+        key: linux-cpp23-ccache-${{ matrix.idx }}-${{ github.sha }}
+        restore-keys: linux-cpp23-ccache-${{ matrix.idx }}
+
+    - 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 \
+              -C cmake/presets/${{ matrix.idx }}.cmake \
+              -D CMAKE_CXX_STANDARD=23 \
+              -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 FFT=KISS \
+              -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

@@ -0,0 +1,89 @@
+# 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=on \
+              -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@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       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@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/compile-msvc.yml

@@ -1,5 +1,5 @@
-# GitHub action to build LAMMPS on Windows with Visual C++
-name: "Native Windows Compilation and Unit Tests"
+# GitHub action to test LAMMPS on Windows with Visual C++
+name: "Windows Unit Tests"
 
 on:
   push:
@@ -11,48 +11,59 @@ 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@v3
+      uses: actions/checkout@v4
       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@v4
+      uses: actions/setup-python@v5
       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
-        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
+        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
 
     - name: Run LAMMPS executable
-      shell: bash
       run: |
-        ./build/Release/lmp.exe -h
-        ./build/Release/lmp.exe -in bench/in.lj
+        build\lmp.exe -h
+        build\lmp.exe -in bench\in.lj
 
     - name: Run Unit Tests
       working-directory: build
-      shell: bash
-      run: ctest -V -C Release -E FixTimestep:python_move_nve
+      run: ctest -V -E FixTimestep:python_move_nve

.github/workflows/coverity.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
@@ -25,7 +25,7 @@ jobs:
 
     - name: Cache Coverity
       id: cache-coverity
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ./download/
         key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
@@ -59,25 +59,20 @@ 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

@@ -0,0 +1,109 @@
+# 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

@@ -0,0 +1,126 @@
+# 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

@@ -0,0 +1,53 @@
+# 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

@@ -0,0 +1,118 @@
+# 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

@@ -0,0 +1,38 @@
+# 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
+         make check-fmtlib

.github/workflows/unittest-arm64.yml

@@ -0,0 +1,81 @@
+# GitHub action to build LAMMPS on Linux with ARM64 and run standard unit tests
+name: "Unittest for Linux on ARM64"
+
+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: Linux ARM64 Unit Test
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-22.04-arm
+    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 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 -LE unstable

.github/workflows/unittest-linux.yml

@@ -0,0 +1,86 @@
+# 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

@@ -11,17 +11,21 @@ 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-latest
+    runs-on: macos-13
     env:
       CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
@@ -32,7 +36,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}
@@ -43,6 +47,8 @@ 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/
-/Testing
+CMakeCache.txt
+CMakeFiles
 /Makefile
-/Testing
-/cmake_install.cmake
+Testing
+Temporary
+cmake_install.cmake
 /lmp
 out/Debug
 out/RelWithDebInfo
@@ -60,3 +60,4 @@ src/Makefile.package.settings-e
 /cmake/build/x64-Debug-Clang
 /install/x64-GUI-MSVC
 /install
+.Rhistory

README

@@ -23,17 +23,21 @@ more information about the code and its uses.
 The LAMMPS distribution includes the following files and directories:
 
 README                     this file
-LICENSE                    the GNU General Public License (GPL)
-bench                      benchmark problems
+LICENSE                    the GNU General Public License (GPLv2)
+CITATION.cff               Citation information for LAMMPS in CFF format
+bench                      benchmark inputs
 cmake                      CMake build files
 doc                        documentation
-examples                   simple test problems
-fortran                    Fortran wrapper for LAMMPS
+examples                   example inputs for many LAMMPS commands
+fortran                    Fortran 2003 module for LAMMPS
 lib                        additional provided or external libraries
 potentials                 interatomic potential files
-python                     Python wrappers for LAMMPS
+python                     Python module for LAMMPS
 src                        source files
+third_party                Copies of thirdparty software bundled with LAMMPS
 tools                      pre- and post-processing tools
+unittest                   test programs for use with CTest
+.github                    Git and GitHub related files and tools
 
 Point your browser at any of these files to get started:
 
@@ -42,6 +46,8 @@ https://docs.lammps.org/Intro.html          hi-level introduction
 https://docs.lammps.org/Build.html          how to build LAMMPS
 https://docs.lammps.org/Run_head.html       how to run LAMMPS
 https://docs.lammps.org/Commands_all.html   Table of available commands
+https://docs.lammps.org/Howto.html          Short tutorials and HowTo discussions
+https://docs.lammps.org/Errors.html         How to interpret and debug errors
 https://docs.lammps.org/Library.html        LAMMPS library interfaces
 https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
 https://docs.lammps.org/Developer.html      LAMMPS developer info

cmake/CMakeLists.txt

@@ -1,9 +1,13 @@
+# -*- CMake -*- master configuration file for building LAMMPS
 ########################################
 # CMake build system
 # This file is part of LAMMPS
-# Created by Christoph Junghans and Richard Berger
-cmake_minimum_required(VERSION 3.10)
+cmake_minimum_required(VERSION 3.16)
 ########################################
+# initialize version variables with project command
+if(POLICY CMP0048)
+  cmake_policy(SET CMP0048 NEW)
+endif()
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -12,8 +16,8 @@ endif()
 if(POLICY CMP0075)
   cmake_policy(SET CMP0075 NEW)
 endif()
-# set policy to silence warnings about missing executable permissions in
-# pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
+# 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
 if(POLICY CMP0109)
   cmake_policy(SET CMP0109 OLD)
 endif()
@@ -21,19 +25,17 @@ 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)
+project(lammps
+        DESCRIPTION "The LAMMPS Molecular Dynamics Simulator"
+        HOMEPAGE_URL "https://www.lammps.org"
+        LANGUAGES CXX C)
 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
@@ -46,6 +48,7 @@ set(LAMMPS_DOC_DIR        ${LAMMPS_DIR}/doc)
 set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
+set(LAMMPS_THIRDPARTY_DIR ${LAMMPS_DIR}/third_party)
 
 set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
 set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
@@ -107,44 +110,55 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
       set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
     endif()
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /QxCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /QxHost")
     endif()
   else()
     set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
 if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "PGI"))
-  set(CMAKE_TUNE_DEFAULT "-Minform=severe")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Minform=severe")
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT
+    ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
+    OR (CMAKE_CXX_COMPILER_ID STREQUAL "XLClang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")))
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
+# we *require* C++11 without extensions but prefer C++17.
+# Kokkos requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
-  set(CMAKE_CXX_STANDARD 11)
+  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
+    set(CMAKE_CXX_STANDARD 17)
+  else()
+    set(CMAKE_CXX_STANDARD 11)
+  endif()
 endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
-if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
-  set(CMAKE_CXX_STANDARD 14)
+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)
 endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@@ -155,30 +169,61 @@ 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)
 endif()
 
+# do not include the (obsolete) MPI C++ bindings which makes for leaner object files
+# and avoids namespace conflicts. Put this early to increase its visbility.
+set(MPI_CXX_SKIP_MPICXX TRUE CACHE BOOL "Skip MPI C++ Bindings" FORCE)
+
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# 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)
-  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
-  else()
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
-  endif()
+# backward compatibility with older LAMMPS documentation
+if (PYTHON_EXECUTABLE)
   set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+# set path to python interpreter and thus enforcing python version when
+# in a virtual environment and Python_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
+  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+  else()
+    set(Python_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+  endif()
   message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
-    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
+    "   Setting Python interpreter to: ${Python_EXECUTABLE}")
+endif()
+
+find_package(Python COMPONENTS Interpreter QUIET)
+# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
+if(Python_VERSION VERSION_LESS 3.6)
+  message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
 endif()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@@ -191,20 +236,10 @@ 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,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()
-
-include(GNUInstallDirs)
-file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
+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})
 
@@ -216,6 +251,10 @@ 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)
@@ -223,6 +262,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD
@@ -246,6 +286,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -271,15 +312,14 @@ set(STANDARD_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
+  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-POD
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   ORIENT
   PERI
@@ -295,6 +335,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -318,12 +359,12 @@ endforeach()
 # packages with special compiler needs or external libs
 ######################################################
 target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}>)
+target_include_directories(lammps PUBLIC $<BUILD_INTERFACE:${LAMMPS_THIRDPARTY_DIR}>)
 
 if(PKG_ADIOS)
   # The search for ADIOS2 must come before MPI because
   # it includes its own MPI search with the latest FindMPI.cmake
   # script that defines the MPI::MPI_C target
-  enable_language(C)
   find_package(ADIOS2 REQUIRED)
   if(BUILD_MPI)
     if(NOT ADIOS2_HAVE_MPI)
@@ -338,21 +379,18 @@ if(PKG_ADIOS)
 endif()
 
 if(NOT CMAKE_CROSSCOMPILING)
-  find_package(MPI QUIET)
+  find_package(MPI QUIET COMPONENTS CXX)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
 endif()
 
 if(BUILD_MPI)
-  # do not include the (obsolete) MPI C++ bindings which makes
-  # for leaner object files and avoids namespace conflicts
-  set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
     include(MPI4WIN)
   else()
-    find_package(MPI REQUIRED)
+    find_package(MPI REQUIRED COMPONENTS CXX)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps PRIVATE -DLAMMPS_LONGLONG_TO_LONG)
@@ -366,8 +404,8 @@ else()
   target_link_libraries(lammps PUBLIC mpi_stubs)
 endif()
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
@@ -385,15 +423,22 @@ 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)" ${ENABLE_TESTING})
-if(LAMMPS_EXCEPTIONS)
-  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by CMake version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    target_compile_definitions(lammps PRIVATE -DFMT_STATIC_THOUSANDS_SEPARATOR)
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    target_compile_definitions(lammps PRIVATE -DFMT_STATIC_THOUSANDS_SEPARATOR)
+  endif()
 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)
@@ -404,6 +449,9 @@ 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)
+pkg_depends(APIP ML-PACE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -429,6 +477,7 @@ 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.
@@ -439,16 +488,42 @@ 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 "${CMAKE_SHARED_LINKER_FLAGS} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS "${CMAKE_STATIC_LINKER_FLAGS} -fopenmp")
+    endif()
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+      set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS "${CMAKE_STATIC_LINKER_FLAGS} -fopenmp")
+    endif()
+  endif()
 endif()
 
-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)
+# 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 (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>")
@@ -466,12 +541,7 @@ option(WITH_JPEG "Enable JPEG support" ${JPEG_FOUND})
 if(WITH_JPEG)
   find_package(JPEG REQUIRED)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_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()
+  target_link_libraries(lammps PRIVATE JPEG::JPEG)
 endif()
 
 find_package(PNG QUIET)
@@ -521,12 +591,22 @@ 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 MSCG COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
   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)
@@ -534,24 +614,15 @@ if(WITH_SWIG)
   add_subdirectory(${LAMMPS_SWIG_DIR} swig)
 endif()
 
-set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
-separate_arguments(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 ${_FLAG})
-  endif()
-endforeach()
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
-foreach(HEADER cmath)
-  check_include_file_cxx(${HEADER} FOUND_${HEADER})
-  if(NOT FOUND_${HEADER})
-    message(FATAL_ERROR "Could not find needed header - ${HEADER}")
-  endif(NOT FOUND_${HEADER})
-endforeach(HEADER)
+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()
 
 # 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")
@@ -583,8 +654,8 @@ 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})
@@ -600,19 +671,12 @@ 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})
@@ -626,7 +690,7 @@ 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}${LAMMPS_MACHINE})
@@ -670,7 +734,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -778,9 +842,15 @@ 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})
+  install(TARGETS lammps EXPORT LAMMPS_Targets
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   if(NOT BUILD_MPI)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets
+            LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   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)
@@ -821,20 +891,8 @@ install(
 # This is primarily for people that only want to use the Python wrapper.
 ###############################################################################
 if(BUILD_SHARED_LIBS)
-  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()
+  # backward compatibility
+  find_package(Python COMPONENTS Interpreter)
   if(BUILD_IS_MULTI_CONFIG)
     set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
   else()
@@ -860,7 +918,7 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 8.0)
+find_package(ClangFormat 11.0 QUIET)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src
@@ -893,13 +951,23 @@ 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}
+   LAMMPS Version:   ${PROJECT_VERSION} ${GIT_DESCRIBE}
    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
 ###############################################################################
@@ -920,8 +988,12 @@ 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}")
@@ -940,14 +1012,15 @@ 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}")
-if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-  get_target_property(OPTIONS lammps LINK_OPTIONS)
-  if(OPTIONS)
-    message(STATUS "Linker options:   ${OPTIONS}")
-  endif()
+get_target_property(OPTIONS lammps LINK_OPTIONS)
+if(OPTIONS)
+  message(STATUS "Linker options:   ${OPTIONS}")
 endif()
 if(CMAKE_EXE_LINKER_FLAGS)
   message(STATUS "Executable linker flags: ${CMAKE_EXE_LINKER_FLAGS}")
@@ -989,34 +1062,37 @@ if(PKG_KOKKOS)
   endif()
 endif()
 if(PKG_KSPACE)
-  message(STATUS "<<< FFT settings >>>
+  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 >>>
 -- 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")
+    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")
   endif()
   if(PKG_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()
+    message(STATUS "Kokkos FFT: ${FFT_KOKKOS}")
   endif()
 endif()
 if(BUILD_DOC)
@@ -1025,8 +1101,16 @@ endif()
 if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
-if(BUILD_LAMMPS_SHELL)
-  message(STATUS "<<< Building LAMMPS Shell >>>")
+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()
 endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")

cmake/Modules/CodeCoverage.cmake

@@ -7,76 +7,76 @@
 # For Python coverage the coverage package needs to be installed
 ###############################################################################
 if(ENABLE_COVERAGE)
-    find_program(GCOVR_BINARY gcovr)
-    find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
+  find_program(GCOVR_BINARY gcovr)
+  find_package_handle_standard_args(GCOVR DEFAULT_MSG GCOVR_BINARY)
 
-    find_program(COVERAGE_BINARY coverage)
-    find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
+  find_program(COVERAGE_BINARY coverage)
+  find_package_handle_standard_args(COVERAGE DEFAULT_MSG COVERAGE_BINARY)
 
-    if(GCOVR_FOUND)
-        get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
+  if(GCOVR_FOUND)
+    get_filename_component(ABSOLUTE_LAMMPS_SOURCE_DIR ${LAMMPS_SOURCE_DIR} ABSOLUTE)
 
-        add_custom_target(
-            gen_coverage_xml
-            COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating XML coverage report..."
-        )
+    add_custom_target(
+        gen_coverage_xml
+        COMMAND ${GCOVR_BINARY} -s -x -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o coverage.xml
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Generating XML coverage report..."
+    )
 
-        set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
+    set(COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/coverage_html)
 
-        add_custom_target(coverage_html_folder
-            COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
+    add_custom_target(coverage_html_folder
+        COMMAND ${CMAKE_COMMAND} -E make_directory ${COVERAGE_HTML_DIR})
 
-        add_custom_target(
-            gen_coverage_html
-            COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Generating HTML coverage report..."
-        )
-        add_dependencies(gen_coverage_html coverage_html_folder)
+    add_custom_target(
+        gen_coverage_html
+        COMMAND ${GCOVR_BINARY} -s  --html --html-details -r ${ABSOLUTE_LAMMPS_SOURCE_DIR} --object-directory=${CMAKE_BINARY_DIR} -o ${COVERAGE_HTML_DIR}/index.html
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Generating HTML coverage report..."
+    )
+    add_dependencies(gen_coverage_html coverage_html_folder)
 
-        add_custom_target(clean_coverage_html
-            ${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
-            COMMENT "Deleting HTML coverage report..."
-        )
+    add_custom_target(clean_coverage_html
+        ${CMAKE_COMMAND} -E remove_directory ${COVERAGE_HTML_DIR}
+        COMMENT "Deleting HTML coverage report..."
+    )
 
-        add_custom_target(reset_coverage
-            ${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
-                              */*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
-                              */*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
-                              */*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
-            WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
-            COMMENT "Deleting coverage data files..."
-        )
-        add_dependencies(reset_coverage clean_coverage_html)
-    endif()
+    add_custom_target(reset_coverage
+        ${CMAKE_COMMAND} -E remove -f */*.gcda */*/*.gcda */*/*/*.gcda
+                          */*/*/*/*.gcda */*/*/*/*/*.gcda */*/*/*/*/*/*.gcda
+                          */*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*.gcda
+                          */*/*/*/*/*/*/*/*/*.gcda */*/*/*/*/*/*/*/*/*/*.gcda
+        WORKIND_DIRECTORY ${CMAKE_BINARY_DIR}
+        COMMENT "Deleting coverage data files..."
+    )
+    add_dependencies(reset_coverage clean_coverage_html)
+  endif()
 
-    if(COVERAGE_FOUND)
-        set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
-        configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
+  if(COVERAGE_FOUND)
+    set(PYTHON_COVERAGE_HTML_DIR ${CMAKE_BINARY_DIR}/python_coverage_html)
+    configure_file(.coveragerc.in ${CMAKE_BINARY_DIR}/.coveragerc @ONLY)
 
-        add_custom_command(
-            OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
-            COMMAND ${COVERAGE_BINARY} combine
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
-            COMMENT "Combine Python coverage files..."
-        )
+    add_custom_command(
+        OUTPUT ${CMAKE_BINARY_DIR}/unittest/python/.coverage
+        COMMAND ${COVERAGE_BINARY} combine
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+        COMMENT "Combine Python coverage files..."
+    )
 
-        add_custom_target(
-            gen_python_coverage_html
-            COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
-            COMMENT "Generating HTML Python coverage report..."
-        )
+    add_custom_target(
+        gen_python_coverage_html
+        COMMAND ${COVERAGE_BINARY} html --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -d ${PYTHON_COVERAGE_HTML_DIR}
+        DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+        COMMENT "Generating HTML Python coverage report..."
+    )
 
-        add_custom_target(
-            gen_python_coverage_xml
-            COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
-            DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
-            COMMENT "Generating XML Python coverage report..."
-        )
-    endif()
+    add_custom_target(
+        gen_python_coverage_xml
+        COMMAND ${COVERAGE_BINARY} xml --rcfile=${CMAKE_BINARY_DIR}/.coveragerc -o ${CMAKE_BINARY_DIR}/python_coverage.xml
+        DEPENDS ${CMAKE_BINARY_DIR}/unittest/python/.coverage ${CMAKE_BINARY_DIR}/.coveragerc
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/unittest/python
+        COMMENT "Generating XML Python coverage report..."
+    )
+  endif()
 endif()

cmake/Modules/CodingStandard.cmake

@@ -1,48 +1,39 @@
-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)
+# use default (or custom) Python executable.
+# Python version check is in main CMakeLists.txt file
+if(Python_EXECUTABLE)
+  set(Python3_EXECUTABLE ${Python_EXECUTABLE})
 endif()
+find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
-        add_custom_target(
-          check-whitespace
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for whitespace errors")
-        add_custom_target(
-          check-homepage
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for homepage URL errors")
-        add_custom_target(
-          check-permissions
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for permission errors")
-        add_custom_target(
-          fix-whitespace
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix whitespace errors")
-        add_custom_target(
-          fix-homepage
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix homepage URL errors")
-        add_custom_target(
-          fix-permissions
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix permission errors")
-    endif()
+  add_custom_target(
+    check-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for whitespace errors")
+  add_custom_target(
+    check-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for homepage URL errors")
+  add_custom_target(
+    check-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for permission errors")
+  add_custom_target(
+    fix-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix whitespace errors")
+  add_custom_target(
+    fix-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix homepage URL errors")
+  add_custom_target(
+    fix-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix permission errors")
 endif()

cmake/Modules/DetectHIPInstallation.cmake

@@ -1,11 +1,3 @@
-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")
@@ -13,4 +5,4 @@ if(NOT DEFINED ROCM_PATH)
         set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
     endif()
 endif()
-list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

cmake/Modules/Documentation.cmake

@@ -4,33 +4,21 @@
 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
-  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)
+  # 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 LAMMPS 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)
-
-
-  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)
+  file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
   set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
   set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
@@ -50,17 +38,35 @@ if(BUILD_DOC)
   # configure paths in conf.py, since relative paths change when file is copied
   configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
-  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
-  )
+  if(BUILD_DOC_VENV)
+    add_custom_command(
+      OUTPUT docenv
+      COMMAND ${VIRTUALENV} docenv
+    )
 
-  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")
+    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()
+
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.2.2.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "08dd6ef33ca08870220d9aade2a62845" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
   GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
 
@@ -80,7 +86,7 @@ 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()
 
@@ -103,8 +109,9 @@ if(BUILD_DOC)
   endif()
   add_custom_command(
     OUTPUT 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
+    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
     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")
+    "${CMAKE_BINARY_DIR}/_deps/${target}-build" EXCLUDE_FROM_ALL)
 endfunction(ExternalCMakeProject)

cmake/Modules/FindClangFormat.cmake

@@ -1,5 +1,10 @@
 # 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
@@ -19,7 +24,7 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
+  if(clang_format_version MATCHES "^(Ubuntu |Debian |)clang-format version .*")
     # Arch Linux output:
     # clang-format version 10.0.0
     #
@@ -32,9 +37,15 @@ 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 |)clang-format version ([0-9.]+).*"
+    string(REGEX REPLACE "^(Ubuntu |Debian |)clang-format version ([0-9.]+).*"
                          "\\2"
                          ClangFormat_VERSION
                          "${clang_format_version}")

cmake/Modules/FindCythonize.cmake

@@ -7,15 +7,7 @@
 # adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
 #=============================================================================
 
-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()
+find_package(Python 3.6 COMPONENTS Interpreter QUIET)
 
 # Use the Cython executable that lives next to the Python executable
 # if it is a local installation.

cmake/Modules/FindSphinx.cmake

@@ -0,0 +1,29 @@
+# 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

@@ -28,15 +28,32 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    if(LAMMPS_EXCEPTIONS)
-      add_compile_options(/EHsc)
-    endif()
+    add_compile_options(/wd4250)
+    add_compile_options(/EHsc)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-# C++11 is required
-set(CMAKE_CXX_STANDARD 11)
+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()
+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)
+endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 # Need -restrict with Intel compilers
@@ -45,6 +62,9 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
 endif()
 set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
 
+# skip over obsolete MPI-2 C++ bindings
+set(MPI_CXX_SKIP_MPICXX TRUE)
+
 #######
 # helper functions from LAMMPSUtils.cmake
 function(validate_option name values)
@@ -65,7 +85,7 @@ 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})
@@ -111,8 +131,7 @@ endif()
 ################################################################################
 # MPI configuration
 if(NOT CMAKE_CROSSCOMPILING)
-  set(MPI_CXX_SKIP_MPICXX TRUE)
-  find_package(MPI QUIET)
+  find_package(MPI QUIET COMPONENTS CXX)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()
   option(BUILD_MPI "Build MPI version" OFF)
@@ -124,78 +143,38 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure MinGW compatible MPICH development files for Windows
-    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
-    if(USE_MSMPI)
-      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-      set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+    message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+    set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
 
-      include(ExternalProject)
-      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-        ExternalProject_Add(mpi4win_build
-          URL     ${MPICH2_WIN64_DEVEL_URL}
-          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
-      else()
-        message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
-      endif()
-
-      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-      set_target_properties(MPI::MPI_CXX PROPERTIES
-        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-      add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-      # set variables for status reporting at the end of CMake run
-      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
+    include(ExternalProject)
+    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN64_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
     else()
-      # Download and configure custom MPICH files for Windows
-      message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-      set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-
-      include(ExternalProject)
-      if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-        ExternalProject_Add(mpi4win_build
-          URL     ${MPICH2_WIN64_DEVEL_URL}
-          URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
-      else()
-        ExternalProject_Add(mpi4win_build
-          URL     ${MPICH2_WIN32_DEVEL_URL}
-          URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
-      endif()
-
-      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-      set_target_properties(MPI::MPI_CXX PROPERTIES
-        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-        INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-        INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-      add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-      # set variables for status reporting at the end of CMake run
-      set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-      set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-      set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
+      message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
     endif()
+
+    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+    set_target_properties(MPI::MPI_CXX PROPERTIES
+      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
+    add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+    # set variables for status reporting at the end of CMake run
+    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
+    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
   else()
-    find_package(MPI REQUIRED)
+    find_package(MPI REQUIRED COMPONENTS CXX)
     option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
     if(LAMMPS_LONGLONG_TO_LONG)
       target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
@@ -243,8 +222,8 @@ endif()
 
 ################
 # integer size selection
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)

cmake/Modules/LAMMPSUtils.cmake

@@ -30,9 +30,15 @@ function(check_omp_h_include)
   if(OpenMP_CXX_FOUND)
     set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
-    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    separate_arguments(CMAKE_REQUIRED_LINK_OPTIONS NATIVE_COMMAND ${OpenMP_CXX_FLAGS}) # needs to be a list
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-    check_include_file_cxx(omp.h _have_omp_h)
+    # 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()
   else()
     set(_have_omp_h FALSE)
   endif()
@@ -41,7 +47,7 @@ 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 ${_dirs})
@@ -69,31 +75,43 @@ function(get_lammps_version version_header variable)
     list(FIND MONTHS "${month}" month)
     string(LENGTH ${day} day_length)
     string(LENGTH ${month} month_length)
-    if(day_length EQUAL 1)
-        set(day "0${day}")
+    # no leading zero needed for new version string with dots
+    # if(day_length EQUAL 1)
+    #   set(day "0${day}")
+    # endif()
+    # if(month_length EQUAL 1)
+    #   set(month "0${month}")
+    #endif()
+    file(STRINGS ${version_header} line REGEX LAMMPS_UPDATE)
+    string(REGEX REPLACE "#define LAMMPS_UPDATE \"Update ([0-9]+)\"" "\\1" tweak "${line}")
+    if (line MATCHES "#define LAMMPS_UPDATE \"(Maintenance|Development)\"")
+      set(tweak "99")
     endif()
-    if(month_length EQUAL 1)
-        set(month "0${month}")
+    if(NOT tweak)
+      set(tweak "0")
     endif()
-    set(${variable} "${year}${month}${day}" PARENT_SCOPE)
+    # new version string with dots
+    set(${variable} "${year}.${month}.${day}.${tweak}" PARENT_SCOPE)
+    # old version string without dots
+    # set(${variable} "${year}${month}${day}" PARENT_SCOPE)
 endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${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 ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
+    list(APPEND SRC_AUTOGEN_FILES ${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(s) generated by the make-based build system\n"
-                              "\n"
-                              "Please run\n"
-                              "make -C ${source_dir} purge\n"
-                              "to remove\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"
+                            "########################################################################")
       endif()
     endforeach()
 endfunction()

cmake/Modules/MPI4WIN.cmake

@@ -1,74 +1,31 @@
-# Download and configure MinGW compatible MPICH development files for Windows
-option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+# set-up MS-MPI library for Windows with MinGW compatibility
+message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
+set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
+set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
+mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
 
-if(USE_MSMPI)
-  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-  set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-
-  include(ExternalProject)
-  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-    ExternalProject_Add(mpi4win_build
-      URL     ${MPICH2_WIN64_DEVEL_URL}
-      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
-  else()
-    message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
-  endif()
-
-  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-  set_target_properties(MPI::MPI_CXX PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-  add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-  # set variables for status reporting at the end of CMake run
-  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")
+include(ExternalProject)
+if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+  ExternalProject_Add(mpi4win_build
+    URL     ${MPICH2_WIN64_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
 else()
-  message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
-  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-  set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
-  set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-  set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
-  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-  mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
-  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-  mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
-
-  include(ExternalProject)
-  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-    ExternalProject_Add(mpi4win_build
-      URL     ${MPICH2_WIN64_DEVEL_URL}
-      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
-  else()
-    ExternalProject_Add(mpi4win_build
-      URL     ${MPICH2_WIN32_DEVEL_URL}
-      URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
-      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
-  endif()
-
-  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-  set_target_properties(MPI::MPI_CXX PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
-    INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
-    INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-  add_dependencies(MPI::MPI_CXX mpi4win_build)
-
-  # set variables for status reporting at the end of CMake run
-  set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
-  set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
-  set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
+  message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
 endif()
+
+ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+set_target_properties(MPI::MPI_CXX PROPERTIES
+  IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
+  INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+  INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
+add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+# set variables for status reporting at the end of CMake run
+set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX=1")
+set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmsmpi.a")

cmake/Modules/OpenCLLoader.cmake

@@ -1,6 +1,6 @@
 message(STATUS "Downloading and building OpenCL loader library")
-set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2022.01.04.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-set(OPENCL_LOADER_MD5 "8d3a801e87a2c6653bf0e27707063914" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+set(OPENCL_LOADER_URL "${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")
 mark_as_advanced(OPENCL_LOADER_URL)
 mark_as_advanced(OPENCL_LOADER_MD5)
 
@@ -8,4 +8,3 @@ 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)
 
@@ -14,16 +14,22 @@ endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
 target_compile_definitions(colvars PRIVATE -DCOLVARS_LAMMPS)
-separate_arguments(CMAKE_TUNE_FLAGS)
-foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  target_compile_options(colvars PRIVATE ${_FLAG})
-endforeach()
 set_target_properties(colvars PROPERTIES OUTPUT_NAME lammps_colvars${LAMMPS_MACHINE})
 target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 # The line below is needed to locate math_eigen_impl.h
 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(BUILD_MPI)
+  target_link_libraries(colvars PUBLIC MPI::MPI_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

@@ -0,0 +1,9 @@
+# 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

@@ -0,0 +1,18 @@
+# the geturl command needs libcurl
+
+find_package(CURL QUIET)
+option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
+if(WITH_CURL)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
+
+  # need to use pkgconfig for fully static bins to find custom static libs
+  if (CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
+    include(FindPkgConfig)
+    pkg_check_modules(CURL IMPORTED_TARGET libcurl libssl libcrypto)
+    target_link_libraries(lammps PUBLIC PkgConfig::CURL)
+  else()
+    find_package(CURL REQUIRED)
+    target_link_libraries(lammps PRIVATE CURL::libcurl)
+  endif()
+endif()
+

cmake/Modules/Packages/GPU.cmake

@@ -1,3 +1,10 @@
+
+# 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
@@ -39,7 +46,7 @@ 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")
@@ -70,7 +77,7 @@ 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"
@@ -80,15 +87,15 @@ 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
@@ -151,10 +158,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -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})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -allow-unsupported-compiler -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)
@@ -182,7 +189,7 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
+  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR -DLAMMPS_${LAMMPS_SIZES})
   target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
@@ -205,7 +212,7 @@ 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
@@ -335,7 +342,7 @@ 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 "")
@@ -482,7 +489,7 @@ else()
   target_link_libraries(gpu PRIVATE mpi_stubs)
 endif()
 
-target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
+target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
 target_sources(lammps PRIVATE ${GPU_SOURCES})
 target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

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 REQUIRED)
+find_package(HDF5 COMPONENTS C 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

@@ -72,6 +72,10 @@ if(INTEL_ARCH STREQUAL "KNL")
   if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     message(FATAL_ERROR "Must use Intel compiler with INTEL for KNL architecture")
   endif()
+  message(WARNING, "Support for Intel Xeon Phi accelerators and Knight's Landing CPUs "
+          "will be removed from LAMMPS in Summer 2025 due to lack of available machines "
+          "in labs and HPC centers and removed support in recent compilers "
+          "Please contact developers@lammps.org if you have any concerns about this step.")
   set(CMAKE_EXE_LINKER_FLAGS  "${CMAKE_EXE_LINKER_FLAGS} -xHost -qopenmp -qoffload")
   set(MIC_OPTIONS "-qoffload-option,mic,compiler,\"-fp-model fast=2 -mGLOB_default_function_attrs=\\\"gather_scatter_loop_unroll=4\\\"\"")
   target_compile_options(lammps PRIVATE -xMIC-AVX512 -qoffload -fno-alias -ansi-alias -restrict -qoverride-limits ${MIC_OPTIONS})
@@ -111,6 +115,9 @@ 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

@@ -1,12 +1,7 @@
 set(KIM-API_MIN_VERSION 2.1.3)
 find_package(CURL)
 if(CURL_FOUND)
-  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_link_libraries(lammps PRIVATE CURL::libcurl)
   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

@@ -1,25 +1,33 @@
 ########################################################################
-# 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")
+# 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")
 endif()
 
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
-if(Kokkos_ENABLE_CUDA)
-  message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
-  set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
+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)
 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")
-  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()
+
+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)
   endif()
 endif()
 ########################################################################
@@ -49,8 +57,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "34d7860d548c06a4040236d959c9f99a" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.02.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "14c02fac07bfcec48a1654f88ddee9c6" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -75,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.02 REQUIRED CONFIG)
+  find_package(Kokkos 4.6.02 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -130,19 +138,45 @@ 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 ${FFT_KOKKOS} FFT_KOKKOS)
+
   if(Kokkos_ENABLE_CUDA)
-    if(NOT (FFT STREQUAL "KISS"))
-      target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
-      target_link_libraries(lammps PRIVATE cufft)
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "CUFFT")))
+      message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
+    elseif(FFT_KOKKOS STREQUAL "CUFFT")
+      find_package(CUDAToolkit REQUIRED)
+      target_link_libraries(lammps PRIVATE CUDA::cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
-    if(NOT (FFT STREQUAL "KISS"))
+    if(NOT ((FFT_KOKKOS STREQUAL "KISS") OR (FFT_KOKKOS STREQUAL "HIPFFT")))
+      message(FATAL_ERROR "The HIP backend of Kokkos requires either KISS FFT or HIPFFT.")
+    elseif(FFT_KOKKOS STREQUAL "KISS")
+      message(WARNING "Using KISS FFT with the HIP backend of Kokkos may be sub-optimal.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "HIPFFT")
       include(DetectHIPInstallation)
       find_package(hipfft REQUIRED)
-      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
       target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
+  elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
+    if(NOT Kokkos_ENABLE_SYCL)
+      message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
+    endif()
+    find_package(MKL REQUIRED)
+    target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
+  elseif(FFT_KOKKOS STREQUAL "MKL")
+    find_package(MKL REQUIRED)
+  elseif(FFT_KOKKOS STREQUAL "NVPL")
+      find_package(nvpl_fft REQUIRED)
+      target_link_libraries(lammps PRIVATE nvpl::fftw)
   endif()
+  target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS})
 endif()
 
 if(PKG_ML-IAP)
@@ -155,7 +189,7 @@ 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)
+set(FFT_VALUES KISS FFTW3 MKL NVPL)
 set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
 validate_option(FFT FFT_VALUES)
 string(TOUPPER ${FFT} FFT)
@@ -41,11 +41,70 @@ 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/MC.cmake

@@ -7,3 +7,23 @@ if(NOT PKG_MANYBODY)
   list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
   set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
 endif()
+
+# fix hmc may only be installed if also fix rigid/small from RIGID is installed
+if(NOT PKG_RIGID)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_hmc.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_hmc.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()
+
+# fix neighbor/swap may only be installed if also the VORONOI package is installed
+if(NOT PKG_VORONOI)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_neighbor_swap.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

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/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
+  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")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   GetFallbackURL(MDI_URL MDI_FALLBACK)
@@ -26,29 +26,9 @@ if(DOWNLOAD_MDI)
 
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    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()
+  find_package(Python QUIET COMPONENTS Development)
+  if(Python_Development_FOUND)
+    set(MDI_USE_PYTHON_PLUGINS ON)
   endif()
   # python plugins are not supported and thus must be always off on Windows
   if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
@@ -102,13 +82,9 @@ if(DOWNLOAD_MDI)
   # if compiling with python plugins we need
   # to add python libraries as dependency.
   if(MDI_USE_PYTHON_PLUGINS)
-    if(CMAKE_VERSION VERSION_LESS 3.12)
-      list(APPEND MDI_DEP_LIBS ${PYTHON_LIBRARIES})
-    else()
-      list(APPEND MDI_DEP_LIBS Python::Python)
-    endif()
-
+    list(APPEND MDI_DEP_LIBS Python::Python)
   endif()
+
   # need to add support for dlopen/dlsym, except when compiling for Windows.
   if(NOT (CMAKE_SYSTEM_NAME STREQUAL "Windows"))
     list(APPEND MDI_DEP_LIBS "${CMAKE_DL_LIBS}")

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,12 +2,7 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize 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()
+  find_package(Python COMPONENTS NumPy QUIET)
   if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
@@ -15,26 +10,24 @@ 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)
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
-    find_package(Python COMPONENTS NumPy REQUIRED)
-  endif()
+  find_package(Python COMPONENTS NumPy REQUIRED)
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
-      message(FATAL_ERROR "Python support in 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()
+  # Python version check is in main CMakeLists.txt file
 
   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)
@@ -49,3 +42,10 @@ 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

@@ -1,37 +1,68 @@
-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")
+# PACE library support for ML-PACE package
+find_package(pace QUIET)
 
-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)
-
-# 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()
+if(pace_FOUND)
+    find_package(pace)
+    target_link_libraries(lammps PRIVATE pace::pace)
 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)
+    # 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_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()
+
+    # fixup yaml-cpp/emitterutils.cpp for GCC 15+ until patch is applied
+    file(READ ${lib-pace}/yaml-cpp/src/emitterutils.cpp yaml_emitterutils)
+    string(REPLACE "#include <sstream>" "#include <sstream>\n#include <cinttypes>" yaml_tmp_emitterutils "${yaml_emitterutils}")
+    string(REPLACE "#include <cinttypes>\n#include <cinttypes>" "#include <cinttypes>" yaml_emitterutils "${yaml_tmp_emitterutils}")
+    file(WRITE ${lib-pace}/yaml-cpp/src/emitterutils.cpp "${yaml_emitterutils}")
+
+    add_subdirectory(${lib-pace} build-pace EXCLUDE_FROM_ALL)
+    set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE pace)
+    endif()
 endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -18,14 +18,16 @@ 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)
-    set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
+    # 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}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -x f95-cpp-input -ffree-line-length-none -ffree-form -fno-second-underscore -fPIC\n")
     set(temp "${temp}F77FLAGS += -x f77-cpp-input -fno-second-underscore -fPIC\n")
   else()
     message(FATAL_ERROR "The ${CMAKE_Fortran_COMPILER_ID} Fortran compiler is not (yet) supported for building QUIP")
   endif()
-  set(temp "${temp}CFLAGS += -fPIC \nCPLUSPLUSFLAGS += -fPIC\nAR_ADD=src\n")
+  set(temp "${temp}CFLAGS += -fPIC -Wno-return-mismatch \nCPLUSPLUSFLAGS += -fPIC -Wno-return-mismatch\nAR_ADD=src\n")
   set(temp "${temp}MATH_LINKOPTS=")
   foreach(flag ${BLAS_LIBRARIES})
     set(temp "${temp} ${flag}")
@@ -35,7 +37,7 @@ if(DOWNLOAD_QUIP)
   endforeach()
   # Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
   set(temp "${temp} -L/_DUMMY_PATH_\n")
-  set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
+  set(temp "${temp}PYTHON=${Python_EXECUTABLE}\nPIP=pip\nEXTRA_LINKOPTS=\n")
   set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
   set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
   set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")
@@ -56,7 +58,7 @@ if(DOWNLOAD_QUIP)
     GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
-    BUILD_COMMAND env QUIP_ARCH=lammps make libquip
+    BUILD_COMMAND env QUIP_ARCH=lammps make -j1 libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
     BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}

cmake/Modules/Packages/MSCG.cmake

@@ -1,28 +0,0 @@
-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

@@ -1,5 +1,14 @@
 # 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})
@@ -21,14 +30,23 @@ else()
   set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.2/plumed-src-2.8.2.tgz"
+# 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/v2.9.3/plumed-src-2.9.3.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "599092b6a0aa6fff992612537ad98994" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
 GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
 
+# adjust C++ standard support for self-compiled Plumed2
+if(CMAKE_CXX_STANDARD GREATER 11)
+  set(PLUMED_CXX_STANDARD 14)
+else()
+  set(PLUMED_CXX_STANDARD 11)
+endif()
+
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
   if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
     set(CROSS_CONFIGURE mingw64-configure)
@@ -44,7 +62,7 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
-                                         --disable-python --enable-cxx=11
+                                         --disable-python --enable-cxx=${PLUMED_CXX_STANDARD}
                                          --enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
                                          ${PLUMED_CONFIG_OMP}
                                          ${PLUMED_CONFIG_MPI}
@@ -75,6 +93,9 @@ 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()
 
@@ -128,7 +149,7 @@ else()
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
                                              --enable-modules=all
-                                             --enable-cxx=11
+                                             --enable-cxx=${PLUMED_CXX_STANDARD}
                                              --disable-python
                                              ${PLUMED_CONFIG_MPI}
                                              ${PLUMED_CONFIG_OMP}
@@ -149,21 +170,26 @@ else()
     endif()
     set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
     file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
+    endif()
   else()
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(PLUMED REQUIRED plumed)
+    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
     add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
     if(PLUMED_MODE STREQUAL "STATIC")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
     elseif(PLUMED_MODE STREQUAL "SHARED")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/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}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-      include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.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)
     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

@@ -1,29 +1,11 @@
-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()
+
+if(NOT Python_INTERPRETER)
+  # backward compatibility with older LAMMPS documentation
+  if(PYTHON_EXECUTABLE)
+    set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
   endif()
-  # 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)
+  find_package(Python COMPONENTS Interpreter)
 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/SCAFACOS.cmake

@@ -14,27 +14,16 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
-  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
-  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.4/scafacos-1.0.4.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "23867540ec32e63ce71d6ecc105278d2" CACHE STRING "MD5 checksum of SCAFACOS tarball")
   mark_as_advanced(SCAFACOS_URL)
   mark_as_advanced(SCAFACOS_MD5)
   GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
 
-
-  # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
-  file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
-          EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
-
-  find_program(HAVE_PATCH patch)
-  if(NOT HAVE_PATCH)
-    message(FATAL_ERROR "The 'patch' program is required to build the ScaFaCoS library")
-  endif()
-
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
     URL     ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
     URL_MD5 ${SCAFACOS_MD5}
-    PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m
                                              --with-internal-fftw --with-internal-pfft

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

@@ -1,3 +1,5 @@
+# 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}")
@@ -19,13 +19,13 @@ 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") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  if((CMAKE_SYSTEM_NAME STREQUAL "Linux")
       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)))
+    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_GREATER_EQUAL 22.04))
         OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
+      check_cxx_compiler_flag(--ld-path=${CMAKE_LINKER} HAVE_LD_PATH_FLAG)
       check_cxx_compiler_flag(-fuse-ld=mold HAVE_MOLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
       check_cxx_compiler_flag(-fuse-ld=gold HAVE_GOLD_LINKER_FLAG)
@@ -50,6 +50,17 @@ if(ENABLE_TESTING)
       if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
         target_link_options(lammps PUBLIC -fuse-ld=${CMAKE_CUSTOM_LINKER})
       endif()
+      if(HAVE_LD_PATH_FLAG)
+        if("${CMAKE_CUSTOM_LINKER}" STREQUAL "mold")
+          target_link_options(lammps PUBLIC --ld-path=${HAVE_MOLD_LINKER_BIN})
+        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "lld")
+          target_link_options(lammps PUBLIC --ld-path=${HAVE_LLD_LINKER_BIN})
+        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "gold")
+          target_link_options(lammps PUBLIC --ld-path=${HAVE_GOLD_LINKER_BIN})
+        elseif("${CMAKE_CUSTOM_LINKER}" STREQUAL "bfd")
+          target_link_options(lammps PUBLIC --ld-path=${HAVE_BFD_LINKER_BIN})
+        endif()
+      endif()
     endif()
   endif()
 
@@ -66,16 +77,8 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
   mark_as_advanced(ENABLE_COVERAGE)
   if(ENABLE_COVERAGE)
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC --coverage)
-      target_link_options(lammps PUBLIC --coverage)
-    endif()
+    target_compile_options(lammps PUBLIC --coverage)
+    target_link_options(lammps PUBLIC --coverage)
   endif()
 endif()
 
@@ -110,24 +113,16 @@ endif()
 #######################################
 # select code sanitizer options
 #######################################
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, hwaddress, leak, thread, undefined)")
 mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set(ENABLE_SANITIZER_VALUES none address hwaddress leak thread undefined)
 set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
 validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
 string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
 if(NOT ENABLE_SANITIZER STREQUAL "none")
   if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-    endif()
+    target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
   else()
     message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
     set(ENABLE_SANITIZER "none")

cmake/Modules/Tools.cmake

@@ -6,6 +6,10 @@ if(BUILD_TOOLS)
   add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
   install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
+  add_executable(reformat-json ${LAMMPS_TOOLS_DIR}/json/reformat-json.cpp)
+  target_include_directories(reformat-json PRIVATE ${LAMMPS_SOURCE_DIR})
+  install(TARGETS reformat-json DESTINATION ${CMAKE_INSTALL_BINDIR})
+
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
     include(CheckLanguage)
@@ -26,7 +30,7 @@ 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 ${STANDARD_MATH_LIB})
@@ -37,40 +41,6 @@ if(BUILD_TOOLS)
   add_subdirectory(${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</string>
+	<string>LAMMPS_GUI</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.app/Contents
+   LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.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

@@ -2,9 +2,10 @@
 
 APP_NAME=lammps-gui
 DESTDIR=${PWD}/../LAMMPS_GUI
+VERSION="$1"
 
 echo "Delete old files, if they exist"
-rm -rf ${DESTDIR} ../LAMMPS-Linux-amd64.tar.gz
+rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
@@ -59,17 +60,19 @@ 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-Linux-amd64.tar.gz LAMMPS_GUI
+tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
 popd
 
 echo "Cleanup dir"

cmake/packaging/build_macos_dmg.sh

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

cmake/packaging/build_windows_cross_zip.sh

@@ -1,26 +1,65 @@
-#!/bin/bash -vx
+#!/bin/bash
 
 APP_NAME=lammps-gui
-DESTDIR=${PWD}/../LAMMPS_GUI
+DESTDIR=${PWD}/LAMMPS_GUI
+SYSROOT="$1"
+VERSION="$2"
 
 echo "Delete old files, if they exist"
-rm -rvf ${DESTDIR} LAMMPS-Win10-amd64.zip
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
 
 echo "Create staging area for deployment and populate"
 DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
 
-echo "Add required dependencies for Qt"
-for dll in Qt5Core.dll Qt5Gui.dll Qt5Widgets.dll
+# no static libs needed
+rm -rvf ${DESTDIR}/lib
+# but the LAMMPS lib
+
+echo "Copying required DLL files"
+for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
 do \
-    cp /usr/x86_64-w64-mingw32/sys-root/mingw/bin/${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}
+    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
 
-pushd ..
-zip -9rv LAMMPS-Win10-amd64.zip LAMMPS_GUI
-popd
-exit 0
+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
+

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-Win10-amd64.zip)
+file(REMOVE LAMMPS_GUI-Win10-amd64.zip)
 file(REMOVE_RECURSE LAMMPS_GUI)
 file(RENAME ${INSTNAME} LAMMPS_GUI)
 
@@ -21,8 +21,15 @@ 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-Win10-amd64.zip")
+file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-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

@@ -1,15 +1,27 @@
 #!/bin/sh
 # wrapper for bundled executables
 
-BASEDIR=$(dirname "$0")
-EXENAME=$(basename "$0")
+# reset locale to avoid problems with decimal numbers
+export LC_ALL=C
+
+BASEDIR="$(dirname "$0")"
+EXENAME="$(basename "$0")"
+
+# save old settings (for restoring them later)
+OLDPATH="${PATH}"
+OLDLDLIB="${LD_LIBRARY_PATH}"
+
+# prepend path to find our custom executables
+PATH="${BASEDIR}/bin:${PATH}"
 
 # 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
+LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
+MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
+
+# export everything
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH OLDPATH OLDLDLIB
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/presets/all_off.cmake

@@ -4,6 +4,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD
@@ -26,8 +27,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -60,11 +62,10 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT
@@ -82,6 +83,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -6,6 +6,7 @@
 set(ALL_PACKAGES
   ADIOS
   AMOEBA
+  APIP
   ASPHERE
   ATC
   AWPMD
@@ -28,8 +29,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -62,11 +64,10 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT
@@ -84,6 +85,7 @@ 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 gfortran f95)
+find_program(CLANG_FORTRAN NAMES flang-new flang gfortran f95)
 set(ENV{OMPI_FC} ${CLANG_FORTRAN})
 get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
-if (_tmp_fc STREQUAL "flang")
+if ((_tmp_fc STREQUAL "flang") OR (_tmp_fc STREQUAL "flang-new"))
   set(FC_STD_VERSION "-std=f2018")
   set(BUILD_MPI OFF)
 else()

cmake/presets/download.cmake

@@ -9,7 +9,6 @@ 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

@@ -0,0 +1,11 @@
+# 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/hip_amd.cmake

@@ -19,12 +19,19 @@ set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
 
 set(MPI_CXX "hipcc" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(MPI_C "hipcc" CACHE STRING "" FORCE)
+set(MPI_C_COMPILER "mpicc" CACHE STRING "" FORCE)
+
+# change as needed. This is for Fedora Linux 41 and 42
+set(_libomp_root "/usr/lib/clang/18")
+# we need to explicitly specify the include dir, since hipcc will
+# compile each file twice and doesn't find omp.h the second time
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "hipcc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "hipcc" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp=libomp -I${_libomp_root}/include" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/kokkos-cuda.cmake

@@ -1,11 +1,14 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. This preselects CC 5.0 as default GPU arch, since
-# that is compatible with all higher CC, but not the default CC 3.5
+# enabled as well. The GPU architecture *must* match your hardware (If not manually set, Kokkos will try to autodetect it).
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 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

@@ -1,19 +1,21 @@
-# preset that enables KOKKOS and selects HIP compilation with OpenMP
-# enabled as well. Also sets some performance related compiler flags.
+# preset that enables KOKKOS and selects HIP compilation withOUT OpenMP.
+# Kokkos OpenMP is not compatible with the second pass of hipcc.
 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_OPENMP OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_HIP    ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_VEGA90A on CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS ON CACHE BOOL "" FORCE)
 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)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -munsafe-fp-atomics" CACHE STRING "" FORCE)
+
+# If KSPACE is also enabled, use HIPFFT 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)
+#set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
 
 # these flags are needed to build with Cray MPICH on OLCF Crusher
 #-D CMAKE_CXX_FLAGS="-I/${MPICH_DIR}/include"

cmake/presets/kokkos-sycl-intel.cmake

@@ -0,0 +1,30 @@
+# 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)
+
+# set(_intel_sycl_flags " -w -fsycl -flink-huge-device-code -fsycl-targets=spir64_gen "
+set(_intel_sycl_flags " -w -fsycl -fsycl-device-code-split=per_kernel -fsycl-targets=spir64_gen ")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)
+
+#set(CMAKE_EXE_LINKER_FLAGS "-fsycl -flink-huge-device-code -fsycl-targets=spir64_gen " CACHE STRING "" FORCE)
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -fsycl -flink-huge-device-code " CACHE STRING "" FORCE)

cmake/presets/kokkos-sycl-nvidia.cmake

@@ -0,0 +1,20 @@
+# 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(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
+set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+
+set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
+set(CMAKE_SHARED_LINKER_FLAGS "${CMAKE_SHARED_LINKER_FLAGS} -Xsycl-target-frontend -O3 " CACHE STRING "" FORCE)
+
+set(_intel_sycl_flags "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${_intel_sycl_flags}" CACHE STRING "" FORCE)

cmake/presets/kokkos-sycl.cmake

@@ -1,18 +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(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
-set(BUILD_OMP ON CACHE BOOL "" FORCE)
-
-# hide deprecation warnings temporarily for stable release
-set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
-
-set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
-set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)
-set(CMAKE_SHARED_LINKER_FLAGS "-Xsycl-target-frontend -O3" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-fgpu-inline-threshold=100000 -Xsycl-target-frontend -O3  -Xsycl-target-frontend -ffp-contract=on -Wno-unknown-cuda-version" CACHE STRING "" FORCE)

cmake/presets/macos-multiarch.cmake

@@ -10,5 +10,3 @@ 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

@@ -22,8 +22,9 @@ set(WIN_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -32,7 +33,6 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
   LEPTON
@@ -50,6 +50,7 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -66,6 +67,7 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SMTBQ
@@ -83,14 +85,13 @@ 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()
 
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(LAMMPS_MEMALIGN "0" CACHE STRING "" FORCE)
-set(CMAKE_TUNE_FLAGS "-Wno-missing-include-dirs" CACHE STRING "" FORCE)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-missing-include-dirs" CACHE STRING "" FORCE)
 set(CMAKE_EXE_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(CMAKE_SHARED_LINKER_FLAGS "-Wl,--enable-stdcall-fixup,--as-needed,-lssp" CACHE STRING "" FORCE)
 set(BUILD_TOOLS ON CACHE BOOL "" FORCE)

cmake/presets/most.cmake

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

cmake/presets/nolib.cmake

@@ -3,6 +3,7 @@
 
 set(PACKAGES_WITH_LIB
   ADIOS
+  APIP
   ATC
   AWPMD
   COMPRESS
@@ -19,8 +20,6 @@ set(PACKAGES_WITH_LIB
   ML-PACE
   ML-QUIP
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   PLUMED
   PYTHON

cmake/presets/oneapi.cmake

@@ -3,26 +3,9 @@
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
-unset(HAVE_OMP_H_INCLUDE CACHE)
-set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -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)
+# force using internal BLAS/LAPCK since external ones may not be ABI compatible
+set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)
 

cmake/presets/windows-intel-llvm.cmake

@@ -5,4 +5,4 @@ set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
 set(INTEL_LRT_MODE "C++11" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
-set(CMAKE_TUNE_FLAGS -Wno-unused-command-line-argument)
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-unused-command-line-argument" CACHE STRING "" FORCE)

cmake/presets/windows.cmake

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

doc/.gitignore

@@ -17,3 +17,10 @@
 *.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

@@ -17,9 +17,11 @@ MATHJAXTAG     = 3.2.2
 
 PYTHON         = $(word 3,$(shell type python3))
 DOXYGEN        = $(word 3,$(shell type doxygen))
+PANDOC         = $(word 3,$(shell type pandoc))
 HAS_PYTHON3    = NO
 HAS_DOXYGEN    = NO
 HAS_PDFLATEX   = NO
+HAS_PANDOC     = NO
 
 ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3    = YES
@@ -31,10 +33,14 @@ endif
 
 ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
 ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
-HAS_PDFLATEX = YES
+HAS_PDFLATEX   = YES
 endif
 endif
 
+ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 0)
+HAS_PANDOC     = YES
+endif
+
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
@@ -45,8 +51,9 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml fasthtml-init 
 
+FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst))
 # ------------------------------------------
 
 help:
@@ -63,6 +70,7 @@ 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"
 
 # ------------------------------------------
@@ -82,14 +90,15 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+globbed-tocs:
+	$(PYTHON) $(BUILDDIR)/utils/make-globbed-tocs.py -d $(RSTDIR)
+
+html: xmlgen globbed-tocs $(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
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
@@ -98,7 +107,11 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		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 ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -110,26 +123,24 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-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
-	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		deactivate ;\
-	)
-	@rm -rf fasthtml/_sources
-	@rm -rf fasthtml/PDF
-	@rm -rf fasthtml/USER
-	@rm -rf fasthtml/JPG
-	@cp -r src/PDF fasthtml/PDF
-	@rm -rf fasthtml/PDF/.[sg]*
+fasthtml: fasthtml-init $(FASTHTMLFILES)
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
-spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
+fasthtml-init:
+	@mkdir -p fasthtml/JPG
+	@cp src/JPG/*.* fasthtml/JPG
+	@cp $(RSTDIR)/accel_styles.rst $(RSTDIR)/lepton_expression.rst fasthtml/
+	@cp $(BUILDDIR)/utils/pandoc.css fasthtml/
+
+fasthtml/%.html: $(RSTDIR)/%.rst
+	@if [ "$(HAS_PANDOC)" == "NO" ] ; then echo "Make 'fasthtml' requires the 'pandoc' software" 1>&2; exit 1; fi
+	@mkdir -p fasthtml
+	@echo converting $< to $@
+	@sed -e 's/\\AA/\\mathring{\\mathrm{A}}/g' $< > fasthtml/$*.temp.rst
+	@pandoc -s --mathml --css="pandoc.css" --template=$(BUILDDIR)/utils/pandoc.html --metadata title="$@" -o $@ fasthtml/$*.temp.rst
+	@rm -f fasthtml/$*.temp.rst
+
+spelling: xmlgen globbed-tocs $(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 ; \
@@ -140,7 +151,7 @@ spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives
 	)
 	@echo "Spell check finished."
 
-epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+epub: xmlgen globbed-tocs $(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
@@ -149,8 +160,6 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
 	)
@@ -163,15 +172,13 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+pdf: xmlgen globbed-tocs $(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
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
@@ -179,7 +186,11 @@ pdf: xmlgen $(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 ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -227,6 +238,10 @@ 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 || : )
+	@( env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                        $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\
@@ -235,6 +250,15 @@ link_check : $(VENV) html
 		deactivate ;\
 	)
 
+upgrade: $(VENV)
+	@(\
+		. $(VENV)/bin/activate; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install --upgrade wheel; \
+		pip $(PIP_OPTIONS) install --upgrade -r $(BUILDDIR)/utils/requirements.txt; \
+		deactivate;\
+	)
+
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in

doc/README

@@ -22,12 +22,12 @@ doxygen-warn.log  logfile with warnings from running doxygen
 and:
 
 github-development-workflow.md   notes on the LAMMPS development workflow
-include-file-conventions.md      notes on LAMMPS' include file conventions
 documentation_conventions.md     notes on writing documentation for LAMMPS
 
 If you downloaded a LAMMPS tarball from www.lammps.org, then the html
 folder and the PDF manual should be included. If you downloaded LAMMPS
-from GitHub then you either need to build them.
+using GitHub then you either need to build them yourself or read the
+online version at https://docs.lammps.org/
 
 You can build the HTML and PDF files yourself, by typing "make html"
 or by "make pdf", respectively.  This requires various tools and files.
@@ -39,10 +39,10 @@ environment and local folders.
 
 Installing prerequisites for the documentation build
 
-To run the HTML documention build toolchain, python 3.x, doxygen, git,
-and the venv python module have to be installed if not already available.
-Also internet access is initially required to download external files
-and tools.
+To run the HTML documention build toolchain, python 3.8 or later,
+doxygen 1.8.10 or later, git, and the venv python module have to be
+installed if not already available.  Also internet access is initially
+required to download external files and tools.
 
 Building the PDF format manual requires in addition a compatible LaTeX
 installation with support for PDFLaTeX and several add-on LaTeX packages
@@ -52,16 +52,24 @@ installed.  This includes:
 - babel
 - capt-of
 - cmap
+- dvipng
+- ellipse
 - fncychap
+- fontawesom
 - framed
 - geometry
+- gyre
 - hyperref
 - hypcap
 - needspace
+- pict2e
 - times
 - tabulary
+- titlesec
 - upquote
 - wrapfig
+- xindy
+
 Also the latexmk script is required to run PDFLaTeX and related tools.
 the required number of times to have self-consistent output and include
 updated bibliography and indices.

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
@@ -45,8 +45,7 @@ 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.
@@ -64,7 +63,7 @@ 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
@@ -84,7 +83,7 @@ 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         = "4 May 2022"
+PROJECT_NUMBER         = "19 November 2024"
 PROJECT_BRIEF          = "Documentation of the LAMMPS library interface and Python wrapper"
 PROJECT_LOGO           = lammps-logo.png
 CREATE_SUBDIRS         = NO

doc/github-development-workflow.md

@@ -6,7 +6,9 @@ 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
 
@@ -36,10 +38,10 @@ 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 or stable releases based on the associated
-tags.  Updates to the stable release in between stable releases
+updated upon "feature releases" 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 update releases.
+branch and then into the "stable" branch as "stable update releases".
 
 Pull requests may also be submitted to (long-running) feature branches
 created by LAMMPS developers inside the LAMMPS project, if needed. Those
@@ -72,7 +74,7 @@ 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
@@ -86,9 +88,9 @@ 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 in 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 at 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.
@@ -131,7 +133,7 @@ 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 4-6 weeks at a point, when the LAMMPS
+releases of LAMMPS made about every 4-8 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
@@ -147,7 +149,8 @@ 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.
+as update releases. Further explanation of LAMMPS versions can be found
+[in the documentation](https://docs.lammps.org/Manual_version.html).
 
 ## Project Management
 

doc/graphviz/Makefile

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

doc/graphviz/lammps-releases.dot

@@ -0,0 +1,34 @@
+// 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:" fontname="bold"]
+        develop [label="'develop' branch" height=0.75];
+        maintenance [label="'maintenance' branch" height=0.75];
+    };
+    {
+        rank = "same";
+        upload [shape="none" label="Release branches:" fontname="bold"]
+        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:" fontname="bold"];
+        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" "2 August 2023" "2023-08-2"
+.TH LAMMPS "1" "12 June 2025" "2025-06-12"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 2 August 2023
+\- Molecular Dynamics Simulator.  Version 12 June 2025
 
 .SH SYNOPSIS
 .B lmp
@@ -226,6 +226,20 @@ 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
@@ -297,7 +311,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2022 Sandia Corporation
+© 2003--2025 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" "v3.9.10" "2023-03-10"
+.TH MSI2LMP "1" "v3.9.11" "2024-09-06"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
@@ -101,7 +101,7 @@ msi2lmp decane -c 0 -f oplsaa
 
 
 .SH COPYRIGHT
-© 2003--2022 Sandia Corporation
+© 2003--2024 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

@@ -1,6 +1,12 @@
 Bibliography
 ************
 
+**(Abascal1)**
+   Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
+
+**(Abascal2)**
+   Abascal, J Chem Phys, 123, 234505 (2005)
+
 **(Ackland)**
    Ackland, Jones, Phys Rev B, 73, 054104 (2006).
 
@@ -22,21 +28,24 @@ Bibliography
 **(Agnolin and Roux 2007)**
    Agnolin, I. & Roux, J-N. (2007). Internal states of model isotropic granular packings. I. Assembling process, geometry, and contact networks. Phys. Rev. E, 76, 061302.
 
+**(Ahrens-Iwers2022)**
+   Ahrens-Iwers *et al.*, J. Chem. Phys. 157, 084801 (2022).
+
+**(Ahrens-Iwers)**
+   Ahrens-Iwers and Meissner, J. Chem. Phys. 155, 104104 (2021).
+
 **(Aktulga)**
    Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38, 245-259 (2012).
 
 **(Albe)**
    J.\  Nord, K. Albe, P. Erhart, and K. Nordlund, J. Phys.: Condens. Matter, 15, 5649(2003).
 
-**(Albe)**
+**(Albe1)**
    K.\  Albe, K. Nordlund, J. Nord, and A. Kuronen, Phys. Rev. B, 66, 035205 (2002).
 
 **(Allen)**
    Allen and Germano, Mol Phys 104, 3225-3235 (2006).
 
-**(Allen)**
-   Allen and Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1987.
-
 **(AllenTildesley)**
    Allen and Tildesley, Computer Simulation of Liquids, Oxford University Press (1987)
 
@@ -49,6 +58,9 @@ Bibliography
 **(Anderson)**
    Anderson, Mukherjee, Critchley, Ziegler, and Lipton "POEMS: Parallelizable Open-source Efficient Multibody Software ", Engineering With Computers (2006).
 
+**(Appshaw)**
+   Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
+
 **(Avendano)**
    C.\  Avendano, T. Lafitte, A. Galindo, C. S. Adjiman, G. Jackson, E. Muller, J Phys Chem B, 115, 11154 (2011).
 
@@ -58,7 +70,7 @@ Bibliography
 **(Babadi)**
    Babadi, Ejtehadi, Everaers, J Comp Phys, 219, 770-779 (2006).
 
-**(Babadi)**
+**(Babadi2)**
    Babadi and Ejtehadi, EPL, 77 (2007) 23002.
 
 **(Baczewski)**
@@ -73,23 +85,23 @@ Bibliography
 **(Ballenegger)**
    Ballenegger, Arnold, Cerda, J Chem Phys, 131, 094107 (2009).
 
-**(Banna)**
-   Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
-
 **(Barrat)**
    Barrat and Rodney, J. Stat. Phys, 144, 679 (2011).
 
 **(Barrett)**
    Barrett, Tschopp, El Kadiri, Scripta Mat. 66, p.666 (2012).
 
+**(Barros)**
+   Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
+
 **(Bartok)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
 **(Bartok2010)**
    Bartok, Payne, Risi, Csanyi, Phys Rev Lett, 104, 136403 (2010).
 
-**(Bartok_2010)**
-   AP Bartok, MC Payne, R Kondor, and G Csanyi, Physical Review Letters 104, 136403 (2010).
+**(Bartok2013)**
+   Bartok, Kondor, Csanyi, Phys Rev B, 87, 184115 (2013).
 
 **(Bartok_PhD)**
    A Bartok-Partay, PhD Thesis, University of Cambridge, (2010).
@@ -97,36 +109,51 @@ Bibliography
 **(Baskes)**
    Baskes, Phys Rev B, 46, 2727-2742 (1992).
 
+**(Baskes2)**
+   Baskes, Phys Rev B, 75, 094113 (2007).
+
 **(Beck)**
    Beck, Molecular Physics, 14, 311 (1968).
 
+**(Becton)**
+   Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).
+
+**(Behler and Parrinello 2007)**
+   Behler, J.; Parrinello, M. Phys. Rev. Lett.  2007, 98 (14), 146401.
+
 **(Bennet)**
    Bennet, J Comput Phys, 22, 245 (1976)
 
 **(Berardi)**
    Berardi, Fava, Zannoni, Chem Phys Lett, 297, 8-14 (1998). Berardi, Muccioli, Zannoni, J Chem Phys, 128, 024905 (2008).
 
-**(Berendsen)**
-   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
-
 **(Berendsen)**
    Berendsen, Postma, van Gunsteren, DiNola, Haak, J Chem Phys, 81, 3684 (1984).
 
+**(Berendsen2)**
+   Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
+
 **(Bessarab)**
    Bessarab, Uzdin, Jonsson, Comp Phys Comm, 196, 335-347 (2015).
 
 **(Beutler)**
    Beutler, Mark, van Schaik, Gerber, van Gunsteren, Chem Phys Lett, 222, 529 (1994).
 
-**(Bialke)**
-   J.\  Bialke, T. Speck, and H Loewen, Phys. Rev. Lett. 108, 168301, 2012.
-
 **(Bird)**
    G.\  A. Bird, "Molecular Gas Dynamics and the Direct Simulation of Gas Flows" (1994).
 
 **(Bitzek)**
    Bitzek, Koskinen, Gahler, Moseler, Gumbsch, Phys Rev Lett, 97, 170201 (2006).
 
+**(Bolintineanu1)**
+   Bolintineanu, Lechman, Plimpton, Grest, Phys Rev E, 86, 066703 (2012).
+
+**(Bolintineanu2)**
+  Bolintineanu, Grest, Lechman, Pierce, Plimpton, Schunk, Comp Particle Mechanics, 1, 321-356 (2014).
+
+**(Bomont)**
+   Bomont, Bretonnet, J. Chem. Phys. 124, 054504 (2006).
+
 **(Bond)**
    Bond and Leimkuhler, SIAM J Sci Comput, 30, p 134 (2007).
 
@@ -134,7 +161,7 @@ Bibliography
    Boone, Babaei, Wilmer, J Chem Theory Comput, 15, 5579--5587 (2019).
 
 **(BoreschKarplus)**
-   Boresch and Karplus, J Phys Chem A, 103, 103 (1999)
+   Boresch and Karplus, J Phys Chem A, 103, 103 (1999).
 
 **(Botu1)**
    V.\  Botu and R. Ramprasad, Int. J. Quant. Chem., 115(16), 1074 (2015).
@@ -169,8 +196,11 @@ Bibliography
 **(Buck)**
    Buck, Bouguet-Bonnet, Pastor, MacKerell Jr., Biophys J, 90, L36 (2006).
 
+**(Bulacu)**
+   Bulacu, Goga, Zhao, Rossi, Monticelli, Periole, Tieleman, Marrink, J Chem Theory Comput, 9, 3282-3292
+
 **(Bussi)**
-   G.\  Bussi, M. Parrinello, Phs. Rev. E 75, 056707 (2007)
+   G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
 
 **(Bussi1)**
    Bussi, Donadio and Parrinello, J. Chem. Phys. 126, 014101(2007)
@@ -178,20 +208,20 @@ Bibliography
 **(Bussi2)**
    Bussi and Parrinello, Phys. Rev. E 75, 056707 (2007)
 
-**(COMB)**
+**(COMB_1)**
+   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
+
+**(COMB_2)**
    T.-R. Shan, B. D. Devine, T. W. Kemper, S. B. Sinnott, and S. R. Phillpot, Phys. Rev. B 81, 125328 (2010)
 
 **(COMB3)**
    T.\  Liang, T.-R. Shan, Y.-T. Cheng, B. D. Devine, M. Noordhoek, Y. Li, Z. Lu, S. R. Phillpot, and S. B. Sinnott, Mat. Sci. & Eng: R 74, 255-279 (2013).
 
-**(COMB_1)**
-   J.\  Yu, S. B. Sinnott, S. R. Phillpot, Phys Rev B, 75, 085311 (2007),
-
 **(Calhoun)**
    A.\  Calhoun, M. Pavese, G. Voth, Chem Phys Letters, 262, 415 (1996).
 
 **(Campana)**
-   C.\  Campana and M. H. Muser, *Practical Green's function approach to the simulation of elastic semi-infinite solids*, `Phys. Rev. B [74], 075420 (2006) <https://doi.org/10.1103/PhysRevB.74.075420>`_
+   C.\  Campana and M. H. Muser, Phys. Rev. B [74], 075420 (2006).
 
 **(Cao1)**
    J.\  Cao and B. Berne, J Chem Phys, 99, 2902 (1993).
@@ -215,6 +245,9 @@ Bibliography
    Cerda, Ballenegger, Lenz, Holm, J Chem Phys 129, 234104 (2008)
 
 **(Ceriotti)**
+   M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
+
+**(Ceriotti1)**
    Ceriotti, Bussi and Parrinello, J Chem Theory Comput 6, 1170-80 (2010)
 
 **(Ceriotti2)**
@@ -232,6 +265,18 @@ Bibliography
 **(Clarke)**
    Clarke and Smith, J Chem Phys, 84, 2290 (1986).
 
+**(Clavier)**
+   G. Clavier, N. Desbiens, E. Bourasseau, V. Lachet, N. Brusselle-Dupend and B. Rousseau, Mol Sim, 43, 1413 (2017).
+
+**(Clemmer)**
+   Clemmer and Robbins, Phys. Rev. Lett. (2022).
+
+**(Clemmer1)**
+   Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).
+
+**(Clemmer2)**
+   Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).
+
 **(Coleman)**
    Coleman, Spearot, Capolungo, MSMSE, 21, 055020 (2013).
 
@@ -244,8 +289,17 @@ Bibliography
 **(Cornell)**
    Cornell, Cieplak, Bayly, Gould, Merz, Ferguson, Spellmeyer, Fox, Caldwell, Kollman, JACS 117, 5179-5197 (1995).
 
+**(Cundall, 1987)**
+   Cundall, P. A. Distinct Element Models of Rock and Soil
+
+**(Curk1)**
+   T. Curk, J. Yuan, and E. Luijten, JCP 156 (2022).
+
+**(Curk2)**
+   T. Curk and E. Luijten, PRL 126 (2021)
+
 **(Cusentino)**
-   Cusentino, Wood, and Thompson, J Phys Chem A, xxx, xxxxx, (2020)
+   Cusentino, Wood, Thompson, J Phys Chem A, 124, 5456, (2020)
 
 **(Daivis and Todd)**
    Daivis and Todd, J Chem Phys, 124, 194103 (2006).
@@ -268,6 +322,15 @@ Bibliography
 **(Daw2)**
    M.\  S. Daw, and M. I. Baskes, Phys. Rev. B, 29, 6443 (1984).
 
+**(de Buyl)**
+   de Buyl, Colberg and Hofling, Comp. Phys. Comm. 185(6), 1546-1553 (2014) -
+
+**(Deissenbeck)**
+   Deissenbeck *et al.*, Phys. Rev. Letters 126, 136803 (2021).
+
+**(de Koning)**
+   de Koning and Antonelli, Phys Rev E, 53, 465 (1996).
+
 **(DeVane)**
    Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
 
@@ -277,12 +340,24 @@ Bibliography
 **(Destree)**
    M.\  Destree, F. Laupretre, A. Lyulin, and J.-P.  Ryckaert, J Chem Phys, 112, 9632 (2000).
 
+**(Dickel)**
+   Dickel, Francis, and Barrett, Computational Materials Science 171 (2020): 109157.
+
+**(Dietz)**
+   Dietz and Hoy, J. Chem Phys, 156, 014103 (2022).
+
 **(Dobson)**
    Dobson, J Chem Phys, 141, 184103 (2014).
 
+**(Drautz)**
+   Drautz, Phys Rev B, 99, 014104 (2019).
+
 **(Duffy)**
    D M Duffy and A M Rutherford, J. Phys.: Condens. Matter, 19, 016207-016218 (2007).
 
+**(Dufils)**
+   Dufils *et al.*, Phys. Rev. Letters 123, 195501 (2019).
+
 **(Dullweber)**
    Dullweber, Leimkuhler and McLachlan, J Chem Phys, 107, 5840 (1997).
 
@@ -295,6 +370,9 @@ Bibliography
 **(Dunweg)**
    Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).
 
+**(EcheverriRestrepo)**
+  Echeverri Restrepo, Andric, Comput Mater Sci, 218, 111978 (2023).
+
 **(EDIP)**
    J F Justo et al, Phys Rev B 58, 2539 (1998).
 
@@ -304,12 +382,21 @@ Bibliography
 **(Elliott)**
    Elliott, Tadmor and Bernstein, `https://openkim.org/kim-api <https://openkim.org/kim-api>`_ (2011) doi: `https://doi.org/10.25950/FF8F563A <https://doi.org/10.25950/FF8F563A>`_
 
+**(Ellis)**
+   Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam,  Phys Rev B, 104, 035120, (2021)
+
+**(Emmrich)**
+   Emmrich, Weckner, Commun. Math. Sci., 5, 851-864 (2007),
+
 **(Elstner)**
    M.\  Elstner, D. Poresag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B, 58, 7260 (1998).
 
 **(Erdmann)**
    U.\  Erdmann , W. Ebeling, L. Schimansky-Geier, and F. Schweitzer, Eur. Phys. J. B 15, 105-113, 2000.
 
+**(Eshelby)**
+  J.D. Eshelby, Philos. Trans. Royal Soc. London A, Math. Phys. Sci., Vol. 244, No. 877 (1951) pp. 87-112; J. Elasticity, Vol. 5, Nos. 3-4 (1975) pp. 321-335]
+
 **(Espanol and Revenga)**
    Espanol, Revenga, Physical Review E, 67, 026705 (2003).
 
@@ -328,9 +415,18 @@ Bibliography
 **(Faken)**
    Faken, Jonsson, Comput Mater Sci, 2, 279 (1994).
 
+**(Falk)**
+   Falk and Langer PRE, 57, 7192 (1998).
+
 **(Fath)**
    Fath, Hochbruck, Singh, J Comp Phys, 333, 180-198 (2017).
 
+**(Feng1)**
+   Z. Feng, ..., and W. Ouyang, J. Phys. Chem. C. 127(18), 8704-8713 (2023).
+
+**(Feng2)**
+   Z. Feng, ..., and W. Ouyang, Langmuir 39(50), 18198-18207 (2023).
+
 **(Fennell)**
    C.\  J. Fennell, J. D. Gezelter, J Chem Phys, 124, 234104 (2006).
 
@@ -367,18 +463,36 @@ Bibliography
 **(Frenkel)**
    Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
 
-**(GLE4MD)**
-   `https://gle4md.org/ <https://gle4md.org/>`_
+**(Fu)**
+   Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
 
 **(Gao)**
    Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
 
+**(Gingrich)**
+   Gingrich, `MSc thesis` <https://gingrich.chem.northwestern.edu/papers/ThesiswCorrections.pdf>` (2010).
+
+**(Gissinger2017)**
+   Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+
+**(Gissinger2020)**
+   Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
+
 **(Gissinger)**
-   Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
+   Jacob R. Gissinger, Scott R. Zavada, Joseph G. Smith, Josh Kemppainen, Ivan Gallegos, Gregory M. Odegard, Emilie J. Siochi, and Kristopher E. Wise, Carbon, 202, 336-347 (2023).
+
+**(Gissinger2024)**
+   J. R. Gissinger, I. Nikiforov, Y. Afshar, B. Waters, M. Choi, D. S. Karls, A. Stukowski, W. Im, H. Heinz, A. Kohlmeyer, and E. B. Tadmor, J Phys Chem B, 128, 3282-3297 (2024).
+
+**(Gloor)**
+   Gloor, J Chem Phys, 123, 134703 (2005)
 
 **(Glosli)**
    Glosli, unpublished, 2005. Streitz, Glosli, Patel, Chan, Yates, de Supinski, Sexton and Gunnels, Journal of Physics: Conference Series, 46, 254 (2006).
 
+**(Goff)**
+   Goff, Zhang, Negre, Rohskopf, Niklasson, Journal of Chemical Theory and Computation 19, no. 13 (2023).
+
 **(Goldman1)**
    Goldman, Reed and Fried, J. Chem. Phys. 131, 204103 (2009)
 
@@ -412,6 +526,9 @@ Bibliography
 **(Guo)**
    Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
 
+**(Gupta)**
+   Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
+
 **(Hardy)**
    David Hardy thesis: Multilevel Summation for the Fast Evaluation of Forces for the Simulation of Biomolecules, University of Illinois at Urbana-Champaign, (2006).
 
@@ -433,6 +550,9 @@ Bibliography
 **(Henrich)**
    O.\  Henrich, Y. A. Gutierrez-Fosado, T. Curk, T. E. Ouldridge, Eur. Phys. J. E 41, 57 (2018).
 
+**(Herman)**
+   M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
+
 **(Hess)**
    Hess, B. The Journal of Chemical Physics 2002, 116 (1), 209-217.
 
@@ -454,24 +574,42 @@ Bibliography
 **(Hoover)**
    Hoover, Phys Rev A, 31, 1695 (1985).
 
+**(Huang)**
+   Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
+
+**(Huang2014)**
+   X. Huang, "Exploring critical-state behavior using DEM", Doctoral dissertation, Imperial College. (2014). https://doi.org/10.25560/25316
+
+**(Hu)**
+   Hu, and Adams J. Comp. Physics, 213, 844-861 (2006).
+
+**(Hu)**
+   Hu, J. Chem. Theory Comput. 10, 5254 (2014).
+
 **(Hummer)**
    Hummer, Gronbech-Jensen, Neumann, J Chem Phys, 109, 2791 (1998)
 
 **(Hunt)**
    Hunt, Mol Simul, 42, 347 (2016).
 
+**(Ikeshoji)**
+   Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
+
+**(Ikeshoji2)**
+   Ikeshoji, Hafskjold, Furuholt, Mol Sim, 29, 101-109, (2003).
+
+**(Ilie)**
+   Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
+
+**(In 't Veld)**
+   In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
+
 **(IPI)**
    `https://ipi-code.org/ <https://ipi-code.org/>`
 
 **(IPI-CPC)**
    Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
 
-**(Ikeshoji)**
-   Ikeshoji and Hafskjold, Molecular Physics, 81, 251-261 (1994).
-
-**(In 't Veld)**
-   In 't Veld, Ismail, Grest, J Chem Phys (accepted) (2007).
-
 **(Isele-Holder)**
    Isele-Holder, Mitchell, Ismail, J Chem Phys, 137, 174107 (2012).
 
@@ -490,6 +628,9 @@ Bibliography
 **(Izvekov)**
    Izvekov, Voth, J Chem Phys 123, 134105 (2005).
 
+**(Jadhao)**
+   Jadhao, Solis, Olvera de la Cruz, J Chem Phys, 138, 054119 (2013)
+
 **(Janssens)**
    Janssens, Olmsted, Holm, Foiles, Plimpton, Derlet, Nature Materials, 5, 124-127 (2006).
 
@@ -502,6 +643,15 @@ Bibliography
 **(Jiang)**
    Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux,  J Phys Chem Lett, 2, 87-92 (2011).
 
+**(Jiang1)**
+   Jiang, Hardy, Phillips, MacKerell, Schulten, and Roux, J Phys Chem Lett, 2, 87-92 (2011).
+
+**(Jiang2)**
+   J.-W. Jiang, Nanotechnology 26, 315706 (2015).
+
+**(Jiang3)**
+   J.-W. Jiang, Acta Mech. Solida. Sin 32, 17 (2019).
+
 **(Johnson et al, 1971)**
    Johnson, K. L., Kendall, K., & Roberts, A. D. (1971).  Surface energy and the contact of elastic solids. Proc. R. Soc. Lond. A, 324(1558), 301-313.
 
@@ -562,27 +712,33 @@ Bibliography
 **(Kumar)**
    Kumar and Skinner, J. Phys. Chem. B, 112, 8311 (2008)
 
+**(Lafourcade)**
+  Lafourcade, Maillet, Denoual, Duval, Allera, Goryaeva, and Marinica, `Comp. Mat. Science, 230, 112534 (2023) <https://doi.org/10.1016/j.commatsci.2023.112534>`_
+
 **(Lamoureux and Roux)**
    G.\  Lamoureux, B. Roux, J. Chem. Phys 119, 3025 (2003)
 
 **(Lamoureux)**
    Lamoureux and Roux, J Chem Phys, 119, 3025-3039 (2003).
 
-**(Larentzos)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+**(Landsgesell)**
+   J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, Macromolecules 53, 3007-3020 (2020).
 
 **(Larentzos1)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, "Parallel Implementation of Isothermal and Isoenergetic Dissipative Particle Dynamics Using Shardlow-Like Splitting
+   J.P. Larentzos, J.K. Brennan, J.D. Moore, M. Lisal and W.D. Mattson, Comput. Phys. Commun., 185, 1987-1998 (2014).
 
 **(Larentzos2)**
-   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, "LAMMPS Implementation of Constant Energy Dissipative Particle Dynamics (DPD-E)", ARL-TR-6863, U.S. Army Research
+   J.P. Larentzos, J.K. Brennan, J.D. Moore, and W.D. Mattson, ARL-TR-6863, U.S. Army Research Laboratory, Aberdeen Proving Ground, MD (2014).
 
 **(Larsen)**
    Larsen, Schmidt, Schiotz, Modelling Simul Mater Sci Eng, 24, 055007 (2016).
 
-**(Lebedeva et al.)**
+**(Lebedeva1)**
    I.\  V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
 
+**(Lebedeva2)**
+  I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
+
 **(Lechman)**
    Lechman, et al, in preparation (2010).
 
@@ -592,6 +748,9 @@ Bibliography
 **(Lee2)**
    Lee, Baskes, Kim, Cho.  Phys. Rev. B, 64, 184102 (2001).
 
+**(Lee2020)**
+   C.W. Lee, et al. (2020) Physical Review B, 102(2), 024107.
+
 **(Lenart)**
    Lenart , Jusufi, and Panagiotopoulos, J Chem Phys, 126, 044509 (2007).
 
@@ -616,8 +775,11 @@ Bibliography
 **(Li2015_JCP)**
    Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015).  DOI:10.1063/1.4923254.
 
+**(Liang)**
+   Liang, Phillpot, Sinnott Phys. Rev. B79 245110, (2009), Erratum: Phys. Rev. B85 199903(E), (2012)
+
 **(Lisal)**
-   M.\  Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
+   M.\  Lisal, J.K. Brennan, J. Bonet Avalos, J. Chem. Phys., 135, 204105 (2011).
 
 **(Liu1)**
    L.\  Liu, Y. Liu, S. V. Zybin, H. Sun and W. A. Goddard, Journal of Physical Chemistry A, 115, 11016-11022 (2011).
@@ -634,6 +796,15 @@ Bibliography
 **(Luding, 2008)**
    Luding, S. (2008). Cohesive, frictional powders: contact models for tension. Granular matter, 10(4), 235.
 
+**(Lysogorskiy)**
+   Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+**(Lysogorskiy21)**
+   Lysogorskiy, van der Oord, Bochkarev, Menon, Rinaldi, Hammerschmidt, Mrovec, Thompson, Csanyi, Ortner, Drautz, npj Comp Mat, 7, 97 (2021).
+
+**(Lysogorskiy23)**
+   Lysogorskiy, Bochkarev, Mrovec, Drautz, Phys Rev Mater, 7, 043801 (2023) / arXiv:2212.08716 (2022).
+
 **(Maaravi)**
    T.\  Maaravi et al, J. Phys. Chem. C 121, 22826-22835 (2017).
 
@@ -652,12 +823,18 @@ Bibliography
 **(Maginn)**
    Kelkar, Rafferty, Maginn, Siepmann, Fluid Phase Equilibria, 260, 218-231 (2007).
 
+**(Mahoney)**
+   Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
+
 **(Malolepsza)**
    Malolepsza, Secor, Keyes, J Phys Chem B 119 (42), 13379-13384 (2015).
 
 **(Mandadapu)**
    Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.  Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
 
+**(Mandelli_1)**
+   D. Mandelli, W. Ouyang, M. Urbakh, and O. Hod, ACS Nano 13(7), 7603-7609 (2019).
+
 **(Maras)**
    Maras, Trushin, Stukowski, Ala-Nissila, Jonsson, Comp Phys Comm, 205, 13-21 (2016).
 
@@ -673,6 +850,9 @@ Bibliography
 **(Martyna1994)**
    Martyna, Tobias and Klein, J Chem Phys, 101, 4177 (1994).
 
+**(Martyna2)**
+  G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
+
 **(Mason)**
    J.\  K. Mason, Acta Cryst A65, 259 (2009).
 
@@ -712,6 +892,9 @@ Bibliography
 **(Mie)**
    G.\  Mie, Ann Phys, 316, 657 (1903).
 
+**(Milano)**
+   G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).
+
 **(Miller1)**
    T.\  F. Miller III, M. Eleftheriou, P. Pattnaik, A. Ndirango, G. J. Martyna, J. Chem. Phys., 116, 8649-8659 (2002).
 
@@ -742,12 +925,18 @@ Bibliography
 **(Mitchell2011a)**
    Mitchell. A Nonlocal, Ordinary, State-Based Plasticity Model for Peridynamics. Sandia National Lab Report, 3166:1-34 (2011).
 
+**(Miyazaki)**
+   Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).
+
 **(Mniszewski)**
    S.\  M. Mniszewski, M. J. Cawkwell, M. E. Wall, J. Mohd-Yusof, N. Bock, T. C.  Germann, and A. M. N. Niklasson, J. Chem. Theory Comput., 11, 4644 (2015).
 
 **(Monaghan)**
    Monaghan and Gingold, Journal of Computational Physics, 52, 374-389 (1983).
 
+**(Monti)**
+   Monti, Clemmer, Srivastava, Silbert, Grest, and Lechman, Phys. Rev. E, (2022).
+
 **(Moore)**
    Moore, J Chem Phys, 144, 104501 (2016).
 
@@ -767,7 +956,7 @@ Bibliography
    Morris, Fox, Zhu, J Comp Physics, 136, 214-226 (1997).
 
 **(Moustafa)**
-   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, *Very fast averaging of thermal properties of crystals by molecular simulation*, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
+   Sabry G. Moustafa, Andrew J. Schultz, and David A. Kofke, `Phys. Rev. E [92], 043303 (2015) <https://link.aps.org/doi/10.1103/PhysRevE.92.043303>`_
 
 **(Muller-Plathe1)**
    Muller-Plathe, J Chem Phys, 106, 6082 (1997).
@@ -787,9 +976,6 @@ Bibliography
 **(Neelov)**
    Neelov, Holm, J Chem Phys 132, 234103 (2010)
 
-**(Negre2016)**
-   C.\  F. A. Negre, S. M. Mniszewski, M. J. Cawkwell, N. Bock, M. E. Wall, and A. M. N. Niklasson, J. Chem. Theory Comp., 12, 3063 (2016).
-
 **(Nelson)**
    Nelson, Halperin, Phys Rev B, 19, 2457 (1979).
 
@@ -799,12 +985,24 @@ Bibliography
 **(Neyts)**
    E.\  C. Neyts and A. Bogaerts, Theor. Chem. Acc. 132, 1320 (2013).
 
+**(Nguyen2023)**
+   Nguyen, Physical Review B, 107(14), 144103, (2023).
+
+**(Nguyen2024)**
+   Nguyen, Journal of Computational Physics, 113102, (2024).
+
+**(Nguyen and Rohskopf)**
+  Nguyen and Rohskopf,  Journal of Computational Physics, 480, 112030, (2023).
+
+**(Nguyen and Sema)**
+   Nguyen and Sema, https://arxiv.org/abs/2405.00306, (2024).
+
+**(NguyenTD)**
+   Nguyen, Li, Bagchi, Solis, Olvera de la Cruz, Comput Phys Commun 241, 80-19 (2019)
+
 **(Nicholson and Rutledge)**
    Nicholson and Rutledge, J Chem Phys, 145, 244903 (2016).
 
-**(Nicklas)**
-   The spline-based MEAM+SW format was first devised and used to develop potentials for bcc transition metals by Jeremy Nicklas, Michael Fellinger,
-
 **(Niklasson2002)**
    A.\  M. N. Niklasson, Phys. Rev. B, 66, 155115 (2002).
 
@@ -817,6 +1015,9 @@ Bibliography
 **(Niklasson2017)**
    A.\  M. N. Niklasson, J. Chem. Phys., 147, 054103 (2017).
 
+**(Nitol)**
+   Nitol, Dickel, and Barrett, Computational Materials Science 188 (2021): 110207.
+
 **(Noid)**
    Noid, Chu, Ayton, Krishna, Izvekov, Voth, Das, Andersen, J Chem Phys 128, 134105 (2008).
 
@@ -838,6 +1039,9 @@ Bibliography
 **(O'Connor)**
    O'Connor et al., J. Chem. Phys. 142, 024903 (2015).
 
+**(O'Hearn)**
+   O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1--C22 (2020).
+
 **(Okabe)**
    T.\  Okabe, M. Kawata, Y. Okamoto, M. Masuhiro, Chem. Phys. Lett., 335, 435-439 (2001).
 
@@ -847,6 +1051,8 @@ Bibliography
 **(Omelyan)**
    Omelyan, Mryglod, and Folk. Phys. Rev. Lett. 86(5), 898. (2001).
 
+**(OPLS-AA96)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
+
 **(Oppelstrup)**
    Oppelstrup, unpublished, 2015. Oppelstrup and Moriarty, to be published.
 
@@ -868,11 +1074,17 @@ Bibliography
 **(Ouyang2)**
    W.\  Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
 
-**(PASS)**
-   PASS webpage: https://www.sdu.dk/en/DPASS
+**(Ouyang_1)**
+   W. Ouyang et al., J. Chem. Theory Comput. 16(1), 666-676 (2020).
 
-**(PLUMED)**
-   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+**(Ouyang6)**
+   W. Ouyang, O. Hod, and R. Guerra, J. Chem. Theory Comput. 17, 7215 (2021).
+
+**(Ouyang7)**
+   W. Ouyang, et al., J. Chem. Theory Comput. 17, 7237 (2021).
+
+**(Palkar)**
+   Palkar V, Kuksenok O, J. Phys. Chem. B, 126 (1), 336-346, 2022
 
 **(Paquay)**
    Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
@@ -883,21 +1095,33 @@ Bibliography
 **(Parks)**
    Parks, Lehoucq, Plimpton, Silling, Comp Phys Comm, 179(11), 777-783 (2008).
 
-**(Parrinello1981)**
+**(Parrinello)**
    Parrinello and Rahman, J Appl Phys, 52, 7182 (1981).
 
+**(PASS)**
+   PASS webpage: https://www.sdu.dk/en/DPASS
+
 **(Paula Leite2016)**
    Paula Leite , Freitas, Azevedo, and de Koning, J Chem Phys, 126, 044509 (2016).
 
 **(Paula Leite2017)**
    Paula Leite, Santos-Florez, and de Koning, Phys Rev E, 96, 32115 (2017).
 
+**(Pavlov1)**
+   D Pavlov, V Galigerov, D Kolotinskii, V Nikolskiy, V Stegailov, International Journal of High Performance Computing Applications, 38, 34-49 (2024).
+
+**(Pavlov2)**
+   Pavlov, Galigerov, Kolotinskii, Nikolskiy, Stegailov, "GPU-based Molecular Dynamics of Fluid Flows: Reaching for Turbulence", Int. J. High Perf. Comp. Appl., (2024)
+
 **(Pearlman)**
    Pearlman, J Chem Phys, 98, 1487 (1994)
 
 **(Pedersen)**
    Pedersen, J. Chem. Phys., 139, 104102 (2013).
 
+**(Pedone)**
+   A. Pedone, G. Malavasi, M. C. Menziani, A. N. Cormack, and U. Segre, J. Phys. Chem. B, 110, 11780 (2006)
+
 **(Peng)**
    Peng, Ren, Dudarev, Whelan, Acta Crystallogr. A, 52, 257-76 (1996).
 
@@ -919,6 +1143,9 @@ Bibliography
 **(Pettifor_3)**
    D.G. Pettifor and I.I. Oleinik, Phys. Rev. B, 65, 172103 (2002).
 
+**(PFC)**
+   PFC Particle Flow Code 6.0 Documentation. Itasca Consulting Group.
+
 **(Phillips)**
    C.\  L. Phillips, J. A. Anderson, S. C. Glotzer, Comput Phys Comm, 230, 7191-7201 (2011).
 
@@ -928,9 +1155,21 @@ Bibliography
 **(Pisarev)**
    V V Pisarev and S V Starikov, J. Phys.: Condens. Matter, 26, 475401 (2014).
 
+**(Plimpton)**
+   Plimpton and Knight, JPDC, 147, 184-195 (2021).
+
+**(PLUMED)**
+   G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
+
 **(Pollock)**
    Pollock and Glosli, Comp Phys Comm, 95, 93 (1996).
 
+**(Ponder)**
+   Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque,  Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark,  Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
+
+**(Popov1)**
+   A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
+
 **(Price1)**
    Price and Brooks, J Chem Phys, 121, 10096 (2004).
 
@@ -970,6 +1209,12 @@ Bibliography
 **(Rick)**
    S.\  W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 16141 (1994).
 
+**(Rick2)**
+   S. W. Rick, S. J. Stuart, B. J. Berne, J Chem Phys 101, 6141
+
+**(Roberts)**
+   R. Roberts (2019) "Evenly Distributing Points in a Triangle." Extreme Learning.  `<http://extremelearning.com.au/evenly-distributing-points-in-a-triangle/>`_
+
 **(Rohart)**
    Rohart and Thiaville, Physical Review B, 88(18), 184422. (2013).
 
@@ -1006,9 +1251,18 @@ Bibliography
 **(Sadigh)**
    B Sadigh, P Erhart, A Stukowski, A Caro, E Martinez, and L Zepeda-Ruiz, Phys. Rev. B, 85, 184203 (2012).
 
+**(Sadigh1)**
+   B. Sadigh, P. Erhart, A. Stukowski, A. Caro, E. Martinez, and L. Zepeda-Ruiz, Phys. Rev. B **85**, 184203 (2012)
+
+**(Sadigh2)**
+  B. Sadigh and P. Erhart, Phys. Rev. B **86**, 134204 (2012)
+
 **(Safran)**
    Safran, Statistical Thermodynamics of Surfaces, Interfaces, And Membranes, Westview Press, ISBN: 978-0813340791 (2003).
 
+**(Salanne)**
+   Salanne, Rotenberg, Jahn, Vuilleumier, Simon, Christian and Madden, Theor Chem Acc, 131, 1143 (2012).
+
 **(Salerno)**
    Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).
 
@@ -1018,9 +1272,18 @@ Bibliography
 **(Sanyal2)**
    Sanyal and Shell, Journal of Physical Chemistry B, 122 (21), 5678-5693.
 
+**(Scalfi)**
+   Scalfi *et al.*, J. Chem. Phys., 153, 174704 (2020).
+
 **(Schelling)**
    Patrick K. Schelling, Comp. Mat. Science, 44, 274 (2008).
 
+**(Scherer1)**
+   C. Scherer and D. Andrienko, Phys. Chem. Chem. Phys. 20, 22387-22394 (2018).
+
+**(Scherer2)**
+   C. Scherer, R. Scheid, D. Andrienko, and T. Bereau, J. Chem. Theor. Comp. 16, 3194-3204 (2020).
+
 **(Schlitter1)**
    Schlitter, Swegat, Mulders, "Distance-type reaction coordinates for modelling activated processes", J Molecular Modeling, 7, 171-177 (2001).
 
@@ -1039,21 +1302,36 @@ Bibliography
 **(Schroeder)**
    Schroeder and Steinhauser, J Chem Phys, 133, 154511 (2010).
 
+**(Seleson 2010)**
+   Seleson, Parks, Int J Mult Comp Eng 9(6), pp. 689-706, 2011.
+
 **(Semaev)**
    Semaev, Cryptography and Lattices, 181 (2001).
 
+**(Seo)**
+   Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
+
 **(Sheppard)**
    Sheppard, Terrell, Henkelman, J Chem Phys, 128, 134106 (2008).  See ref 1 in this paper for original reference to Qmin in Jonsson, Mills, Jacobsen.
 
+**(Shi)**
+   Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
+
 **(Shinoda)**
    Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
 
 **(Shinoda)**
    Shinoda, Shiga, and Mikami, Phys Rev B, 69, 134103 (2004).
 
+**(Shire)**
+   Shire, Hanley and Stratford, Comp. Part. Mech., (2020).
+
 **(Sides)**
    Sides, Grest, Stevens, Plimpton, J Polymer Science B, 42, 199-208 (2004).
 
+**(Siepmann)**
+   Siepmann and Sprik, J. Chem. Phys. 102, 511 (1995).
+
 **(Silbert)**
    Silbert, Ertas, Grest, Halsey, Levine, Plimpton, Phys Rev E, 64, p 051302 (2001).
 
@@ -1063,12 +1341,21 @@ Bibliography
 **(Silling 2000)**
    Silling, J Mech Phys Solids, 48, 175-209 (2000).
 
+**(Silling 2005)**
+   Silling Askari, Computer and Structures, 83, 1526-1535 (2005).
+
 **(Silling 2007)**
    Silling, Epton, Weckner, Xu, Askari, J Elasticity, 88, 151-184 (2007).
 
 **(Singh)**
    Singh and Warner, Acta Mater, 58, 5797-5805 (2010),
 
+**(Singraber, Behler and Dellago 2019)**
+   Singraber, A.; Behler, J.; Dellago, C. J., Chem.  Theory Comput. 2019, 15 (3), 1827-1840
+
+**(Singraber et al 2019)**
+   Singraber, A.; Morawietz, T.; Behler, J.; Dellago, C., J. Chem. Theory Comput.  2019, 15 (5), 3075-3092.
+
 **(Sirk1)**
    Sirk TW, Sliozberg YR, Brennan JK, Lisal M, Andzelm JW, J Chem Phys, 136 (13) 134903, 2012.
 
@@ -1081,6 +1368,9 @@ Bibliography
 **(Snodin)**
    B.E. Snodin, F. Randisi, M. Mosayebi, et al., J. Chem. Phys. 142, 234901 (2015).
 
+**(Son)**
+   Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).
+
 **(Srivastava)**
    Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
 
@@ -1090,6 +1380,12 @@ Bibliography
 **(Steinhardt)**
    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).
 
@@ -1147,12 +1443,21 @@ 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).
 
@@ -1195,6 +1500,9 @@ 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),
 
@@ -1213,6 +1521,9 @@ 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
 
@@ -1222,6 +1533,15 @@ 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).
 
@@ -1234,6 +1554,9 @@ 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).
 
@@ -1258,6 +1581,9 @@ 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).
 
@@ -1297,6 +1623,9 @@ 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).
 
@@ -1309,9 +1638,27 @@ 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.
 
@@ -1381,17 +1728,6 @@ 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

@@ -1,10 +1,14 @@
 Build LAMMPS
 ============
 
-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).
+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.
 
 As an alternative, you can download a package with pre-built executables
 or automated build trees, as described in the :doc:`Install <Install>`
@@ -13,6 +17,7 @@ section of the manual.
 .. toctree::
    :maxdepth: 1
 
+   Build_prerequisites
    Build_cmake
    Build_make
    Build_link

doc/src/Build_basics.rst

@@ -37,8 +37,9 @@ 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, else no
-         -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
+         -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
 
@@ -54,9 +55,9 @@ 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
@@ -74,15 +75,15 @@ 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
@@ -90,7 +91,7 @@ standard. A more detailed discussion of that is below.
       directory, or ``make`` from the ``src/STUBS`` dir.  If the build
       fails, you may need to edit the ``STUBS/Makefile`` for your
       platform.  The stubs library does not provide MPI/IO functions
-      required by some LAMMPS packages, e.g. ``MPIIO`` or ``LATBOLTZ``,
+      required by some LAMMPS packages, e.g. ``LATBOLTZ``,
       and thus is not compatible with those packages.
 
       .. note::
@@ -128,14 +129,13 @@ and adds vectorization support when compiled with compatible compilers,
 in particular the Intel compilers on top of OpenMP. Also, the ``KOKKOS``
 package can be compiled to include OpenMP threading.
 
-In addition, there are a few commands in LAMMPS that have native
-OpenMP support included as well.  These are commands in the ``MPIIO``,
-``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 ``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
+``LMP_INC`` variable in your makefile, or add it to the command-line flags
 while configuring with CMake.  LAMMPS will auto-detect a suitable setting
 for most GNU, Clang, and Intel compilers.
 
@@ -196,22 +196,23 @@ LAMMPS.
 
    .. tab:: CMake build
 
-      By default CMake will use the compiler it finds according to
+      By default CMake will use the compiler it finds according to its
       internal preferences, and it will add optimization flags
       appropriate to that compiler and any :doc:`accelerator packages
       <Speed_packages>` you have included in the build.  CMake will
       check if the detected or selected compiler is compatible with the
       C++ support requirements of LAMMPS and stop with an error, if this
-      is not the case.
+      is not the case.  A C++11 compatible compiler is currently
+      required, but a transition to require C++17 is in progress and
+      planned to be completed in Summer 2025. Currently, setting
+      ``-DLAMMPS_CXX11=yes`` is required when configuring with CMake while
+      using a C++11 compatible compiler that does not support C++17,
+      otherwise setting ``-DCMAKE_CXX_STANDARD=17`` is preferred.
 
       You can tell CMake to look for a specific compiler with setting
       CMake variables (listed below) during configuration.  For a few
       common choices, there are also presets in the ``cmake/presets``
-      folder.  For convenience, there is a ``CMAKE_TUNE_FLAGS`` variable
-      that can be set to apply global compiler options (applied to
-      compilation only), to be used for adding compiler or host specific
-      optimization flags in addition to the "flags" variables listed
-      below. You may also specify the corresponding ``CMAKE_*_FLAGS``
+      folder.  You may also specify the corresponding ``CMAKE_*_FLAGS``
       variables individually, if you want to experiment with alternate
       optimization flags.  You should specify all 3 compilers, so that
       the (few) LAMMPS source files written in C or Fortran are built
@@ -223,6 +224,8 @@ LAMMPS.
          -D CMAKE_C_COMPILER=name              # name of C compiler
          -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
 
+         -D CMAKE_CXX_STANDARD=17              # put compiler in C++17 mode
+         -D LAMMPS_CXX11=yes                   # enforce compilation in C++11 mode
          -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
          -D CMAKE_C_FLAGS=string               # flags to use with C compiler
          -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
@@ -232,35 +235,39 @@ LAMMPS.
       .. code-block:: bash
 
          # Building with GNU Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
-         # Building with Intel Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         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
          # Building with Intel oneAPI Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
+         cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx \
+               -DCMAKE_Fortran_COMPILER=ifx ../cmake
          # Building with LLVM/Clang Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
+         cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ \
+               -DCMAKE_Fortran_COMPILER=flang ../cmake
          # Building with PGI/Nvidia Compilers:
-         cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
+         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
 
       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,
-      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.
-      This variable is empty by default.
+      ``-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.
 
       .. note::
 
          When the cmake command completes, it prints a summary to the
          screen which compilers it is using and what flags and settings
          will be used for the compilation.  Note that if the top-level
-         compiler is mpicxx, it is simply a wrapper on a real compiler.
+         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.
@@ -279,19 +286,19 @@ 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::
 
@@ -313,15 +320,23 @@ LAMMPS.
          you would have to install a newer compiler that supports C++11;
          either as a binary package or through compiling from source.
 
-         If you build LAMMPS with any :doc:`Speed_packages` included,
-         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
-         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
-         accelerator packages and their hardware variants:
+      While a C++11 compatible compiler is currently sufficient to compile
+      LAMMPS, a transition to require C++17 is in progress and planned to
+      be completed in Summer 2025. Currently, setting ``-DLAMMPS_CXX11``
+      in the ``LMP_INC =`` line in the machine makefile is required when
+      using a C++11 compatible compiler that does not support C++17.
+      Otherwise, to enable C++17 support (if not enabled by default) using
+      a compiler flag like ``-std=c++17`` in CCFLAGS may needed.
+
+      If you build LAMMPS with any :doc:`Speed_packages` included,
+      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
+      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
+      accelerator packages and their hardware variants:
 
          .. code-block:: bash
 
@@ -389,7 +404,8 @@ 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``\ ,
@@ -451,7 +467,7 @@ 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
@@ -464,7 +480,7 @@ 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).
@@ -489,8 +505,12 @@ using CMake or Make.
 
       .. code-block:: bash
 
-         -D BUILD_TOOLS=value         # yes or no (default)
-         -D BUILD_LAMMPS_SHELL=value  # yes or no (default)
+         -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
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).
@@ -504,10 +524,10 @@ 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
 
-         cd lammps/tools/lammps-shell
-         make                  # build LAMMPS shell
+      .. note::
+
+         Building the LAMMPS-GUI *requires* building LAMMPS with CMake.
 
 ----------
 

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
@@ -16,8 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
-   LAMMPS currently requires that CMake version 3.10 or later is available;
-   version 3.12 or later is preferred.
+   LAMMPS currently requires that CMake version 3.20 or later is available.
 
 .. warning::
 
@@ -33,30 +32,29 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 Advantages of using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-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
+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
 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 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 manual editing of files,
+  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.
 - Simplified packaging of LAMMPS for Linux distributions, environment
-  modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
-- Integration of automated unit and regression testing (the LAMMPS side
-  of this is still under active development).
+  modules, or automated build tools like `Spack <https://spack.io>`_
+  or `Homebrew <https://brew.sh/>`_.
+- Integration of automated unit and regression testing.
 
 .. _cmake_build:
 
@@ -70,7 +68,7 @@ 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
@@ -121,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
 potential and force field files.  The location of the installation tree
 defaults to ``${HOME}/.local``.
 
+.. note::
+
+   If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
+   system location on a Linux machine , you may also have to run (as
+   root) the `ldconfig` program to update the cache file for fast lookup
+   of system shared libraries.
+
 .. _cmake_options:
 
 Configuration and build options
@@ -133,21 +138,21 @@ 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 line.
+by adding one or more ``-D`` flags to the CMake command.
 
 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:
@@ -173,19 +178,19 @@ 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" 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.
+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.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -28,28 +28,6 @@ variable VERBOSE set to 1:
 
 ----------
 
-.. _clang-tidy:
-
-Enable static code analysis with clang-tidy (CMake only)
---------------------------------------------------------
-
-The `clang-tidy tool <https://clang.llvm.org/extra/clang-tidy/>`_ is a
-static code analysis tool to diagnose (and potentially fix) typical
-programming errors or coding style violations.  It has a modular framework
-of tests that can be adjusted to help identifying problems before they
-become bugs and also assist in modernizing large code bases (like LAMMPS).
-It can be enabled for all C++ code with the following CMake flag
-
-.. code-block:: bash
-
-   -D ENABLE_CLANG_TIDY=value    # value = no (default) or yes
-
-With this flag enabled all source files will be processed twice, first to
-be compiled and then to be analyzed. Please note that the analysis can be
-significantly more time-consuming than the compilation itself.
-
-----------
-
 .. _iwyu_processing:
 
 Report missing and unneeded '#include' statements (CMake only)
@@ -88,8 +66,8 @@ on recording all commands required to do the compilation.
 
 .. _sanitizer:
 
-Address, Undefined Behavior, and Thread Sanitizer Support (CMake only)
-----------------------------------------------------------------------
+Address, Leak, 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
@@ -110,6 +88,7 @@ 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
@@ -122,32 +101,59 @@ Code Coverage and Unit Testing (CMake only)
 -------------------------------------------
 
 The LAMMPS code is subject to multiple levels of automated testing
-during development: integration testing (i.e. whether the code compiles
-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>`_.
+during development:
 
-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.
+- 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 unit testing facility is integrated into the CMake build process
-of the LAMMPS source code distribution itself.  It can be enabled by
+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
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-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.
+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``.
 
-.. admonition:: Software version requirements for testing
+.. admonition:: Software version and LAMMPS configuration requirements
    :class: note
 
    The compiler and library version requirements for the testing
@@ -155,7 +161,7 @@ for implementing the tests.
    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 tests will depend on
+   stop with an error.  Also the number of available tests will depend on
    installed LAMMPS packages, development environment, operating system,
    and configuration settings.
 
@@ -168,24 +174,24 @@ 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
 
@@ -200,24 +206,25 @@ 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
@@ -234,12 +241,31 @@ 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 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.
+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.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -255,16 +281,18 @@ 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``, 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:
+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:
 
 .. code-block:: console
 
@@ -302,16 +330,17 @@ 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
@@ -325,10 +354,10 @@ 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
@@ -369,7 +398,7 @@ 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
@@ -416,15 +445,16 @@ 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 ``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.
+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.
 
 Tests for other components and utility functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -471,33 +501,57 @@ to do this to install it via pip:
 
 .. code-block:: bash
 
-   pip install git+https://github.com/gcovr/gcovr.git
+   python3 -m pip install gcovr
 
 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.
 
-.. list-table::
+.. only:: not latex
 
-      * - .. figure:: JPG/coverage-overview-top.png
-             :scale: 25%
+   .. list-table::
 
-          Top of the overview page
+         * - .. figure:: JPG/coverage-overview-top.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-overview-manybody.png
-             :scale: 25%
+             Top of the overview page
 
-          Styles with good coverage
+           - .. figure:: JPG/coverage-overview-manybody.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-file-top.png
-             :scale: 25%
+             Styles with good coverage
 
-          Top of individual source page
+           - .. figure:: JPG/coverage-file-top.png
+                :scale: 25%
 
-        - .. figure:: JPG/coverage-file-branches.png
-             :scale: 25%
+             Top of individual source page
 
-          Source page with branches
+           - .. 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
 
 Coding style utilities
 ----------------------
@@ -518,6 +572,8 @@ 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
@@ -564,14 +620,38 @@ The following target are available for both, GNU make and CMake:
 
 .. _gh-cli:
 
-GitHub command line interface
+GitHub command-line interface
 -----------------------------
 
-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.
+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:
 
-The capabilities of the ``gh`` command is continually expanding, so
-please see the documentation at https://cli.github.com/manual/
+.. 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.