temporarily comment out incomplete run WHAM and plot results dialog for release

this way its contribution is not double counted when determining
the "Other" time data.

.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
@@ -58,15 +60,26 @@ 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-FIX/fix_deform_pressure.* @jtclemm
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps
+src/REAXFF/compute_reaxff_atom.*    @rbberger
+src/KOKKOS/compute_reaxff_atom_kokkos.*    @rbberger
+src/REPLICA/fix_pimd_langevin.*     @Yi-FanLi
+src/DPD-BASIC/pair_dpd_coul_slater_long.* @Eddy-Barraud
+src/GPU/pair_dpd_coul_slater_long.* @Eddy-Barraud
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -78,7 +91,7 @@ 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
@@ -86,9 +99,10 @@ 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/library.*             @sjplimp @akohlmey
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
@@ -96,12 +110,12 @@ 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
@@ -134,6 +148,7 @@ 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
@@ -150,12 +165,12 @@ tools/vim/*           @hammondkd
 unittest/*            @akohlmey
 
 # cmake
-cmake/*               @junghans @rbberger
+cmake/*               @akohlmey
 cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
 cmake/Modules/MPI4WIN.cmake @akohlmey
 cmake/Modules/OpenCLLoader.cmake @akohlmey
-cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
-cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
+cmake/Modules/Packages/COLVARS.cmake @giacomofiorin
+cmake/Modules/Packages/KIM.cmake @ellio167
 cmake/presets/*.cmake @akohlmey
 
 # python

.github/CONTRIBUTING.md

@@ -1,13 +1,13 @@
 # Contributing to LAMMPS via GitHub
 
-Thank your for considering to contribute to the LAMMPS software project.
+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/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

@@ -19,12 +19,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 

.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.*') }}
@@ -59,16 +59,13 @@ 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 \
@@ -77,7 +74,6 @@ jobs:
         -D PKG_PTM=on \
         -D PKG_QTB=on \
         -D PKG_SMTBQ=on \
-        -D PKG_TALLY=on \
         ../cmake
 
     - name: Run Coverity Scan

.github/workflows/unittest-macos.yml

@@ -15,13 +15,13 @@ 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 +32,7 @@ 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 +43,8 @@ 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
@@ -57,3 +57,7 @@ out/x86
 out/x64
 src/Makefile.package-e
 src/Makefile.package.settings-e
+/cmake/build/x64-Debug-Clang
+/install/x64-GUI-MSVC
+/install
+.Rhistory

SECURITY.md

@@ -32,17 +32,21 @@ for unicode characters and only all-ASCII source code is accepted.
 
 LAMMPS follows a continuous release development model.  We aim to keep
 the development version (`develop` branch) always fully functional and
-employ a variety of automatic testing procedures to detect failures
-of existing functionality from adding or modifying features.  Most of
-those tests are run on pull requests *before* merging to the `develop`
-branch.  The `develop` branch is protected, so all changes *must* be
-submitted as a pull request and thus cannot avoid the automated tests.
+employ a variety of automatic testing procedures to detect failures of
+existing functionality from adding or modifying features.  Most of those
+tests are run on pull requests and must be passed *before* merging to
+the `develop` branch.  The `develop` branch is protected, so all changes
+*must* be submitted as a pull request and thus cannot avoid the
+automated tests.
 
 Additional tests are run *after* merging.  Before releases are made
 *all* tests must have cleared.  Then a release tag is applied and the
-`release` branch is fast-forwarded to that tag.  This is often referred
-to as a patch release. Bug fixes and updates are
-applied first to the `develop` branch.  Later, they appear in the `release`
-branch when the next patch release occurs.
-For stable releases, selected bug fixes, updates, and new functionality
-are pushed to the `stable` branch and a new stable tag is applied.
+`release` branch is fast-forwarded to that tag.  This is referred to to
+as a "feature release".  Bug fixes and updates are applied first to the
+`develop` branch.  Later, they appear in the `release` branch when the
+next patch release occurs.  For stable releases, backported bug fixes
+and infrastructure updates are first applied to the `maintenance` branch
+and then merged to `stable` and published as "updates".  For a new
+stable release the `stable` branch is updated to the corresponding state
+of the `release` branch and a new stable tag is applied in addition to
+the release tag.

bench/in.chain

@@ -1,25 +1,25 @@
 # FENE beadspring benchmark
 
-units		lj
-atom_style	bond
+units           lj
+atom_style      bond
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
+neighbor        0.4 bin
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_style      lj/cut 1.12
+pair_modify     shift yes
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             1 all nve
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chain.scaled

@@ -1,32 +1,32 @@
 # FENE beadspring benchmark
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-units		lj
-atom_style	bond
-atom_modify	map hash
+units           lj
+atom_style      bond
+atom_modify     map hash
 special_bonds   fene
 
-read_data	data.chain
+read_data       data.chain
 
-replicate	$x $y $z
+replicate       $x $y $z
 
-neighbor	0.4 bin
-neigh_modify	every 1 delay 1
+neighbor        0.4 bin
+neigh_modify    every 1 delay 1
 
 bond_style      fene
-bond_coeff	1 30.0 1.5 1.0 1.0
+bond_coeff      1 30.0 1.5 1.0 1.0
 
-pair_style	lj/cut 1.12
-pair_modify	shift yes
-pair_coeff	1 1 1.0 1.0 1.12
+pair_style      lj/cut 1.12
+pair_modify     shift yes
+pair_coeff      1 1 1.0 1.0 1.12
 
-fix		1 all nve
-fix		2 all langevin 1.0 1.0 10.0 904297
+fix             1 all nve
+fix             2 all langevin 1.0 1.0 10.0 904297
 
 thermo          100
-timestep	0.012
+timestep        0.012
 
-run		100
+run             100

bench/in.chute

@@ -1,33 +1,33 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
+units           lj
+atom_style      sphere
+boundary        p p fs
+newton          off
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff      * *
 
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
+neighbor        0.1 bin
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
-group		active subtract all bottom
-neigh_modify	exclude group bottom bottom
+group           bottom type 2
+group           active subtract all bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
+fix             1 all gravity 1.0 chute 26.0
+fix             2 bottom freeze
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
+compute         1 all erotate/sphere
+thermo_style    custom step atoms ke c_1 vol
+thermo_modify   norm no
+thermo          100
 
-run		100
+run             100

bench/in.chute.scaled

@@ -1,38 +1,38 @@
 # LAMMPS benchmark of granular flow
 # chute flow of 32000 atoms with frozen base at 26 degrees
 
-variable	x index 1
-variable	y index 1
+variable        x index 1
+variable        y index 1
 
-units		lj
-atom_style	sphere
-boundary	p p fs
-newton		off
-comm_modify	vel yes
+units           lj
+atom_style      sphere
+boundary        p p fs
+newton          off
+comm_modify     vel yes
 
-read_data	data.chute
+read_data       data.chute
 
-replicate	$x $y 1
+replicate       $x $y 1
 
-pair_style	gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
-pair_coeff	* *
+pair_style      gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0
+pair_coeff      * *
 
-neighbor	0.1 bin
-neigh_modify	every 1 delay 0
+neighbor        0.1 bin
+neigh_modify    every 1 delay 0
 
-timestep	0.0001
+timestep        0.0001
 
-group		bottom type 2
-group		active subtract all bottom
-neigh_modify	exclude group bottom bottom
+group           bottom type 2
+group           active subtract all bottom
+neigh_modify    exclude group bottom bottom
 
-fix		1 all gravity 1.0 chute 26.0
-fix		2 bottom freeze
-fix		3 active nve/sphere
+fix             1 all gravity 1.0 chute 26.0
+fix             2 bottom freeze
+fix             3 active nve/sphere
 
-compute		1 all erotate/sphere
-thermo_style	custom step atoms ke c_1 vol
-thermo_modify	norm no
-thermo		100
+compute         1 all erotate/sphere
+thermo_style    custom step atoms ke c_1 vol
+thermo_modify   norm no
+thermo          100
 
-run		100
+run             100

bench/in.eam

@@ -1,32 +1,32 @@
 # bulk Cu lattice
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
 
-units		metal
-atom_style	atomic
+units           metal
+atom_style      atomic
 
-lattice		fcc 3.615
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
+lattice         fcc 3.615
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
 
-pair_style	eam
-pair_coeff	1 1 Cu_u3.eam
+pair_style      eam
+pair_coeff      1 1 Cu_u3.eam
 
-velocity	all create 1600.0 376847 loop geom
+velocity        all create 1600.0 376847 loop geom
 
-neighbor	1.0 bin
+neighbor        1.0 bin
 neigh_modify    every 1 delay 5 check yes
 
-fix		1 all nve
+fix             1 all nve
 
-timestep	0.005
-thermo		50
+timestep        0.005
+thermo          50
 
-run		100
+run             100

bench/in.lj

@@ -1,30 +1,30 @@
 # 3d Lennard-Jones melt
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-variable	xx equal 20*$x
-variable	yy equal 20*$y
-variable	zz equal 20*$z
+variable        xx equal 20*$x
+variable        yy equal 20*$y
+variable        zz equal 20*$z
 
-units		lj
-atom_style	atomic
+units           lj
+atom_style      atomic
 
-lattice		fcc 0.8442
-region		box block 0 ${xx} 0 ${yy} 0 ${zz}
-create_box	1 box
-create_atoms	1 box
-mass		1 1.0
+lattice         fcc 0.8442
+region          box block 0 ${xx} 0 ${yy} 0 ${zz}
+create_box      1 box
+create_atoms    1 box
+mass            1 1.0
 
-velocity	all create 1.44 87287 loop geom
+velocity        all create 1.44 87287 loop geom
 
-pair_style	lj/cut 2.5
-pair_coeff	1 1 1.0 1.0 2.5
+pair_style      lj/cut 2.5
+pair_coeff      1 1 1.0 1.0 2.5
 
-neighbor	0.3 bin
-neigh_modify	delay 0 every 20 check no
+neighbor        0.3 bin
+neigh_modify    delay 0 every 20 check no
 
-fix		1 all nve
+fix             1 all nve
 
-run		100
+run             100

bench/in.rhodo

@@ -1,27 +1,27 @@
 # Rhodopsin model
 
-units           real  
-neigh_modify    delay 5 every 1   
+units           real
+neigh_modify    delay 5 every 1
 
-atom_style      full  
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
 
 read_data       data.rhodo
 
 fix             1 all shake 0.0001 5 0 m 1.0 a 232
 fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
- 
+
 thermo          50
-thermo_style    multi 
+thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

bench/in.rhodo.scaled

@@ -1,34 +1,34 @@
 # Rhodopsin model
 
-variable	x index 1
-variable	y index 1
-variable	z index 1
+variable        x index 1
+variable        y index 1
+variable        z index 1
 
-units           real  
-neigh_modify    delay 5 every 1   
+units           real
+neigh_modify    delay 5 every 1
 
-atom_style      full  
-atom_modify	map hash
-bond_style      harmonic 
-angle_style     charmm 
-dihedral_style  charmm 
-improper_style  harmonic 
-pair_style      lj/charmm/coul/long 8.0 10.0 
-pair_modify     mix arithmetic 
-kspace_style    pppm 1e-4 
+atom_style      full
+atom_modify     map hash
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+pair_style      lj/charmm/coul/long 8.0 10.0
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
 
 read_data       data.rhodo
 
-replicate	$x $y $z
+replicate       $x $y $z
 
 fix             1 all shake 0.0001 5 0 m 1.0 a 232
 fix             2 all npt temp 300.0 300.0 100.0 &
-		z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
+                z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
 
 special_bonds   charmm
- 
+
 thermo          50
-thermo_style    multi 
+thermo_style    multi
 timestep        2.0
 
-run		100
+run             100

cmake/CMakeLists.jpeg

@@ -1,615 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-if(CMAKE_EXECUTABLE_SUFFIX)
-  set(CMAKE_EXECUTABLE_SUFFIX_TMP ${CMAKE_EXECUTABLE_SUFFIX})
-endif()
-
-project(libjpeg-turbo C)
-set(VERSION 2.1.3)
-set(COPYRIGHT_YEAR "1991-2022")
-string(REPLACE "." ";" VERSION_TRIPLET ${VERSION})
-list(GET VERSION_TRIPLET 0 VERSION_MAJOR)
-list(GET VERSION_TRIPLET 1 VERSION_MINOR)
-list(GET VERSION_TRIPLET 2 VERSION_REVISION)
-function(pad_number NUMBER OUTPUT_LEN)
-  string(LENGTH "${${NUMBER}}" INPUT_LEN)
-  if(INPUT_LEN LESS OUTPUT_LEN)
-    math(EXPR ZEROES "${OUTPUT_LEN} - ${INPUT_LEN} - 1")
-    set(NUM ${${NUMBER}})
-    foreach(C RANGE ${ZEROES})
-      set(NUM "0${NUM}")
-    endforeach()
-    set(${NUMBER} ${NUM} PARENT_SCOPE)
-  endif()
-endfunction()
-pad_number(VERSION_MINOR 3)
-pad_number(VERSION_REVISION 3)
-set(LIBJPEG_TURBO_VERSION_NUMBER ${VERSION_MAJOR}${VERSION_MINOR}${VERSION_REVISION})
-
-# CMake 3.14 and later sets CMAKE_MACOSX_BUNDLE to TRUE by default when
-# CMAKE_SYSTEM_NAME is iOS, tvOS, or watchOS, which breaks the libjpeg-turbo
-# build.  (Specifically, when CMAKE_MACOSX_BUNDLE is TRUE, executables for
-# Apple platforms are built as application bundles, which causes CMake to
-# complain that our install() directives for executables do not specify a
-# BUNDLE DESTINATION.  Even if CMake did not complain, building executables as
-# application bundles would break our iOS packages.)
-set(CMAKE_MACOSX_BUNDLE FALSE)
-
-string(TIMESTAMP DEFAULT_BUILD "%Y%m%d")
-set(BUILD ${DEFAULT_BUILD} CACHE STRING "Build string (default: ${DEFAULT_BUILD})")
-
-# NOTE: On Windows, this does nothing except when using MinGW or Cygwin.
-# CMAKE_BUILD_TYPE has no meaning in Visual Studio, and it always defaults to
-# Debug when using NMake.
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE Release)
-endif()
-message(STATUS "CMAKE_BUILD_TYPE = ${CMAKE_BUILD_TYPE}")
-
-message(STATUS "VERSION = ${VERSION}, BUILD = ${BUILD}")
-
-include(cmakescripts/PackageInfo.cmake)
-
-# Detect CPU type and whether we're building 64-bit or 32-bit code
-math(EXPR BITS "${CMAKE_SIZEOF_VOID_P} * 8")
-string(TOLOWER ${CMAKE_SYSTEM_PROCESSOR} CMAKE_SYSTEM_PROCESSOR_LC)
-set(COUNT 1)
-foreach(ARCH ${CMAKE_OSX_ARCHITECTURES})
-  if(COUNT GREATER 1)
-    message(FATAL_ERROR "The libjpeg-turbo build system does not support multiple values in CMAKE_OSX_ARCHITECTURES.")
-  endif()
-  math(EXPR COUNT "${COUNT}+1")
-endforeach()
-if(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86_64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "amd64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "i[0-9]86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "x86" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "ia32")
-  if(BITS EQUAL 64 OR CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-    set(CPU_TYPE x86_64)
-  else()
-    set(CPU_TYPE i386)
-  endif()
-  if(NOT CMAKE_SYSTEM_PROCESSOR STREQUAL ${CPU_TYPE})
-    set(CMAKE_SYSTEM_PROCESSOR ${CPU_TYPE})
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC STREQUAL "aarch64" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^arm")
-  if(BITS EQUAL 64)
-    set(CPU_TYPE arm64)
-  else()
-    set(CPU_TYPE arm)
-  endif()
-elseif(CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^ppc" OR
-  CMAKE_SYSTEM_PROCESSOR_LC MATCHES "^powerpc")
-  set(CPU_TYPE powerpc)
-else()
-  set(CPU_TYPE ${CMAKE_SYSTEM_PROCESSOR_LC})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "x86_64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "arm64" OR
-  CMAKE_OSX_ARCHITECTURES MATCHES "i386")
-  set(CPU_TYPE ${CMAKE_OSX_ARCHITECTURES})
-endif()
-if(CMAKE_OSX_ARCHITECTURES MATCHES "ppc")
-  set(CPU_TYPE powerpc)
-endif()
-if(MSVC_IDE AND CMAKE_GENERATOR_PLATFORM MATCHES "arm64")
-  set(CPU_TYPE arm64)
-endif()
-
-message(STATUS "${BITS}-bit build (${CPU_TYPE})")
-
-macro(report_directory var)
-  if(CMAKE_INSTALL_${var} STREQUAL CMAKE_INSTALL_FULL_${var})
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}}")
-  else()
-    message(STATUS "CMAKE_INSTALL_${var} = ${CMAKE_INSTALL_${var}} (${CMAKE_INSTALL_FULL_${var}})")
-  endif()
-  mark_as_advanced(CLEAR CMAKE_INSTALL_${var})
-endmacro()
-
-set(DIRLIST "BINDIR;DATAROOTDIR;DOCDIR;INCLUDEDIR;LIBDIR")
-if(UNIX)
-  list(APPEND DIRLIST "MANDIR")
-endif()
-foreach(dir ${DIRLIST})
-  report_directory(${dir})
-endforeach()
-
-
-###############################################################################
-# CONFIGURATION OPTIONS
-###############################################################################
-
-macro(boolean_number var)
-  if(${var})
-    set(${var} 1 ${ARGN})
-  else()
-    set(${var} 0 ${ARGN})
-  endif()
-endmacro()
-
-option(ENABLE_SHARED "Build shared libraries" FALSE)
-boolean_number(ENABLE_SHARED)
-option(ENABLE_STATIC "Build static libraries" TRUE)
-boolean_number(ENABLE_STATIC)
-option(REQUIRE_SIMD "Generate a fatal error if SIMD extensions are not available for this platform (default is to fall back to a non-SIMD build)" FALSE)
-boolean_number(REQUIRE_SIMD)
-option(WITH_12BIT "Encode/decode JPEG images with 12-bit samples (implies WITH_ARITH_DEC=0 WITH_ARITH_ENC=0 WITH_JAVA=0 WITH_SIMD=0 WITH_TURBOJPEG=0 )" FALSE)
-boolean_number(WITH_12BIT)
-option(WITH_ARITH_DEC "Include arithmetic decoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_DEC)
-option(WITH_ARITH_ENC "Include arithmetic encoding support when emulating the libjpeg v6b API/ABI" TRUE)
-boolean_number(WITH_ARITH_ENC)
-if(CMAKE_C_COMPILER_ABI MATCHES "ELF X32")
-  set(WITH_JAVA 0)
-else()
-  option(WITH_JAVA "Build Java wrapper for the TurboJPEG API library (implies ENABLE_SHARED=1)" FALSE)
-  boolean_number(WITH_JAVA)
-endif()
-option(WITH_JPEG7 "Emulate libjpeg v7 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG7)
-option(WITH_JPEG8 "Emulate libjpeg v8 API/ABI (this makes ${CMAKE_PROJECT_NAME} backward-incompatible with libjpeg v6b)" FALSE)
-boolean_number(WITH_JPEG8)
-option(WITH_MEM_SRCDST "Include in-memory source/destination manager functions when emulating the libjpeg v6b or v7 API/ABI" TRUE)
-boolean_number(WITH_MEM_SRCDST)
-option(WITH_SIMD "Include SIMD extensions, if available for this platform" FALSE)
-boolean_number(WITH_SIMD)
-option(WITH_TURBOJPEG "Include the TurboJPEG API library and associated test programs" FALSE)
-boolean_number(WITH_TURBOJPEG)
-option(WITH_FUZZ "Build fuzz targets" FALSE)
-
-macro(report_option var desc)
-  if(${var})
-    message(STATUS "${desc} enabled (${var} = ${${var}})")
-  else()
-    message(STATUS "${desc} disabled (${var} = ${${var}})")
-  endif()
-endmacro()
-
-if(WITH_JAVA)
-  set(ENABLE_SHARED 1)
-endif()
-
-# Explicitly setting CMAKE_POSITION_INDEPENDENT_CODE=FALSE disables PIC for all
-# targets, which will cause the shared library builds to fail.  Thus, if shared
-# libraries are enabled and CMAKE_POSITION_INDEPENDENT_CODE is explicitly set
-# to FALSE, we need to unset it, thus restoring the default behavior
-# (automatically using PIC for shared library targets.)
-if(DEFINED CMAKE_POSITION_INDEPENDENT_CODE AND
-  NOT CMAKE_POSITION_INDEPENDENT_CODE AND ENABLE_SHARED)
-  unset(CMAKE_POSITION_INDEPENDENT_CODE CACHE)
-endif()
-
-report_option(ENABLE_SHARED "Shared libraries")
-report_option(ENABLE_STATIC "Static libraries")
-
-if(ENABLE_SHARED)
-  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
-endif()
-
-if(WITH_JPEG8 OR WITH_JPEG7)
-  set(WITH_ARITH_ENC 1)
-  set(WITH_ARITH_DEC 1)
-endif()
-if(WITH_JPEG8)
-  set(WITH_MEM_SRCDST 0)
-endif()
-
-if(WITH_12BIT)
-  set(WITH_ARITH_DEC 0)
-  set(WITH_ARITH_ENC 0)
-  set(WITH_JAVA 0)
-  set(WITH_SIMD 0)
-  set(WITH_TURBOJPEG 0)
-  set(BITS_IN_JSAMPLE 12)
-else()
-  set(BITS_IN_JSAMPLE 8)
-endif()
-report_option(WITH_12BIT "12-bit JPEG support")
-
-if(WITH_ARITH_DEC)
-  set(D_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_DEC "Arithmetic decoding support")
-endif()
-
-if(WITH_ARITH_ENC)
-  set(C_ARITH_CODING_SUPPORTED 1)
-endif()
-if(NOT WITH_12BIT)
-  report_option(WITH_ARITH_ENC "Arithmetic encoding support")
-endif()
-
-if(NOT WITH_12BIT)
-  report_option(WITH_TURBOJPEG "TurboJPEG API library")
-  report_option(WITH_JAVA "TurboJPEG Java wrapper")
-endif()
-
-if(WITH_MEM_SRCDST)
-  set(MEM_SRCDST_SUPPORTED 1)
-  set(MEM_SRCDST_FUNCTIONS "global:  jpeg_mem_dest;  jpeg_mem_src;")
-endif()
-if(NOT WITH_JPEG8)
-  report_option(WITH_MEM_SRCDST "In-memory source/destination managers")
-endif()
-
-set(SO_AGE 2)
-if(WITH_MEM_SRCDST)
-  set(SO_AGE 3)
-endif()
-
-if(WITH_JPEG8)
-  set(JPEG_LIB_VERSION 80)
-elseif(WITH_JPEG7)
-  set(JPEG_LIB_VERSION 70)
-else()
-  set(JPEG_LIB_VERSION 62)
-endif()
-
-math(EXPR JPEG_LIB_VERSION_DIV10 "${JPEG_LIB_VERSION} / 10")
-math(EXPR JPEG_LIB_VERSION_MOD10 "${JPEG_LIB_VERSION} % 10")
-if(JPEG_LIB_VERSION STREQUAL "62")
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION})
-else()
-  set(DEFAULT_SO_MAJOR_VERSION ${JPEG_LIB_VERSION_DIV10})
-endif()
-if(JPEG_LIB_VERSION STREQUAL "80")
-  set(DEFAULT_SO_MINOR_VERSION 2)
-else()
-  set(DEFAULT_SO_MINOR_VERSION 0)
-endif()
-
-# This causes SO_MAJOR_VERSION/SO_MINOR_VERSION to reset to defaults if
-# WITH_JPEG7 or WITH_JPEG8 has changed.
-if((DEFINED WITH_JPEG7_INT AND NOT WITH_JPEG7 EQUAL WITH_JPEG7_INT) OR
-  (DEFINED WITH_JPEG8_INT AND NOT WITH_JPEG8 EQUAL WITH_JPEG8_INT))
-  set(FORCE_SO_VERSION "FORCE")
-endif()
-set(WITH_JPEG7_INT ${WITH_JPEG7} CACHE INTERNAL "")
-set(WITH_JPEG8_INT ${WITH_JPEG8} CACHE INTERNAL "")
-
-set(SO_MAJOR_VERSION ${DEFAULT_SO_MAJOR_VERSION} CACHE STRING
-  "Major version of the libjpeg API shared library (default: ${DEFAULT_SO_MAJOR_VERSION})"
-  ${FORCE_SO_VERSION})
-set(SO_MINOR_VERSION ${DEFAULT_SO_MINOR_VERSION} CACHE STRING
-  "Minor version of the libjpeg API shared library (default: ${DEFAULT_SO_MINOR_VERSION})"
-  ${FORCE_SO_VERSION})
-
-set(JPEG_LIB_VERSION_DECIMAL "${JPEG_LIB_VERSION_DIV10}.${JPEG_LIB_VERSION_MOD10}")
-message(STATUS "Emulating libjpeg API/ABI v${JPEG_LIB_VERSION_DECIMAL} (WITH_JPEG7 = ${WITH_JPEG7}, WITH_JPEG8 = ${WITH_JPEG8})")
-message(STATUS "libjpeg API shared library version = ${SO_MAJOR_VERSION}.${SO_AGE}.${SO_MINOR_VERSION}")
-
-# Because the TurboJPEG API library uses versioned symbols and changes the
-# names of functions whenever they are modified in a backward-incompatible
-# manner, it is always backward-ABI-compatible with itself, so the major and
-# minor SO versions don't change.  However, we increase the middle number (the
-# SO "age") whenever functions are added to the API.
-set(TURBOJPEG_SO_MAJOR_VERSION 0)
-set(TURBOJPEG_SO_AGE 2)
-set(TURBOJPEG_SO_VERSION 0.${TURBOJPEG_SO_AGE}.0)
-
-
-###############################################################################
-# COMPILER SETTINGS
-###############################################################################
-
-if(MSVC)
-  option(WITH_CRT_DLL
-    "Link all ${CMAKE_PROJECT_NAME} libraries and executables with the C run-time DLL (msvcr*.dll) instead of the static C run-time library (libcmt*.lib.)  The default is to use the C run-time DLL only with the libraries and executables that need it."
-    FALSE)
-  if(NOT WITH_CRT_DLL)
-    # Use the static C library for all build types
-    foreach(var CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_RELEASE
-      CMAKE_C_FLAGS_MINSIZEREL CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "/MD")
-        string(REGEX REPLACE "/MD" "/MT" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-  add_definitions(-D_CRT_NONSTDC_NO_WARNINGS)
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_C_COMPILER_ID STREQUAL "Clang")
-  # Use the maximum optimization level for release builds
-  foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-    if(${var} MATCHES "-O2")
-      string(REGEX REPLACE "-O2" "-O3" ${var} "${${var}}")
-    endif()
-  endforeach()
-endif()
-
-if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-  if(CMAKE_C_COMPILER_ID MATCHES "SunPro")
-    # Use the maximum optimization level for release builds
-    foreach(var CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO)
-      if(${var} MATCHES "-xO3")
-        string(REGEX REPLACE "-xO3" "-xO5" ${var} "${${var}}")
-      endif()
-      if(${var} MATCHES "-xO2")
-        string(REGEX REPLACE "-xO2" "-xO5" ${var} "${${var}}")
-      endif()
-    endforeach()
-  endif()
-endif()
-
-string(TOUPPER ${CMAKE_BUILD_TYPE} CMAKE_BUILD_TYPE_UC)
-
-set(EFFECTIVE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Compiler flags = ${EFFECTIVE_C_FLAGS}")
-
-set(EFFECTIVE_LD_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE_UC}}")
-message(STATUS "Linker flags = ${EFFECTIVE_LD_FLAGS}")
-
-include(CheckCSourceCompiles)
-include(CheckIncludeFiles)
-include(CheckTypeSize)
-
-check_type_size("size_t" SIZE_T)
-check_type_size("unsigned long" UNSIGNED_LONG)
-
-if(SIZE_T EQUAL UNSIGNED_LONG)
-  check_c_source_compiles("int main(int argc, char **argv) { unsigned long a = argc;  return __builtin_ctzl(a); }"
-    HAVE_BUILTIN_CTZL)
-endif()
-if(MSVC)
-  check_include_files("intrin.h" HAVE_INTRIN_H)
-endif()
-
-if(UNIX)
-  if(CMAKE_CROSSCOMPILING)
-    set(RIGHT_SHIFT_IS_UNSIGNED 0)
-  else()
-    include(CheckCSourceRuns)
-    check_c_source_runs("
-      #include <stdio.h>
-      #include <stdlib.h>
-      int is_shifting_signed (long arg) {
-        long res = arg >> 4;
-        if (res == -0x7F7E80CL)
-          return 1; /* right shift is signed */
-        /* see if unsigned-shift hack will fix it. */
-        /* we can't just test exact value since it depends on width of long... */
-        res |= (~0L) << (32-4);
-        if (res == -0x7F7E80CL)
-          return 0; /* right shift is unsigned */
-        printf(\"Right shift isn't acting as I expect it to.\\\\n\");
-        printf(\"I fear the JPEG software will not work at all.\\\\n\\\\n\");
-        return 0; /* try it with unsigned anyway */
-      }
-      int main (void) {
-        exit(is_shifting_signed(-0x7F7E80B1L));
-      }" RIGHT_SHIFT_IS_UNSIGNED)
-  endif()
-endif()
-
-if(MSVC)
-  set(INLINE_OPTIONS "__inline;inline")
-else()
-  set(INLINE_OPTIONS "__inline__;inline")
-endif()
-option(FORCE_INLINE "Force function inlining" TRUE)
-boolean_number(FORCE_INLINE)
-if(FORCE_INLINE)
-  if(MSVC)
-    list(INSERT INLINE_OPTIONS 0 "__forceinline")
-  else()
-    list(INSERT INLINE_OPTIONS 0 "inline __attribute__((always_inline))")
-    list(INSERT INLINE_OPTIONS 0 "__inline__ __attribute__((always_inline))")
-  endif()
-endif()
-foreach(inline ${INLINE_OPTIONS})
-  check_c_source_compiles("${inline} static int foo(void) { return 0; } int main(void) { return foo(); }"
-    INLINE_WORKS)
-  if(INLINE_WORKS)
-    set(INLINE ${inline})
-    break()
-  endif()
-endforeach()
-if(NOT INLINE_WORKS)
-  message(FATAL_ERROR "Could not determine how to inline functions.")
-endif()
-message(STATUS "INLINE = ${INLINE} (FORCE_INLINE = ${FORCE_INLINE})")
-
-if(WITH_TURBOJPEG)
-  if(MSVC)
-    set(THREAD_LOCAL "__declspec(thread)")
-  else()
-    set(THREAD_LOCAL "__thread")
-  endif()
-  check_c_source_compiles("${THREAD_LOCAL} int i;  int main(void) { i = 0;  return i; }" HAVE_THREAD_LOCAL)
-  if(HAVE_THREAD_LOCAL)
-    message(STATUS "THREAD_LOCAL = ${THREAD_LOCAL}")
-  else()
-    message(WARNING "Thread-local storage is not available.  The TurboJPEG API library's global error handler will not be thread-safe.")
-    unset(THREAD_LOCAL)
-  endif()
-endif()
-
-if(UNIX AND NOT APPLE)
-  file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map "VERS_1 { global: *; };")
-  set(CMAKE_REQUIRED_FLAGS
-    "-Wl,--version-script,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("int main(void) { return 0; }" HAVE_VERSION_SCRIPT)
-  set(CMAKE_REQUIRED_FLAGS)
-  file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-  if(HAVE_VERSION_SCRIPT)
-    message(STATUS "Linker supports GNU-style version scripts")
-    set(MAPFLAG "-Wl,--version-script,")
-    set(TJMAPFLAG "-Wl,--version-script,")
-  else()
-    message(STATUS "Linker does not support GNU-style version scripts")
-    if(CMAKE_SYSTEM_NAME STREQUAL "SunOS")
-      # The Solaris linker doesn't like our version script for the libjpeg API
-      # library, but the version script for the TurboJPEG API library should
-      # still work.
-      file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map
-        "VERS_1 { global: foo;  local: *; }; VERS_2 { global: foo2; } VERS_1;")
-      set(CMAKE_REQUIRED_FLAGS "-Wl,-M,${CMAKE_CURRENT_BINARY_DIR}/conftest.map -shared")
-      check_c_source_compiles("int foo() { return 0; } int foo2() { return 2; }"
-        HAVE_MAPFILE)
-      set(CMAKE_REQUIRED_FLAGS)
-      file(REMOVE ${CMAKE_CURRENT_BINARY_DIR}/conftest.map)
-      if(HAVE_MAPFILE)
-        message(STATUS "Linker supports mapfiles")
-        set(TJMAPFLAG "-Wl,-M,")
-      else()
-        message(STATUS "Linker does not support mapfiles")
-      endif()
-    endif()
-  endif()
-endif()
-
-# Generate files
-if(WIN32)
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/win/jconfig.h.in jconfig.h)
-else()
-  configure_file(jconfig.h.in jconfig.h)
-endif()
-configure_file(jconfigint.h.in jconfigint.h)
-configure_file(jversion.h.in jversion.h)
-if(UNIX)
-  configure_file(libjpeg.map.in libjpeg.map)
-endif()
-
-# Include directories and compiler definitions
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_CURRENT_SOURCE_DIR})
-
-
-###############################################################################
-# TARGETS
-###############################################################################
-
-if(CMAKE_EXECUTABLE_SUFFIX_TMP)
-  set(CMAKE_EXECUTABLE_SUFFIX ${CMAKE_EXECUTABLE_SUFFIX_TMP})
-endif()
-message(STATUS "CMAKE_EXECUTABLE_SUFFIX = ${CMAKE_EXECUTABLE_SUFFIX}")
-
-set(JPEG_SOURCES jcapimin.c jcapistd.c jccoefct.c jccolor.c jcdctmgr.c jchuff.c
-  jcicc.c jcinit.c jcmainct.c jcmarker.c jcmaster.c jcomapi.c jcparam.c
-  jcphuff.c jcprepct.c jcsample.c jctrans.c jdapimin.c jdapistd.c jdatadst.c
-  jdatasrc.c jdcoefct.c jdcolor.c jddctmgr.c jdhuff.c jdicc.c jdinput.c
-  jdmainct.c jdmarker.c jdmaster.c jdmerge.c jdphuff.c jdpostct.c jdsample.c
-  jdtrans.c jerror.c jfdctflt.c jfdctfst.c jfdctint.c jidctflt.c jidctfst.c
-  jidctint.c jidctred.c jquant1.c jquant2.c jutils.c jmemmgr.c jmemnobs.c)
-
-if(WITH_ARITH_ENC OR WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jaricom.c)
-endif()
-
-if(WITH_ARITH_ENC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jcarith.c)
-endif()
-
-if(WITH_ARITH_DEC)
-  set(JPEG_SOURCES ${JPEG_SOURCES} jdarith.c)
-endif()
-
-if(WITH_SIMD)
-  add_subdirectory(simd)
-  if(NEON_INTRINSICS)
-    add_definitions(-DNEON_INTRINSICS)
-  endif()
-elseif(NOT WITH_12BIT)
-  message(STATUS "SIMD extensions: None (WITH_SIMD = ${WITH_SIMD})")
-endif()
-if(WITH_SIMD)
-  message(STATUS "SIMD extensions: ${CPU_TYPE} (WITH_SIMD = ${WITH_SIMD})")
-  if(MSVC_IDE OR XCODE)
-    set_source_files_properties(${SIMD_OBJS} PROPERTIES GENERATED 1)
-  endif()
-else()
-  add_library(simd OBJECT jsimd_none.c)
-  if(NOT WIN32 AND (CMAKE_POSITION_INDEPENDENT_CODE OR ENABLE_SHARED))
-    set_target_properties(simd PROPERTIES POSITION_INDEPENDENT_CODE 1)
-  endif()
-endif()
-
-if(WITH_JAVA)
-  add_subdirectory(java)
-endif()
-
-if(ENABLE_SHARED)
-  add_subdirectory(sharedlib)
-endif()
-
-if(ENABLE_STATIC)
-  add_library(jpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-    ${SIMD_OBJS})
-  if(NOT MSVC)
-    set_target_properties(jpeg-static PROPERTIES OUTPUT_NAME jpeg)
-  endif()
-endif()
-
-if(WITH_TURBOJPEG)
-  if(ENABLE_SHARED)
-    set(TURBOJPEG_SOURCES ${JPEG_SOURCES} $<TARGET_OBJECTS:simd> ${SIMD_OBJS}
-      turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c rdppm.c
-      wrbmp.c wrppm.c)
-    set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile)
-    if(WITH_JAVA)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES} turbojpeg-jni.c)
-      include_directories(${JAVA_INCLUDE_PATH} ${JAVA_INCLUDE_PATH2})
-      set(TJMAPFILE ${CMAKE_CURRENT_SOURCE_DIR}/turbojpeg-mapfile.jni)
-    endif()
-    if(MSVC)
-      configure_file(${CMAKE_SOURCE_DIR}/win/turbojpeg.rc.in
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-      set(TURBOJPEG_SOURCES ${TURBOJPEG_SOURCES}
-        ${CMAKE_BINARY_DIR}/win/turbojpeg.rc)
-    endif()
-    add_library(turbojpeg SHARED ${TURBOJPEG_SOURCES})
-    set_property(TARGET turbojpeg PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(WIN32)
-      set_target_properties(turbojpeg PROPERTIES DEFINE_SYMBOL DLLDEFINE)
-    endif()
-    if(MINGW)
-      set_target_properties(turbojpeg PROPERTIES LINK_FLAGS -Wl,--kill-at)
-    endif()
-    if(APPLE AND (NOT CMAKE_OSX_DEPLOYMENT_TARGET OR
-                  CMAKE_OSX_DEPLOYMENT_TARGET VERSION_GREATER 10.4))
-      if(NOT CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG)
-        set(CMAKE_SHARED_LIBRARY_RUNTIME_C_FLAG "-Wl,-rpath,")
-      endif()
-      set_target_properties(turbojpeg PROPERTIES MACOSX_RPATH 1)
-    endif()
-    set_target_properties(turbojpeg PROPERTIES
-      SOVERSION ${TURBOJPEG_SO_MAJOR_VERSION} VERSION ${TURBOJPEG_SO_VERSION})
-    if(TJMAPFLAG)
-      set_target_properties(turbojpeg PROPERTIES
-        LINK_FLAGS "${TJMAPFLAG}${TJMAPFILE}")
-    endif()
-  endif()
-
-  if(ENABLE_STATIC)
-    add_library(turbojpeg-static STATIC ${JPEG_SOURCES} $<TARGET_OBJECTS:simd>
-      ${SIMD_OBJS} turbojpeg.c transupp.c jdatadst-tj.c jdatasrc-tj.c rdbmp.c
-      rdppm.c wrbmp.c wrppm.c)
-    set_property(TARGET turbojpeg-static PROPERTY COMPILE_FLAGS
-      "-DBMP_SUPPORTED -DPPM_SUPPORTED")
-    if(NOT MSVC)
-      set_target_properties(turbojpeg-static PROPERTIES OUTPUT_NAME turbojpeg)
-    endif()
-  endif()
-endif()
-
-if(WIN32)
-  set(USE_SETMODE "-DUSE_SETMODE")
-endif()
-if(WITH_12BIT)
-  set(COMPILE_FLAGS "-DGIF_SUPPORTED -DPPM_SUPPORTED ${USE_SETMODE}")
-else()
-  set(COMPILE_FLAGS "-DBMP_SUPPORTED -DGIF_SUPPORTED -DPPM_SUPPORTED -DTARGA_SUPPORTED ${USE_SETMODE}")
-  set(CJPEG_BMP_SOURCES rdbmp.c rdtarga.c)
-  set(DJPEG_BMP_SOURCES wrbmp.c wrtarga.c)
-endif()

cmake/CMakeLists.png

@@ -1,741 +0,0 @@
-# CMakeLists.txt
-
-# Copyright (C) 2018 Cosmin Truta
-# Copyright (C) 2007,2009-2018 Glenn Randers-Pehrson
-# Written by Christian Ehrlicher, 2007
-# Revised by Roger Lowman, 2009-2010
-# Revised by Clifford Yapp, 2011-2012,2017
-# Revised by Roger Leigh, 2016
-# Revised by Andreas Franek, 2016
-# Revised by Sam Serrels, 2017
-# Revised by Vadim Barkov, 2017
-# Revised by Vicky Pfau, 2018
-# Revised by Cameron Cawley, 2018
-# Revised by Cosmin Truta, 2018
-# Revised by Kyle Bentley, 2018
-
-# This code is released under the libpng license.
-# For conditions of distribution and use, see the disclaimer
-# and license in png.h
-
-cmake_minimum_required(VERSION 3.10)
-cmake_policy(VERSION 3.1)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(libpng C ASM)
-enable_testing()
-
-set(PNGLIB_MAJOR 1)
-set(PNGLIB_MINOR 6)
-set(PNGLIB_RELEASE 37)
-set(PNGLIB_NAME libpng${PNGLIB_MAJOR}${PNGLIB_MINOR})
-set(PNGLIB_VERSION ${PNGLIB_MAJOR}.${PNGLIB_MINOR}.${PNGLIB_RELEASE})
-
-include(GNUInstallDirs)
-
-# needed packages
-
-# Allow users to specify location of Zlib.
-# Useful if zlib is being built alongside this as a sub-project.
-option(PNG_BUILD_ZLIB "Custom zlib Location, else find_package is used" ON)
-
-if(NOT PNG_BUILD_ZLIB)
-  find_package(ZLIB REQUIRED)
-  include_directories(${ZLIB_INCLUDE_DIR})
-endif()
-
-if(UNIX AND NOT APPLE AND NOT BEOS AND NOT HAIKU)
-  find_library(M_LIBRARY m)
-else()
-  # libm is not needed and/or not available
-  set(M_LIBRARY "")
-endif()
-
-# COMMAND LINE OPTIONS
-option(PNG_SHARED "Build shared lib" OFF)
-option(PNG_STATIC "Build static lib" ON)
-option(PNG_TESTS  "Build libpng tests" OFF)
-
-# Many more configuration options could be added here
-option(PNG_FRAMEWORK "Build OS X framework" OFF)
-option(PNG_DEBUG "Build with debug output" OFF)
-option(PNG_HARDWARE_OPTIMIZATIONS "Enable hardware optimizations" OFF)
-
-set(PNG_PREFIX "" CACHE STRING "Prefix to add to the API function names")
-set(DFA_XTRA "" CACHE FILEPATH "File containing extra configuration settings")
-
-if(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-  CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  set(PNG_ARM_NEON_POSSIBLE_VALUES check on off)
-  set(PNG_ARM_NEON "check" CACHE STRING "Enable ARM NEON optimizations:
-     check: (default) use internal checking code;
-     off: disable the optimizations;
-     on: turn on unconditionally.")
-  set_property(CACHE PNG_ARM_NEON PROPERTY STRINGS
-     ${PNG_ARM_NEON_POSSIBLE_VALUES})
-  list(FIND PNG_ARM_NEON_POSSIBLE_VALUES ${PNG_ARM_NEON} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_ARM_NEON must be one of [${PNG_ARM_NEON_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_ARM_NEON} STREQUAL "off")
-    set(libpng_arm_sources
-      arm/arm_init.c
-      arm/filter_neon.S
-      arm/filter_neon_intrinsics.c
-      arm/palette_neon_intrinsics.c)
-
-    if(${PNG_ARM_NEON} STREQUAL "on")
-      add_definitions(-DPNG_ARM_NEON_OPT=2)
-    elseif(${PNG_ARM_NEON} STREQUAL "check")
-      add_definitions(-DPNG_ARM_NEON_CHECK_SUPPORTED)
-    endif()
-  else()
-    add_definitions(-DPNG_ARM_NEON_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  set(PNG_POWERPC_VSX_POSSIBLE_VALUES on off)
-  set(PNG_POWERPC_VSX "on" CACHE STRING "Enable POWERPC VSX optimizations:
-     off: disable the optimizations.")
-  set_property(CACHE PNG_POWERPC_VSX PROPERTY STRINGS
-     ${PNG_POWERPC_VSX_POSSIBLE_VALUES})
-  list(FIND PNG_POWERPC_VSX_POSSIBLE_VALUES ${PNG_POWERPC_VSX} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_POWERPC_VSX must be one of [${PNG_POWERPC_VSX_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_POWERPC_VSX} STREQUAL "off")
-    set(libpng_powerpc_sources
-      powerpc/powerpc_init.c
-      powerpc/filter_vsx_intrinsics.c)
-    if(${PNG_POWERPC_VSX} STREQUAL "on")
-      add_definitions(-DPNG_POWERPC_VSX_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  set(PNG_INTEL_SSE_POSSIBLE_VALUES on off)
-  set(PNG_INTEL_SSE "on" CACHE STRING "Enable INTEL_SSE optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_INTEL_SSE PROPERTY STRINGS
-     ${PNG_INTEL_SSE_POSSIBLE_VALUES})
-  list(FIND PNG_INTEL_SSE_POSSIBLE_VALUES ${PNG_INTEL_SSE} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_INTEL_SSE must be one of [${PNG_INTEL_SSE_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_INTEL_SSE} STREQUAL "off")
-    set(libpng_intel_sources
-      intel/intel_init.c
-      intel/filter_sse2_intrinsics.c)
-    if(${PNG_INTEL_SSE} STREQUAL "on")
-      add_definitions(-DPNG_INTEL_SSE_OPT=1)
-    endif()
-  else()
-    add_definitions(-DPNG_INTEL_SSE_OPT=0)
-  endif()
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  set(PNG_MIPS_MSA_POSSIBLE_VALUES on off)
-  set(PNG_MIPS_MSA "on" CACHE STRING "Enable MIPS_MSA optimizations:
-     off: disable the optimizations")
-  set_property(CACHE PNG_MIPS_MSA PROPERTY STRINGS
-     ${PNG_MIPS_MSA_POSSIBLE_VALUES})
-  list(FIND PNG_MIPS_MSA_POSSIBLE_VALUES ${PNG_MIPS_MSA} index)
-  if(index EQUAL -1)
-    message(FATAL_ERROR
-            "PNG_MIPS_MSA must be one of [${PNG_MIPS_MSA_POSSIBLE_VALUES}]")
-  elseif(NOT ${PNG_MIPS_MSA} STREQUAL "off")
-    set(libpng_mips_sources
-      mips/mips_init.c
-      mips/filter_msa_intrinsics.c)
-    if(${PNG_MIPS_MSA} STREQUAL "on")
-      add_definitions(-DPNG_MIPS_MSA_OPT=2)
-    endif()
-  else()
-    add_definitions(-DPNG_MIPS_MSA_OPT=0)
-  endif()
-endif()
-
-else(PNG_HARDWARE_OPTIMIZATIONS)
-
-# set definitions and sources for arm
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^arm" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^aarch64")
-  add_definitions(-DPNG_ARM_NEON_OPT=0)
-endif()
-
-# set definitions and sources for powerpc
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^powerpc*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^ppc64*")
-  add_definitions(-DPNG_POWERPC_VSX_OPT=0)
-endif()
-
-# set definitions and sources for intel
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "^i?86" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "^x86_64*")
-  add_definitions(-DPNG_INTEL_SSE_OPT=0)
-endif()
-
-# set definitions and sources for MIPS
-if(CMAKE_SYSTEM_PROCESSOR MATCHES "mipsel*" OR
-   CMAKE_SYSTEM_PROCESSOR MATCHES "mips64el*")
-  add_definitions(-DPNG_MIPS_MSA_OPT=0)
-endif()
-
-endif(PNG_HARDWARE_OPTIMIZATIONS)
-
-# SET LIBNAME
-set(PNG_LIB_NAME png${PNGLIB_MAJOR}${PNGLIB_MINOR})
-
-# to distinguish between debug and release lib
-set(CMAKE_DEBUG_POSTFIX "d")
-
-include(CheckCSourceCompiles)
-option(ld-version-script "Enable linker version script" ON)
-if(ld-version-script AND NOT APPLE)
-  # Check if LD supports linker scripts.
-  file(WRITE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map" "VERS_1 {
-        global: sym;
-        local: *;
-};
-
-VERS_2 {
-        global: sym2;
-                main;
-} VERS_1;
-")
-  set(CMAKE_REQUIRED_FLAGS_SAVE ${CMAKE_REQUIRED_FLAGS})
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS} "-Wl,--version-script='${CMAKE_CURRENT_BINARY_DIR}/conftest.map'")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_LD_VERSION_SCRIPT)
-  if(NOT HAVE_LD_VERSION_SCRIPT)
-    set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE} "-Wl,-M -Wl,${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-  check_c_source_compiles("void sym(void) {}
-void sym2(void) {}
-int main(void) {return 0;}
-" HAVE_SOLARIS_LD_VERSION_SCRIPT)
-  endif()
-  set(CMAKE_REQUIRED_FLAGS ${CMAKE_REQUIRED_FLAGS_SAVE})
-  file(REMOVE "${CMAKE_CURRENT_BINARY_DIR}/conftest.map")
-endif()
-
-# Find symbol prefix.  Likely obsolete and unnecessary with recent
-# toolchains (it's not done in many other projects).
-function(symbol_prefix)
-  set(SYMBOL_PREFIX)
-
-  execute_process(COMMAND "${CMAKE_C_COMPILER}" "-E" "-"
-                  INPUT_FILE /dev/null
-                  OUTPUT_VARIABLE OUT
-                  RESULT_VARIABLE STATUS)
-
-  if(CPP_FAIL)
-    message(WARNING "Failed to run the C preprocessor")
-  endif()
-
-  string(REPLACE "\n" ";" OUT "${OUT}")
-  foreach(line ${OUT})
-    string(REGEX MATCH "^PREFIX=" found_match "${line}")
-    if(found_match)
-      string(REGEX REPLACE "^PREFIX=(.*\)" "\\1" prefix "${line}")
-      string(REGEX MATCH "__USER_LABEL_PREFIX__" found_match "${prefix}")
-      if(found_match)
-        string(REGEX REPLACE "(.*)__USER_LABEL_PREFIX__(.*)" "\\1\\2" prefix "${prefix}")
-      endif()
-      set(SYMBOL_PREFIX "${prefix}")
-    endif()
-  endforeach()
-
-  message(STATUS "Symbol prefix: ${SYMBOL_PREFIX}")
-  set(SYMBOL_PREFIX "${SYMBOL_PREFIX}" PARENT_SCOPE)
-endfunction()
-
-if(UNIX)
-  symbol_prefix()
-endif()
-
-find_program(AWK NAMES gawk awk)
-
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
-
-if(NOT AWK OR ANDROID)
-  # No awk available to generate sources; use pre-built pnglibconf.h
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt
-                 ${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h)
-  add_custom_target(genfiles) # Dummy
-else()
-  include(CMakeParseArguments)
-  # Generate .chk from .out with awk
-  # generate_chk(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_chk)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GC "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GC_INPUT)
-      message(FATAL_ERROR "generate_chk: Missing INPUT argument")
-    endif()
-    if(NOT _GC_OUTPUT)
-      message(FATAL_ERROR "generate_chk: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GC_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GC_INPUT}"
-                               "-DOUTPUT=${_GC_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake"
-                       DEPENDS "${_GC_INPUT}" ${_GC_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate .out from .c with awk
-  # generate_out(INPUT inputfile OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_out)
-    set(options)
-    set(oneValueArgs INPUT OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GO_INPUT)
-      message(FATAL_ERROR "generate_out: Missing INPUT argument")
-    endif()
-    if(NOT _GO_OUTPUT)
-      message(FATAL_ERROR "generate_out: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${_GO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DINPUT=${_GO_INPUT}"
-                               "-DOUTPUT=${_GO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake"
-                       DEPENDS "${_GO_INPUT}" ${_GO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Generate specific source file with awk
-  # generate_source(OUTPUT outputfile [DEPENDS dep1 [dep2...]])
-  function(generate_source)
-    set(options)
-    set(oneValueArgs OUTPUT)
-    set(multiValueArgs DEPENDS)
-    cmake_parse_arguments(_GSO "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
-    if(NOT _GSO_OUTPUT)
-      message(FATAL_ERROR "generate_source: Missing OUTPUT argument")
-    endif()
-
-    add_custom_command(OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/${_GSO_OUTPUT}"
-                       COMMAND "${CMAKE_COMMAND}"
-                               "-DOUTPUT=${_GSO_OUTPUT}"
-                               -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                       DEPENDS ${_GSO_DEPENDS}
-                       WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-  endfunction()
-
-  # Copy file
-  function(generate_copy source destination)
-    add_custom_command(OUTPUT "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E remove "${destination}"
-                       COMMAND "${CMAKE_COMMAND}" -E copy "${source}"
-                                                          "${destination}"
-                       DEPENDS "${source}")
-  endfunction()
-
-  # Generate scripts/pnglibconf.h
-  generate_source(OUTPUT "scripts/pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  # Generate pnglibconf.c
-  generate_source(OUTPUT "pnglibconf.c"
-                  DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.dfa"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/scripts/options.awk"
-                          "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h")
-
-  if(PNG_PREFIX)
-    set(PNGLIBCONF_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-        "${CMAKE_CURRENT_SOURCE_DIR}/scripts/macro.lst")
-    set(PNGPREFIX_H_EXTRA_DEPENDS
-        "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out")
-  endif()
-
-  generate_out(INPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pnglibconf.h
-  generate_source(OUTPUT "pnglibconf.h"
-                  DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-                          ${PNGLIBCONF_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/intprefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/prefix.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out")
-
-  # Generate pngprefix.h
-  generate_source(OUTPUT "pngprefix.h"
-                  DEPENDS ${PNGPREFIX_H_EXTRA_DEPENDS})
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/sym.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-               DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/pnglibconf.h.prebuilt")
-
-  generate_out(INPUT "${CMAKE_CURRENT_SOURCE_DIR}/scripts/vers.c"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/png.h"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/pngconf.h"
-                       "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h")
-
-  generate_chk(INPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-               OUTPUT "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-               DEPENDS "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checksym.awk"
-                       "${CMAKE_CURRENT_SOURCE_DIR}/scripts/symbols.def")
-
-  add_custom_target(symbol-check DEPENDS
-                    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk")
-
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-  generate_copy("${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out"
-                "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-
-  add_custom_target(genvers DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers")
-  add_custom_target(gensym DEPENDS "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym")
-
-  add_custom_target("genprebuilt"
-                    COMMAND "${CMAKE_COMMAND}"
-                            "-DOUTPUT=scripts/pnglibconf.h.prebuilt"
-                            -P "${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake"
-                    WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-
-  # A single target handles generation of all generated files.  If
-  # they are depended upon separately by multiple targets, this
-  # confuses parallel make (it would require a separate top-level
-  # target for each file to track the dependencies properly).
-  add_custom_target(genfiles DEPENDS
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.sym"
-    "${CMAKE_CURRENT_BINARY_DIR}/libpng.vers"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/intprefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/pnglibconf.c"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/prefix.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/sym.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.chk"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/symbols.out"
-    "${CMAKE_CURRENT_BINARY_DIR}/scripts/vers.out")
-endif(NOT AWK OR ANDROID)
-
-# OUR SOURCES
-set(libpng_public_hdrs
-  png.h
-  pngconf.h
-  "${CMAKE_CURRENT_BINARY_DIR}/pnglibconf.h"
-)
-set(libpng_private_hdrs
-  pngpriv.h
-  pngdebug.h
-  pnginfo.h
-  pngstruct.h
-)
-if(AWK AND NOT ANDROID)
-  list(APPEND libpng_private_hdrs "${CMAKE_CURRENT_BINARY_DIR}/pngprefix.h")
-endif()
-set(libpng_sources
-  ${libpng_public_hdrs}
-  ${libpng_private_hdrs}
-  png.c
-  pngerror.c
-  pngget.c
-  pngmem.c
-  pngpread.c
-  pngread.c
-  pngrio.c
-  pngrtran.c
-  pngrutil.c
-  pngset.c
-  pngtrans.c
-  pngwio.c
-  pngwrite.c
-  pngwtran.c
-  pngwutil.c
-  ${libpng_arm_sources}
-  ${libpng_intel_sources}
-  ${libpng_mips_sources}
-  ${libpng_powerpc_sources}
-)
-set(pngtest_sources
-  pngtest.c
-)
-set(pngvalid_sources
-  contrib/libtests/pngvalid.c
-)
-set(pngstest_sources
-  contrib/libtests/pngstest.c
-)
-set(pngunknown_sources
-  contrib/libtests/pngunknown.c
-)
-set(pngimage_sources
-  contrib/libtests/pngimage.c
-)
-set(pngfix_sources
-  contrib/tools/pngfix.c
-)
-set(png_fix_itxt_sources
-  contrib/tools/png-fix-itxt.c
-)
-
-if(MSVC)
-  add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-endif()
-
-if(PNG_DEBUG)
-  add_definitions(-DPNG_DEBUG)
-endif()
-
-# NOW BUILD OUR TARGET
-include_directories(${CMAKE_CURRENT_SOURCE_DIR} ${ZLIB_INCLUDE_DIR})
-
-unset(PNG_LIB_TARGETS)
-
-if(PNG_STATIC)
-  # does not work without changing name
-  set(PNG_LIB_NAME_STATIC png_static)
-  add_library(png_static STATIC ${libpng_sources})
-  add_dependencies(png_static genfiles)
-  # MSVC doesn't use a different file extension for shared vs. static
-  # libs.  We are able to change OUTPUT_NAME to remove the _static
-  # for all other platforms.
-  if(NOT MSVC)
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}"
-      CLEAN_DIRECT_OUTPUT 1)
-  else()
-    set_target_properties(png_static PROPERTIES
-      OUTPUT_NAME "${PNG_LIB_NAME}_static"
-      CLEAN_DIRECT_OUTPUT 1)
-  endif()
-  list(APPEND PNG_LIB_TARGETS png_static)
-  if(MSVC)
-    # msvc does not append 'lib' - do it here to have consistent name
-    set_target_properties(png_static PROPERTIES PREFIX "lib")
-  endif()
-  target_link_libraries(png_static ${M_LIBRARY})
-endif()
-
-if(NOT PNG_LIB_TARGETS)
-  message(SEND_ERROR
-    "No library variant selected to build. "
-    "Please enable at least one of the following options: "
-    "PNG_STATIC, PNG_SHARED, PNG_FRAMEWORK")
-endif()
-
-# Set a variable with CMake code which:
-# Creates a symlink from src to dest (if possible) or alternatively
-# copies if different.
-include(CMakeParseArguments)
-
-function(create_symlink DEST_FILE)
-
-  cmake_parse_arguments(S "" "FILE;TARGET" "" ${ARGN})
-
-  if(NOT S_TARGET AND NOT S_FILE)
-    message(FATAL_ERROR "create_symlink: Missing TARGET or FILE argument")
-  endif()
-
-  if(S_TARGET AND S_FILE)
-    message(FATAL_ERROR "create_symlink: Both source file ${S_FILE} and build target ${S_TARGET} arguments are present; can only have one.")
-  endif()
-
-  if(S_FILE)
-    # If we don't need to symlink something that's coming from a build target,
-    # we can go ahead and symlink/copy at configure time.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      execute_process(
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    else()
-      execute_process(
-        COMMAND ${CMAKE_COMMAND} -E create_symlink ${S_FILE} ${DEST_FILE}
-        WORKING_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}")
-    endif()
-  endif()
-
-  if(S_TARGET)
-    # We need to use generator expressions, which can be a bit tricky, so for
-    # simplicity make the symlink a POST_BUILD step and use the TARGET
-    # signature of add_custom_command.
-    if(CMAKE_HOST_WIN32 AND NOT CYGWIN)
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E copy_if_different $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    else()
-      add_custom_command(TARGET ${S_TARGET} POST_BUILD
-        COMMAND "${CMAKE_COMMAND}" -E create_symlink $<TARGET_LINKER_FILE_NAME:${S_TARGET}> $<TARGET_LINKER_FILE_DIR:${S_TARGET}>/${DEST_FILE})
-    endif()
-  endif()
-
-endfunction()
-
-# Create source generation scripts.
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genchk.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genchk.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/genout.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/genout.cmake @ONLY)
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/scripts/gensrc.cmake.in
-               ${CMAKE_CURRENT_BINARY_DIR}/scripts/gensrc.cmake @ONLY)
-
-# libpng is a library so default to 'lib'
-if(NOT DEFINED CMAKE_INSTALL_LIBDIR)
-  set(CMAKE_INSTALL_LIBDIR lib)
-endif()
-
-# CREATE PKGCONFIG FILES
-# We use the same files like ./configure, so we have to set its vars.
-# Only do this on Windows for Cygwin - the files don't make much sense outside
-# of a UNIX look-alike.
-if(NOT WIN32 OR CYGWIN OR MINGW)
-  set(prefix      ${CMAKE_INSTALL_PREFIX})
-  set(exec_prefix ${CMAKE_INSTALL_PREFIX})
-  set(libdir      ${CMAKE_INSTALL_FULL_LIBDIR})
-  set(includedir  ${CMAKE_INSTALL_FULL_INCLUDEDIR})
-  set(LIBS        "-lz -lm")
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng.pc.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc @ONLY)
-  create_symlink(libpng.pc FILE ${PNGLIB_NAME}.pc)
-
-  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/libpng-config.in
-    ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config @ONLY)
-  create_symlink(libpng-config FILE ${PNGLIB_NAME}-config)
-endif()
-
-# SET UP LINKS
-if(PNG_SHARED)
-  set_target_properties(png PROPERTIES
-#   VERSION 16.${PNGLIB_RELEASE}.1.6.37
-    VERSION 16.${PNGLIB_RELEASE}.0
-    SOVERSION 16
-    CLEAN_DIRECT_OUTPUT 1)
-endif()
-
-# INSTALL
-if(NOT SKIP_INSTALL_LIBRARIES AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_LIB_TARGETS}
-          EXPORT libpng
-          RUNTIME DESTINATION bin
-          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
-          FRAMEWORK DESTINATION ${CMAKE_INSTALL_LIBDIR})
-
-  if(PNG_SHARED)
-    # Create a symlink for libpng.dll.a => libpng16.dll.a on Cygwin
-    if(CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_IMPORT_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_IMPORT_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-
-    if(NOT WIN32)
-      create_symlink(libpng${CMAKE_SHARED_LIBRARY_SUFFIX} TARGET png)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png>/libpng${CMAKE_SHARED_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-
-  if(PNG_STATIC)
-    if(NOT WIN32 OR CYGWIN OR MINGW)
-      create_symlink(libpng${CMAKE_STATIC_LIBRARY_SUFFIX} TARGET png_static)
-      install(FILES $<TARGET_LINKER_FILE_DIR:png_static>/libpng${CMAKE_STATIC_LIBRARY_SUFFIX}
-              DESTINATION ${CMAKE_INSTALL_LIBDIR})
-    endif()
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_HEADERS AND NOT SKIP_INSTALL_ALL)
-  install(FILES ${libpng_public_hdrs} DESTINATION include)
-  install(FILES ${libpng_public_hdrs} DESTINATION include/${PNGLIB_NAME})
-endif()
-if(NOT SKIP_INSTALL_EXECUTABLES AND NOT SKIP_INSTALL_ALL)
-  if(NOT WIN32 OR CYGWIN OR MINGW)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config DESTINATION bin)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config DESTINATION bin)
-  endif()
-endif()
-
-if(NOT SKIP_INSTALL_PROGRAMS AND NOT SKIP_INSTALL_ALL)
-  install(TARGETS ${PNG_BIN_TARGETS}
-          RUNTIME DESTINATION bin)
-endif()
-
-if(NOT SKIP_INSTALL_FILES AND NOT SKIP_INSTALL_ALL)
-  # Install man pages
-  if(NOT PNG_MAN_DIR)
-    set(PNG_MAN_DIR "share/man")
-  endif()
-  install(FILES libpng.3 libpngpf.3 DESTINATION ${PNG_MAN_DIR}/man3)
-  install(FILES png.5 DESTINATION ${PNG_MAN_DIR}/man5)
-  # Install pkg-config files
-  if(NOT CMAKE_HOST_WIN32 OR CYGWIN OR MINGW)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/libpng.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/libpng-config
-            DESTINATION bin)
-    install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}.pc
-            DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
-    install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/${PNGLIB_NAME}-config
-            DESTINATION bin)
-  endif()
-endif()
-
-# Create an export file that CMake users can include() to import our targets.
-if(NOT SKIP_INSTALL_EXPORT AND NOT SKIP_INSTALL_ALL)
-  install(EXPORT libpng DESTINATION lib/libpng FILE lib${PNG_LIB_NAME}.cmake)
-endif()
-
-# what's with libpng-manual.txt and all the extra files?
-
-# UNINSTALL
-# do we need this?
-
-# DIST
-# do we need this?
-
-# to create msvc import lib for mingw compiled shared lib
-# pexports libpng.dll > libpng.def
-# lib /def:libpng.def /machine:x86

cmake/CMakeLists.txt

@@ -1,8 +1,8 @@
+# -*- 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)
 ########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
@@ -12,8 +12,8 @@ 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 +21,14 @@ endif()
 if(POLICY CMP0135)
   cmake_policy(SET CMP0135 OLD)
 endif()
-########################################
-# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
-if(CMAKE_VERSION VERSION_LESS 3.12)
-  unset(CONFIGURE_DEPENDS)
-else()
-  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
-endif()
+
 ########################################
 
 project(lammps CXX)
 set(SOVERSION 0)
 get_property(BUILD_IS_MULTI_CONFIG GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
 
+include(GNUInstallDirs)
 get_filename_component(LAMMPS_DIR ${CMAKE_CURRENT_SOURCE_DIR}/.. ABSOLUTE)
 get_filename_component(LAMMPS_LIB_BINARY_DIR ${CMAKE_BINARY_DIR}/lib ABSOLUTE)
 # collect all executables and shared libs in the top level build folder
@@ -116,7 +111,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=11074 -diag-disable=11076 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -131,20 +126,33 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
   set(CMAKE_TUNE_DEFAULT "-Minform=severe")
 endif()
 
+# this hack is required to compile fmt lib with CrayClang version 15.0.2
+# CrayClang is only directly recognized by version 3.28 and later
+if(CMAKE_VERSION VERSION_LESS 3.28)
+  get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+else()
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+    set(CMAKE_TUNE_DEFAULT "-DFMT_STATIC_THOUSANDS_SEPARATOR")
+  endif()
+endif()
+
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
+# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
   set(CMAKE_CXX_STANDARD 11)
 endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
-if(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()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
@@ -155,11 +163,28 @@ if(MSVC)
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
+    add_compile_options(/wd4250)
     add_compile_options(/EHsc)
   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 ${CMAKE_CXX_COMPILER_ID} compiler version 5.x or later")
+    endif()
+  endif()
+endif()
+
 # export all symbols when building a .dll file on windows
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND BUILD_SHARED_LIBS)
   set(CMAKE_WINDOWS_EXPORT_ALL_SYMBOLS ON)
@@ -168,17 +193,20 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version when
-# in a virtual environment and PYTHON_EXECUTABLE is not set on command line
-if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
-  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
-  else()
-    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
-  endif()
+# backward compatibility with CMake before 3.12 and older LAMMPS documentation
+if (PYTHON_EXECUTABLE)
   set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+endif()
+# set path to python interpreter and thus enforcing python version when
+# in a virtual environment and Python_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
+  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()
 
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
@@ -191,19 +219,19 @@ 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")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,readability-qualified-auto,misc-unused-parameters,modernize-deprecated-ios-base-aliases,modernize-loop-convert,modernize-shrink-to-fit,modernize-use-auto,modernize-use-using,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
 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})
 
@@ -215,6 +243,10 @@ 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)
@@ -245,6 +277,7 @@ set(STANDARD_PACKAGES
   DRUDE
   EFF
   ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -257,7 +290,6 @@ set(STANDARD_PACKAGES
   KIM
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -271,15 +303,14 @@ 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 +326,7 @@ set(STANDARD_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK
@@ -385,15 +417,9 @@ if(NOT ${LAMMPS_MEMALIGN} STREQUAL "0")
   target_compile_definitions(lammps PRIVATE -DLAMMPS_MEMALIGN=${LAMMPS_MEMALIGN})
 endif()
 
-option(LAMMPS_EXCEPTIONS "enable the use of C++ exceptions for error messages (useful for library interface)" ${ENABLE_TESTING})
-if(LAMMPS_EXCEPTIONS)
-  target_compile_definitions(lammps PUBLIC -DLAMMPS_EXCEPTIONS)
-endif()
-
 # "hard" dependencies between packages resulting
 # in an error instead of skipping over files
 pkg_depends(ML-IAP ML-SNAP)
-pkg_depends(MPIIO MPI)
 pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
 pkg_depends(SCAFACOS MPI)
@@ -404,6 +430,8 @@ pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
 pkg_depends(EXTRA-MOLECULE MOLECULE)
+pkg_depends(MESONT MOLECULE)
+pkg_depends(RHEO BPM)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -429,6 +457,7 @@ 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 +468,43 @@ if(BUILD_OMP)
   target_compile_definitions(lammps PRIVATE -DLAMMPS_OMP_COMPAT=${LAMMPS_OMP_COMPAT_LEVEL})
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
+
+  # this hack is required to correctly link with OpenMP support when using CrayClang version 15.0.2
+  # CrayClang is only directly recognized by version 3.28 and later
+  if(CMAKE_VERSION VERSION_LESS 3.28)
+    get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
+    if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
+    endif()
+  else()
+    if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
+    endif()
+  endif()
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
+# 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 BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
     find_package(BLAS)
   endif()
   if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
+    file(GLOB LINALG_SOURCES CONFIGURE_DEPENDS ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
     add_library(linalg STATIC ${LINALG_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
@@ -459,6 +515,14 @@ if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR
   endif()
 endif()
 
+find_package(CURL QUIET COMPONENTS HTTP HTTPS)
+option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
+if(WITH_CURL)
+  find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
+  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
+  target_link_libraries(lammps PRIVATE CURL::libcurl)
+endif()
+
 # tweak jpeg library names to avoid linker errors with MinGW cross-compilation
 set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
@@ -466,12 +530,7 @@ 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)
@@ -521,7 +580,7 @@ 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 LATTE MSCG COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -538,17 +597,20 @@ set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine
 separate_arguments(CMAKE_TUNE_FLAGS)
 foreach(_FLAG ${CMAKE_TUNE_FLAGS})
   target_compile_options(lammps PRIVATE ${_FLAG})
-  target_compile_options(lmp 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")
@@ -580,8 +642,8 @@ 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})
@@ -597,19 +659,12 @@ 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})
@@ -623,7 +678,7 @@ 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}${LAMMPS_MACHINE})
@@ -667,7 +722,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-BASIC DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -793,9 +848,11 @@ include(Tools)
 include(Documentation)
 
 ###############################################################################
-# Install potential and force field files in data directory
+# Install bench, potential and force field files in data directory
 ###############################################################################
-set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_FULL_DATADIR}/lammps)
+set(LAMMPS_INSTALL_DATADIR ${CMAKE_INSTALL_DATADIR}/lammps)
+
+install(DIRECTORY ${LAMMPS_DIR}/bench DESTINATION ${LAMMPS_INSTALL_DATADIR})
 install(DIRECTORY ${LAMMPS_POTENTIALS_DIR} DESTINATION ${LAMMPS_INSTALL_DATADIR})
 if(BUILD_TOOLS)
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/msi2lmp/frc_files DESTINATION ${LAMMPS_INSTALL_DATADIR})
@@ -816,20 +873,8 @@ 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()
@@ -838,9 +883,8 @@ if(BUILD_SHARED_LIBS)
   set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
   if(Python_EXECUTABLE)
     add_custom_target(
-      install-python ${CMAKE_COMMAND} -E remove_directory build
-      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
-              -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
+      install-python ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
+      -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR} -v ${LAMMPS_SOURCE_DIR}/version.h
       COMMENT "Installing LAMMPS Python module")
   else()
     add_custom_target(
@@ -853,39 +897,10 @@ else()
     ${CMAKE_COMMAND} -E echo "Must build LAMMPS as a shared library to use the Python module")
 endif()
 
-###############################################################################
-# Add LAMMPS python module to "install" target. This is taylored for building
-# LAMMPS for package managers and with different prefix settings.
-# This requires either a shared library or that the PYTHON package is included.
-###############################################################################
-if(BUILD_SHARED_LIBS OR PKG_PYTHON)
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
-    find_package(PythonInterp) # Deprecated since version 3.12
-    if(PYTHONINTERP_FOUND)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-  else()
-    # backward compatibility
-    if(PYTHON_EXECUTABLE)
-      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
-    endif()
-    find_package(Python COMPONENTS Interpreter)
-  endif()
-  if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
-    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
-  endif()
-endif()
-
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 8.0)
+find_package(ClangFormat 11.0)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src
@@ -918,13 +933,23 @@ 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
 ###############################################################################
@@ -945,6 +970,7 @@ 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}")
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)
@@ -968,11 +994,9 @@ if(_index GREATER -1)
 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}")
@@ -1014,34 +1038,37 @@ 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)
@@ -1050,8 +1077,16 @@ 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/CMakeLists.zlib

@@ -1,195 +0,0 @@
-cmake_minimum_required(VERSION 3.10)
-# When using CMake 3.4 and later, don't export symbols from executables unless
-# the CMAKE_ENABLE_EXPORTS variable is set.
-if(POLICY CMP0065)
-  cmake_policy(SET CMP0065 NEW)
-endif()
-if (POLICY CMP0077)
-  cmake_policy(SET CMP0077 NEW)
-endif()
-set(CMAKE_ALLOW_LOOSE_LOOP_CONSTRUCTS ON)
-
-project(zlib C)
-
-set(VERSION "1.2.11")
-
-option(ASM686 "Enable building i686 assembly implementation" OFF)
-option(AMD64 "Enable building amd64 assembly implementation" OFF)
-
-set(INSTALL_BIN_DIR "${CMAKE_INSTALL_PREFIX}/bin" CACHE PATH "Installation directory for executables")
-set(INSTALL_LIB_DIR "${CMAKE_INSTALL_PREFIX}/lib" CACHE PATH "Installation directory for libraries")
-set(INSTALL_INC_DIR "${CMAKE_INSTALL_PREFIX}/include" CACHE PATH "Installation directory for headers")
-set(INSTALL_MAN_DIR "${CMAKE_INSTALL_PREFIX}/share/man" CACHE PATH "Installation directory for manual pages")
-set(INSTALL_PKGCONFIG_DIR "${CMAKE_INSTALL_PREFIX}/share/pkgconfig" CACHE PATH "Installation directory for pkgconfig (.pc) files")
-
-include(CheckTypeSize)
-include(CheckFunctionExists)
-include(CheckIncludeFile)
-include(CheckCSourceCompiles)
-
-check_include_file(sys/types.h HAVE_SYS_TYPES_H)
-check_include_file(stdint.h    HAVE_STDINT_H)
-check_include_file(stddef.h    HAVE_STDDEF_H)
-
-#
-# Check to see if we have large file support
-#
-set(CMAKE_REQUIRED_DEFINITIONS -D_LARGEFILE64_SOURCE=1)
-# We add these other definitions here because CheckTypeSize.cmake
-# in CMake 2.4.x does not automatically do so and we want
-# compatibility with CMake 2.4.x.
-if(HAVE_SYS_TYPES_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_SYS_TYPES_H)
-endif()
-if(HAVE_STDINT_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDINT_H)
-endif()
-if(HAVE_STDDEF_H)
-    list(APPEND CMAKE_REQUIRED_DEFINITIONS -DHAVE_STDDEF_H)
-endif()
-check_type_size(off64_t OFF64_T)
-check_type_size(off64_t OFF64_T)
-if(HAVE_OFF64_T)
-   add_definitions(-D_LARGEFILE64_SOURCE=1)
-endif()
-set(CMAKE_REQUIRED_DEFINITIONS) # clear variable
-
-#
-# Check for fseeko
-#
-check_function_exists(fseeko HAVE_FSEEKO)
-if(NOT HAVE_FSEEKO)
-    add_definitions(-DNO_FSEEKO)
-endif()
-
-#
-# Check for unistd.h
-#
-check_include_file(unistd.h Z_HAVE_UNISTD_H)
-
-if(MSVC)
-    set(CMAKE_DEBUG_POSTFIX "d")
-    add_definitions(-D_CRT_SECURE_NO_DEPRECATE)
-    add_definitions(-D_CRT_NONSTDC_NO_DEPRECATE)
-    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
-endif()
-
-if(NOT CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
-    # If we're doing an out of source build and the user has a zconf.h
-    # in their source tree...
-    if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h)
-        file(RENAME ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h ${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.included)
-  endif()
-endif()
-
-set(ZLIB_PC ${CMAKE_CURRENT_BINARY_DIR}/zlib.pc)
-configure_file( ${CMAKE_CURRENT_SOURCE_DIR}/zlib.pc.cmakein
-		${ZLIB_PC} @ONLY)
-configure_file(	${CMAKE_CURRENT_SOURCE_DIR}/zconf.h.cmakein
-		${CMAKE_CURRENT_BINARY_DIR}/zconf.h @ONLY)
-include_directories(${CMAKE_CURRENT_BINARY_DIR} ${CMAKE_SOURCE_DIR})
-
-
-#============================================================================
-# zlib
-#============================================================================
-
-set(ZLIB_PUBLIC_HDRS
-    ${CMAKE_CURRENT_BINARY_DIR}/zconf.h
-    zlib.h
-)
-set(ZLIB_PRIVATE_HDRS
-    crc32.h
-    deflate.h
-    gzguts.h
-    inffast.h
-    inffixed.h
-    inflate.h
-    inftrees.h
-    trees.h
-    zutil.h
-)
-set(ZLIB_SRCS
-    adler32.c
-    compress.c
-    crc32.c
-    deflate.c
-    gzclose.c
-    gzlib.c
-    gzread.c
-    gzwrite.c
-    inflate.c
-    infback.c
-    inftrees.c
-    inffast.c
-    trees.c
-    uncompr.c
-    zutil.c
-)
-
-if(NOT MINGW)
-    set(ZLIB_DLL_SRCS
-        win32/zlib1.rc # If present will override custom build rule below.
-    )
-endif()
-
-if(CMAKE_COMPILER_IS_GNUCC)
-    if(ASM686)
-        set(ZLIB_ASMS contrib/asm686/match.S)
-    elseif (AMD64)
-        set(ZLIB_ASMS contrib/amd64/amd64-match.S)
-    endif ()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV)
-		set_source_files_properties(${ZLIB_ASMS} PROPERTIES LANGUAGE C COMPILE_FLAGS -DNO_UNDERLINE)
-	endif()
-endif()
-
-if(MSVC)
-    if(ASM686)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx86/inffas32.asm
-			contrib/masmx86/match686.asm
-		)
-    elseif (AMD64)
-		ENABLE_LANGUAGE(ASM_MASM)
-        set(ZLIB_ASMS
-			contrib/masmx64/gvmat64.asm
-			contrib/masmx64/inffasx64.asm
-		)
-    endif()
-
-	if(ZLIB_ASMS)
-		add_definitions(-DASMV -DASMINF)
-	endif()
-endif()
-
-# parse the full version number from zlib.h and include in ZLIB_FULL_VERSION
-file(READ ${CMAKE_CURRENT_SOURCE_DIR}/zlib.h _zlib_h_contents)
-string(REGEX REPLACE ".*#define[ \t]+ZLIB_VERSION[ \t]+\"([-0-9A-Za-z.]+)\".*"
-    "\\1" ZLIB_FULL_VERSION ${_zlib_h_contents})
-
-if(MINGW)
-    # This gets us DLL resource information when compiling on MinGW.
-    if(NOT CMAKE_RC_COMPILER)
-        set(CMAKE_RC_COMPILER windres.exe)
-    endif()
-
-    add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                       COMMAND ${CMAKE_RC_COMPILER}
-                            -D GCC_WINDRES
-                            -I ${CMAKE_CURRENT_SOURCE_DIR}
-                            -I ${CMAKE_CURRENT_BINARY_DIR}
-                            -o ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj
-                            -i ${CMAKE_CURRENT_SOURCE_DIR}/win32/zlib1.rc)
-    set(ZLIB_DLL_SRCS ${CMAKE_CURRENT_BINARY_DIR}/zlib1rc.obj)
-endif(MINGW)
-
-add_library(zlibstatic STATIC ${ZLIB_SRCS} ${ZLIB_ASMS} ${ZLIB_PUBLIC_HDRS} ${ZLIB_PRIVATE_HDRS})
-
-if(UNIX)
-    # On unix-like platforms the library is almost always called libz
-   set_target_properties(zlibstatic PROPERTIES OUTPUT_NAME z)
-endif()

cmake/CMakeSettings.json

@@ -63,6 +63,11 @@
           "name": "ENABLE_TESTING",
           "value": "True",
           "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "False",
+          "type": "BOOL"
         }
       ]
     },
@@ -303,6 +308,54 @@
           "type": "STRING"
         }
       ]
+    },
+    {
+      "name": "x64-GUI-MSVC",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -D QT_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5  -D Qt5_DIR=C:\\Qt\\5.15.2\\msvc2019_64\\lib\\cmake\\Qt5",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [ "msvc_x64_x64" ],
+      "variables": [
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_MPI",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "WITH_PNG",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_LAMMPS_GUI",
+          "value": "True",
+          "type": "BOOL"
+        }
+      ]
     }
   ]
 }

cmake/Modules/CodingStandard.cmake

@@ -1,15 +1,11 @@
-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()
-    find_package(Python3 COMPONENTS Interpreter QUIET)
+# use default (or custom) Python executable, if version is sufficient
+if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
+  set(Python3_EXECUTABLE ${Python_EXECUTABLE})
 endif()
+find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
+    if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
         add_custom_target(
           check-whitespace
           ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .

cmake/Modules/DetectHIPInstallation.cmake

@@ -0,0 +1,8 @@
+if(NOT DEFINED ROCM_PATH)
+    if(NOT DEFINED ENV{ROCM_PATH})
+        set(ROCM_PATH "/opt/rocm" CACHE PATH "Path to ROCm installation")
+    else()
+        set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
+    endif()
+endif()
+list(APPEND CMAKE_PREFIX_PATH ${ROCM_PATH})

cmake/Modules/Documentation.cmake

@@ -4,21 +4,19 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
-  # Sphinx 3.x requires at least Python 3.5
-  if(CMAKE_VERSION VERSION_LESS 3.12)
-    find_package(PythonInterp 3.5 REQUIRED)
-    set(VIRTUALENV ${PYTHON_EXECUTABLE} -m venv)
-  else()
-    find_package(Python3 REQUIRED COMPONENTS Interpreter)
-    if(Python3_VERSION VERSION_LESS 3.5)
-      message(FATAL_ERROR "Python 3.5 and up is required to build the HTML documentation")
-    endif()
-    set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
+  # Current Sphinx versions require at least Python 3.8
+  # use default (or custom) Python executable, if version is sufficient
+  if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
+    set(Python3_EXECUTABLE ${Python_EXECUTABLE})
   endif()
+  find_package(Python3 REQUIRED COMPONENTS Interpreter)
+  if(Python3_VERSION VERSION_LESS 3.8)
+    message(FATAL_ERROR "Python 3.8 and up is required to build the HTML documentation")
+  endif()
+  set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
+
   find_package(Doxygen 1.8.10 REQUIRED)
-
-  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
-
+  file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
   add_custom_command(
     OUTPUT docenv
@@ -76,7 +74,7 @@ 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()
 

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/LAMMPSInterfacePlugin.cmake

@@ -28,9 +28,8 @@ 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()
@@ -65,7 +64,7 @@ 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 ${_dirs})
@@ -88,6 +87,18 @@ function(get_lammps_version version_header variable)
     set(${variable} "${date}" PARENT_SCOPE)
 endfunction()
 
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
+function(GetFallbackURL input output)
+  string(REPLACE "_URL" "" _tmp ${input})
+  string(TOLOWER ${_tmp} libname)
+  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
+  if ("${newurl}" STREQUAL "${${input}}")
+    set(${output} "" PARENT_SCOPE)
+  else()
+    set(${output} ${newurl} PARENT_SCOPE)
+  endif()
+endfunction(GetFallbackURL)
+
 #################################################################################
 # LAMMPS C++ interface. We only need the header related parts except on windows.
 add_library(lammps INTERFACE)

cmake/Modules/LAMMPSUtils.cmake

@@ -32,7 +32,13 @@ function(check_omp_h_include)
     set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
     set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
     set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-    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})
@@ -80,20 +86,20 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_FILES CONFIGURE_DEPENDS ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES CONFIGURE_DEPENDS ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
-    list(APPEND SRC_AUTOGEN_FILES ${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 ${source_dir} purge\n"
+                            "to remove\n"
+                            "########################################################################")
       endif()
     endforeach()
 endfunction()
@@ -152,13 +158,14 @@ endfunction(FetchPotentials)
 # set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
 if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   file(STRINGS /etc/os-release distro REGEX "^NAME=")
-  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  string(REGEX REPLACE "NAME=\"?([^ ]+).*\"?" "\\1" distro "${distro}")
   file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
   string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
   set(CMAKE_LINUX_DISTRO ${distro})
   set(CMAKE_DISTRO_VERSION ${disversion})
 endif()
 
+# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
 function(GetFallbackURL input output)
   string(REPLACE "_URL" "" _tmp ${input})
   string(TOLOWER ${_tmp} libname)

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)
 
@@ -24,6 +24,12 @@ target_include_directories(colvars PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
+if(BUILD_OMP)
+  # Enable OpenMP for Colvars as well
+  target_compile_options(colvars PRIVATE ${OpenMP_CXX_FLAGS})
+  target_link_libraries(colvars PRIVATE OpenMP::OpenMP_CXX)
+endif()
+
 if(COLVARS_DEBUG)
   # Need to export the define publicly to be valid in interface code
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)

cmake/Modules/Packages/DPD-BASIC.cmake

@@ -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/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")
@@ -60,15 +67,17 @@ if(GPU_API STREQUAL "CUDA")
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
     if(CUDPP_OPT)
-      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DCUDA_MPS_SUPPORT=ON")
     endif()
-    set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
+    set(GPU_CUDA_MPS_FLAGS "-DCUDA_MPS_SUPPORT")
   endif()
+  option(CUDA_BUILD_MULTIARCH "Enable building CUDA kernels for all supported GPU architectures" ON)
+  mark_as_advanced(GPU_BUILD_MULTIARCH)
 
   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"
@@ -78,77 +87,81 @@ 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
   # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
   set(GPU_CUDA_GENCODE "-arch=${GPU_ARCH}")
 
-  # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
-  # only the Kepler achitecture and beyond is supported
-  # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
-  if(CUDA_VERSION VERSION_LESS 8.0)
-    message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-    message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
-    set(GPU_CUDA_GENCODE "-arch=all")
-  else()
-    # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
-    endif()
-    # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
-    if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
-    endif()
-    # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
-    endif()
-    # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
-    endif()
-    # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
-    endif()
-    # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
-    endif()
-    # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
-    endif()
-    # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
-    endif()
-    # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
-    endif()
-    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+  if(CUDA_BUILD_MULTIARCH)
+    # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
+    # only the Kepler achitecture and beyond is supported
+    # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
+    if(CUDA_VERSION VERSION_LESS 8.0)
+      message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
+      message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
+      set(GPU_CUDA_GENCODE "-arch=all")
+    elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+      set(GPU_CUDA_GENCODE "-arch=all")
+    else()
+      # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_30,code=[sm_30,compute_30] ")
+      endif()
+      # Kepler (GPU Arch 3.5) is supported by CUDA 5 to CUDA 11
+      if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "12.0"))
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_35,code=[sm_35,compute_35]")
+      endif()
+      # Maxwell (GPU Arch 5.x) is supported by CUDA 6 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "6.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compute_52,code=[sm_52,compute_52]")
+      endif()
+      # Pascal (GPU Arch 6.x) is supported by CUDA 8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "8.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_60,code=[sm_60,compute_60] -gencode arch=compute_61,code=[sm_61,compute_61]")
+      endif()
+      # Volta (GPU Arch 7.0) is supported by CUDA 9 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "9.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_70,code=[sm_70,compute_70]")
+      endif()
+      # Turing (GPU Arch 7.5) is supported by CUDA 10 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "10.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_75,code=[sm_75,compute_75]")
+      endif()
+      # Ampere (GPU Arch 8.0) is supported by CUDA 11 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
+      endif()
+      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+      endif()
+      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
+      if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+      endif()
     endif()
   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)
@@ -175,8 +188,6 @@ if(GPU_API STREQUAL "CUDA")
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
   endif()
 
-  target_link_libraries(lammps PRIVATE gpu)
-
   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_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
@@ -201,7 +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
@@ -249,29 +260,14 @@ elseif(GPU_API STREQUAL "OPENCL")
   else()
     target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   endif()
-  target_link_libraries(lammps PRIVATE gpu)
 
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
   add_dependencies(ocl_get_devices OpenCL::OpenCL)
+
 elseif(GPU_API STREQUAL "HIP")
-  if(NOT DEFINED HIP_PATH)
-      if(NOT DEFINED ENV{HIP_PATH})
-          message(FATAL_ERROR "GPU_API=HIP 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")
-      else()
-          set(ROCM_PATH $ENV{ROCM_PATH} CACHE PATH "Path to ROCm installation")
-      endif()
-  endif()
-  list(APPEND CMAKE_PREFIX_PATH ${HIP_PATH} ${ROCM_PATH})
+  include(DetectHIPInstallation)
   find_package(hip REQUIRED)
   option(HIP_USE_DEVICE_SORT "Use GPU sorting" ON)
 
@@ -285,7 +281,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+  if(HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "spirv")
     set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
@@ -346,7 +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 "")
@@ -358,7 +354,7 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
+    if(HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
@@ -412,7 +408,8 @@ elseif(GPU_API STREQUAL "HIP")
       set_property(TARGET gpu PROPERTY CXX_STANDARD 14)
     endif()
     # add hipCUB
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+    find_package(hipcub REQUIRED)
+    target_link_libraries(gpu PRIVATE hip::hipcub)
     target_compile_definitions(gpu PRIVATE -DUSE_HIP_DEVICE_SORT)
 
     if(HIP_PLATFORM STREQUAL "nvcc")
@@ -461,35 +458,25 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_executable(hip_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(hip_get_devices PRIVATE -DUCL_HIP)
-  target_link_libraries(hip_get_devices hip::host)
+  target_link_libraries(hip_get_devices PRIVATE hip::host)
 
   if(HIP_PLATFORM STREQUAL "nvcc")
     target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
     target_include_directories(gpu PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_NVCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/include)
     target_include_directories(hip_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
     target_link_libraries(hip_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
-  elseif(HIP_PLATFORM STREQUAL "hcc")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
-  elseif(HIP_PLATFORM STREQUAL "amd")
-    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
-
-    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
-    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
-
-  target_link_libraries(lammps PRIVATE gpu)
 endif()
 
+if(BUILD_OMP)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
+  target_link_libraries(gpu PRIVATE OpenMP::OpenMP_CXX)
+endif()
+target_link_libraries(lammps PRIVATE gpu)
+
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
 # detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)

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

@@ -111,6 +111,9 @@ 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)
@@ -19,7 +14,7 @@ if(CURL_FOUND)
     target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
   endif()
 endif()
-set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
+option(KIM_EXTRA_UNITTESTS "Enable extra unit tests for the KIM package." OFF)
 mark_as_advanced(KIM_EXTRA_UNITTESTS)
 find_package(PkgConfig QUIET)
 set(DOWNLOAD_KIM_DEFAULT ON)

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,7 +1,8 @@
 ########################################################################
-# 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()
 
 ########################################################################
@@ -15,11 +16,6 @@ endif()
 if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
-  else()
-    # NVHPC 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"))
-      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
-    endif()
   endif()
 endif()
 ########################################################################
@@ -49,8 +45,8 @@ 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/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -72,13 +68,11 @@ if(DOWNLOAD_KOKKOS)
   set_target_properties(LAMMPS::KOKKOSCONTAINERS PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkokkoscontainers.a")
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
-  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOSCORE LAMMPS::KOKKOSCONTAINERS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.3.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
-  target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -90,7 +84,7 @@ else()
   if(CMAKE_REQUEST_PIC)
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
   endif()
-  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
+  add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR} EXCLUDE_FROM_ALL)
 
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
@@ -98,7 +92,6 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
-  target_link_libraries(lmp PRIVATE kokkos)
   if(BUILD_SHARED_LIBS_WAS_ON)
     set(BUILD_SHARED_LIBS ON)
   endif()
@@ -124,19 +117,43 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/domain_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/modify_kokkos.cpp)
 
+# fix wall/gran has been refactored in an incompatible way. Use old version of base class for now
+if(PKG_GRANULAR)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fix_wall_gran_old.cpp)
+endif()
+
 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 HIPFFT CUFFT)
+  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.")
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
+    elseif(FFT_KOKKOS STREQUAL "CUFFT")
+      find_package(CUDAToolkit REQUIRED)
+      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
+      target_link_libraries(lammps PRIVATE CUDA::cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
-    if(NOT (FFT STREQUAL "KISS"))
-      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
-      target_link_libraries(lammps PRIVATE hipfft)
+    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_KOKKOS_HIPFFT)
+      target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
   endif()
 endif()
@@ -151,7 +168,7 @@ 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

@@ -46,6 +46,61 @@ else()
   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/LATTE.cmake

@@ -1,54 +0,0 @@
-enable_language(Fortran)
-
-# using lammps in a super-build setting
-if(TARGET LATTE::latte)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-  return()
-endif()
-
-find_package(LATTE 1.2.2 CONFIG)
-if(LATTE_FOUND)
-  set(DOWNLOAD_LATTE_DEFAULT OFF)
-else()
-  set(DOWNLOAD_LATTE_DEFAULT ON)
-endif()
-option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
-if(DOWNLOAD_LATTE)
-  message(STATUS "LATTE download requested - we will build our own")
-  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
-  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
-  mark_as_advanced(LATTE_URL)
-  mark_as_advanced(LATTE_MD5)
-  GetFallbackURL(LATTE_URL LATTE_FALLBACK)
-
-  # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
-  list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
-  list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
-  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
-                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
-  endif()
-
-  include(ExternalProject)
-  ExternalProject_Add(latte_build
-    URL     ${LATTE_URL} ${LATTE_FALLBACK}
-    URL_MD5 ${LATTE_MD5}
-    SOURCE_SUBDIR cmake
-    CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
-    -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}
-    -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=${CMAKE_Fortran_FLAGS}
-    -DCMAKE_Fortran_FLAGS_${BTYPE}=${CMAKE_Fortran_FLAGS_${BTYPE}} -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
-    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM} -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-    BUILD_BYPRODUCTS <INSTALL_DIR>/lib/liblatte.a
-  )
-  ExternalProject_get_property(latte_build INSTALL_DIR)
-  add_library(LAMMPS::LATTE UNKNOWN IMPORTED)
-  set_target_properties(LAMMPS::LATTE PROPERTIES
-    IMPORTED_LOCATION "${INSTALL_DIR}/lib/liblatte.a"
-    INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
-  target_link_libraries(lammps PRIVATE LAMMPS::LATTE)
-  add_dependencies(LAMMPS::LATTE latte_build)
-else()
-  find_package(LATTE 1.2.2 REQUIRED CONFIG)
-  target_link_libraries(lammps PRIVATE LATTE::latte)
-endif()

cmake/Modules/Packages/LEPTON.cmake

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

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" 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 +10,26 @@ endif()
 
 option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
 
+# if ML-PACE package *and* MLIAP with Python is enabled is included we may also include ML-PACE support in ML-IAP
+set(MLIAP_ENABLE_ACE_DEFAULT OFF)
+if(PKG_ML-PACE)
+  set(MLIAP_ENABLE_ACE_DEFAULT ON)
+endif()
+
+option(MLIAP_ENABLE_ACE "Build ML-IAP package with ACE support" ${MLIAP_ENABLE_ACE_DEFAULT})
+
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
-  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()
+  if(Python_VERSION VERSION_LESS 3.6)
+    message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
   foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
     get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
@@ -49,3 +44,10 @@ 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

@@ -1,33 +1,46 @@
-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
 
-set(PACELIB_MD5 "4f0b3b5b14456fe9a73b447de3765caa" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+# 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.fix.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "b45de9a633f42ed65422567e3ce56f9f" 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()
+# 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()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+  # download library sources to build folder
+  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+  endif()
+  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+    message(STATUS "Downloading ${PACELIB_URL}")
+    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    endif()
+  else()
+    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+  endif()
 
-# uncompress downloaded sources
-execute_process(
-  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-)
-get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+
+  # 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()
 
 add_subdirectory(${lib-pace} build-pace)
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})

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}")
@@ -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/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
-  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
-  mark_as_advanced(MSCG_URL)
-  mark_as_advanced(MSCG_MD5)
-
-  include(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

@@ -1,106 +1,188 @@
-set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
-set(PLUMED_MODE_VALUES static shared runtime)
-set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
-validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
-string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+# Plumed2 support for PLUMED package
 
-set(PLUMED_LINK_LIBS)
-if(PLUMED_MODE STREQUAL "STATIC")
-  find_package(LAPACK REQUIRED)
-  find_package(BLAS REQUIRED)
-  find_package(GSL REQUIRED)
-  list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
-  find_package(ZLIB QUIET)
-  if(ZLIB_FOUND)
-    list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
-  endif()
-  find_package(FFTW3 QUIET)
-  if(FFTW3_FOUND)
-    list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
-  endif()
+# 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()
 
-find_package(PkgConfig QUIET)
-set(DOWNLOAD_PLUMED_DEFAULT ON)
-if(PKG_CONFIG_FOUND)
-  pkg_check_modules(PLUMED QUIET plumed)
-  if(PLUMED_FOUND)
-    set(DOWNLOAD_PLUMED_DEFAULT OFF)
-  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})
+  set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+  set(PLUMED_CONFIG_CPP "-I ${MPI_CXX_INCLUDE_PATH}")
+  set(PLUMED_CONFIG_LIB "${MPI_CXX_LIBRARIES}")
+  set(PLUMED_CONFIG_DEP "mpi4win_build")
+else()
+  set(PLUMED_CONFIG_MPI "--disable-mpi")
+  set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
+  set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+  set(PLUMED_CONFIG_CPP "")
+  set(PLUMED_CONFIG_LIB "")
+  set(PLUMED_CONFIG_DEP "")
+endif()
+if(BUILD_OMP)
+  set(PLUMED_CONFIG_OMP "--enable-openmp")
+else()
+  set(PLUMED_CONFIG_OMP "--disable-openmp")
 endif()
 
-option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
-if(DOWNLOAD_PLUMED)
-  if(BUILD_MPI)
-    set(PLUMED_CONFIG_MPI "--enable-mpi")
-    set(PLUMED_CONFIG_CC  ${CMAKE_MPI_C_COMPILER})
-    set(PLUMED_CONFIG_CXX  ${CMAKE_MPI_CXX_COMPILER})
+# 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/v2.9.1/plumed-src-2.9.1.tgz"
+  CACHE STRING "URL for PLUMED tarball")
+set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
+
+mark_as_advanced(PLUMED_URL)
+mark_as_advanced(PLUMED_MD5)
+GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
+
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
+  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+    set(CROSS_CONFIGURE mingw64-configure)
+  elseif(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86")
+    set(CROSS_CONFIGURE mingw32-configure)
   else()
-    set(PLUMED_CONFIG_MPI "--disable-mpi")
-    set(PLUMED_CONFIG_CC  ${CMAKE_C_COMPILER})
-    set(PLUMED_CONFIG_CXX  ${CMAKE_CXX_COMPILER})
+    message(FATAL_ERROR "Unsupported target system: ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR}")
   endif()
-  if(BUILD_OMP)
-    set(PLUMED_CONFIG_OMP "--enable-openmp")
-  else()
-    set(PLUMED_CONFIG_OMP "--disable-openmp")
-  endif()
-  message(STATUS "PLUMED download requested - we will build our own")
-  if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
-  endif()
-
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
-
-  mark_as_advanced(PLUMED_URL)
-  mark_as_advanced(PLUMED_MD5)
-  GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
-
+  message(STATUS "Downloading and cross-compiling Plumed2 for ${CMAKE_SYSTEM_NAME}/${CMAKE_SYSTEM_PROCESSOR} with ${CROSS_CONFIGURE}")
   include(ExternalProject)
   ExternalProject_Add(plumed_build
     URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
-    CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
+    CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
+                                         --disable-python --enable-cxx=11
+                                         --enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
+                                         ${PLUMED_CONFIG_OMP}
+                                         ${PLUMED_CONFIG_MPI}
+                                         CXX=${PLUMED_CONFIG_CXX}
+                                         CC=${PLUMED_CONFIG_CC}
+                                         CPPFLAGS=${PLUMED_CONFIG_CPP}
+                                         LIBS=${PLUMED_CONFIG_LIB}
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<SOURCE_DIR>/src/lib/install/libplumed.a" "<SOURCE_DIR>/src/lib/install/plumed.exe"
+    DEPENDS "${PLUMED_MPI_CONFIG_DEP}"
+  )
+  ExternalProject_Get_Property(plumed_build SOURCE_DIR)
+  set(PLUMED_BUILD_DIR ${SOURCE_DIR})
+  set(PLUMED_INSTALL_DIR ${PLUMED_BUILD_DIR}/src/lib/install)
+  file(MAKE_DIRECTORY ${PLUMED_BUILD_DIR}/src/include)
+
+  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+  add_dependencies(LAMMPS::PLUMED plumed_build)
+  set_target_properties(LAMMPS::PLUMED PROPERTIES
+    IMPORTED_LOCATION "${PLUMED_INSTALL_DIR}/libplumed.a"
+    INTERFACE_LINK_LIBRARIES "-Wl,--image-base -Wl,0x10000000 -lfftw3 -lz  -fstack-protector -lssp -fopenmp"
+    INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_BUILD_DIR}/src/include")
+
+  add_custom_target(plumed_copy ALL ${CMAKE_COMMAND} -E rm -rf ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed_patches
+    COMMAND ${CMAKE_COMMAND} -E copy ${PLUMED_INSTALL_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/plumed.exe
+    COMMAND ${CMAKE_COMMAND} -E copy_directory ${PLUMED_BUILD_DIR}/patches ${CMAKE_BINARY_DIR}/patches
+    BYPRODUCTS ${CMAKE_BINARY_DIR}/plumed.exe ${CMAKE_BINARY_DIR}/patches
+    DEPENDS plumed_build
+    COMMENT "Copying Plumed files"
+  )
+  if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+    target_link_libraries(lammps INTERFACE LAMMPS::PLUMED)
+  endif()
+
+else()
+
+  set(PLUMED_MODE "static" CACHE STRING "Linkage mode for Plumed2 library")
+  set(PLUMED_MODE_VALUES static shared runtime)
+  set_property(CACHE PLUMED_MODE PROPERTY STRINGS ${PLUMED_MODE_VALUES})
+  validate_option(PLUMED_MODE PLUMED_MODE_VALUES)
+  string(TOUPPER ${PLUMED_MODE} PLUMED_MODE)
+
+  set(PLUMED_LINK_LIBS)
+  if(PLUMED_MODE STREQUAL "STATIC")
+    find_package(LAPACK REQUIRED)
+    find_package(BLAS REQUIRED)
+    find_package(GSL REQUIRED)
+    list(APPEND PLUMED_LINK_LIBS ${LAPACK_LIBRARIES} ${BLAS_LIBRARIES} GSL::gsl)
+    find_package(ZLIB QUIET)
+    if(ZLIB_FOUND)
+      list(APPEND PLUMED_LINK_LIBS ZLIB::ZLIB)
+    endif()
+    find_package(FFTW3 QUIET)
+    if(FFTW3_FOUND)
+      list(APPEND PLUMED_LINK_LIBS FFTW3::FFTW3)
+    endif()
+  endif()
+
+  find_package(PkgConfig QUIET)
+  set(DOWNLOAD_PLUMED_DEFAULT ON)
+  if(PKG_CONFIG_FOUND)
+    pkg_check_modules(PLUMED QUIET plumed)
+    if(PLUMED_FOUND)
+      set(DOWNLOAD_PLUMED_DEFAULT OFF)
+    endif()
+  endif()
+
+  option(DOWNLOAD_PLUMED "Download Plumed package instead of using an already installed one" ${DOWNLOAD_PLUMED_DEFAULT})
+  if(DOWNLOAD_PLUMED)
+    message(STATUS "PLUMED download requested - we will build our own")
+    if(PLUMED_MODE STREQUAL "STATIC")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
+    endif()
+
+    include(ExternalProject)
+    ExternalProject_Add(plumed_build
+      URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
+      URL_MD5 ${PLUMED_MD5}
+      BUILD_IN_SOURCE 1
+      CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
                                              --enable-modules=all
+                                             --enable-cxx=11
+                                             --disable-python
                                              ${PLUMED_CONFIG_MPI}
                                              ${PLUMED_CONFIG_OMP}
                                              CXX=${PLUMED_CONFIG_CXX}
                                              CC=${PLUMED_CONFIG_CC}
-    BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
-  )
-  ExternalProject_get_property(plumed_build INSTALL_DIR)
-  add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
-  add_dependencies(LAMMPS::PLUMED plumed_build)
-  if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+      BUILD_BYPRODUCTS ${PLUMED_BUILD_BYPRODUCTS}
+    )
+    ExternalProject_get_property(plumed_build INSTALL_DIR)
+    add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
+    add_dependencies(LAMMPS::PLUMED plumed_build)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    elseif(PLUMED_MODE STREQUAL "SHARED")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    elseif(PLUMED_MODE STREQUAL "RUNTIME")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+      set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    endif()
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
+    file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE LAMMPS::PLUMED)
+    endif()
+  else()
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(PLUMED REQUIRED plumed${PLUMED_SUFFIX})
+    add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
+    if(PLUMED_MODE STREQUAL "STATIC")
+      include(${PLUMED_LIBDIR}/plumed${PLUMED_SUFFIX}/src/lib/Plumed.cmake.static)
+    elseif(PLUMED_MODE STREQUAL "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}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()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
-  file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
-else()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(PLUMED REQUIRED plumed)
-  add_library(LAMMPS::PLUMED INTERFACE IMPORTED)
-  if(PLUMED_MODE STREQUAL "STATIC")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.static)
-  elseif(PLUMED_MODE STREQUAL "SHARED")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
-  elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
-  endif()
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")
-  set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${PLUMED_INCLUDE_DIRS}")
 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 CMake before 3.12 and 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/RHEO.cmake

@@ -0,0 +1,2 @@
+find_package(GSL 2.6 REQUIRED)
+target_link_libraries(lammps PRIVATE GSL::gsl)

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})
@@ -95,73 +95,76 @@ function(RegisterIntegrateStyle path)
 endfunction(RegisterIntegrateStyle)
 
 function(RegisterStyles search_path)
-    FindStyleHeaders(${search_path} ANGLE_CLASS     angle_     ANGLE     ) # angle     ) # force
-    FindStyleHeaders(${search_path} ATOM_CLASS      atom_vec_  ATOM_VEC  ) # atom      ) # atom      atom_vec_hybrid
-    FindStyleHeaders(${search_path} BODY_CLASS      body_      BODY      ) # body      ) # atom_vec_body
-    FindStyleHeaders(${search_path} BOND_CLASS      bond_      BOND      ) # bond      ) # force
-    FindStyleHeaders(${search_path} COMMAND_CLASS   "[^.]"     COMMAND   ) # command   ) # input
-    FindStyleHeaders(${search_path} COMPUTE_CLASS   compute_   COMPUTE   ) # compute   ) # modify
-    FindStyleHeaders(${search_path} DIHEDRAL_CLASS  dihedral_  DIHEDRAL  ) # dihedral  ) # force
-    FindStyleHeaders(${search_path} DUMP_CLASS      dump_      DUMP      ) # dump      ) # output    write_dump
-    FindStyleHeaders(${search_path} FIX_CLASS       fix_       FIX       ) # fix       ) # modify
-    FindStyleHeaders(${search_path} IMPROPER_CLASS  improper_  IMPROPER  ) # improper  ) # force
-    FindStyleHeaders(${search_path} INTEGRATE_CLASS "[^.]"     INTEGRATE ) # integrate ) # update
-    FindStyleHeaders(${search_path} KSPACE_CLASS    "[^.]"     KSPACE    ) # kspace    ) # force
-    FindStyleHeaders(${search_path} MINIMIZE_CLASS  min_       MINIMIZE  ) # minimize  ) # update
-    FindStyleHeaders(${search_path} NBIN_CLASS      nbin_      NBIN      ) # nbin      ) # neighbor
-    FindStyleHeaders(${search_path} NPAIR_CLASS     npair_     NPAIR     ) # npair     ) # neighbor
-    FindStyleHeaders(${search_path} NSTENCIL_CLASS  nstencil_  NSTENCIL  ) # nstencil  ) # neighbor
-    FindStyleHeaders(${search_path} NTOPO_CLASS     ntopo_     NTOPO     ) # ntopo     ) # neighbor
-    FindStyleHeaders(${search_path} PAIR_CLASS      pair_      PAIR      ) # pair      ) # force
-    FindStyleHeaders(${search_path} READER_CLASS    reader_    READER    ) # reader    ) # read_dump
-    FindStyleHeaders(${search_path} REGION_CLASS    region_    REGION    ) # region    ) # domain
+    FindStyleHeaders(${search_path} ANGLE_CLASS        angle_        ANGLE        ) # angle        ) # force
+    FindStyleHeaders(${search_path} ATOM_CLASS         atom_vec_     ATOM_VEC     ) # atom         ) # atom      atom_vec_hybrid
+    FindStyleHeaders(${search_path} BODY_CLASS         body_         BODY         ) # body         ) # atom_vec_body
+    FindStyleHeaders(${search_path} BOND_CLASS         bond_         BOND         ) # bond         ) # force
+    FindStyleHeaders(${search_path} COMMAND_CLASS      "[^.]"        COMMAND      ) # command      ) # input
+    FindStyleHeaders(${search_path} COMPUTE_CLASS      compute_      COMPUTE      ) # compute      ) # modify
+    FindStyleHeaders(${search_path} DIHEDRAL_CLASS     dihedral_     DIHEDRAL     ) # dihedral     ) # force
+    FindStyleHeaders(${search_path} DUMP_CLASS         dump_         DUMP         ) # dump         ) # output    write_dump
+    FindStyleHeaders(${search_path} FIX_CLASS          fix_          FIX          ) # fix          ) # modify
+    FindStyleHeaders(${search_path} GRAN_SUB_MOD_CLASS gran_sub_mod_ GRAN_SUB_MOD ) # gran_sub_mod ) # granular_model
+    FindStyleHeaders(${search_path} IMPROPER_CLASS     improper_     IMPROPER     ) # improper     ) # force
+    FindStyleHeaders(${search_path} INTEGRATE_CLASS    "[^.]"        INTEGRATE    ) # integrate    ) # update
+    FindStyleHeaders(${search_path} KSPACE_CLASS       "[^.]"        KSPACE       ) # kspace       ) # force
+    FindStyleHeaders(${search_path} MINIMIZE_CLASS     min_          MINIMIZE     ) # minimize     ) # update
+    FindStyleHeaders(${search_path} NBIN_CLASS         nbin_         NBIN         ) # nbin         ) # neighbor
+    FindStyleHeaders(${search_path} NPAIR_CLASS        npair_        NPAIR        ) # npair        ) # neighbor
+    FindStyleHeaders(${search_path} NSTENCIL_CLASS     nstencil_     NSTENCIL     ) # nstencil     ) # neighbor
+    FindStyleHeaders(${search_path} NTOPO_CLASS        ntopo_        NTOPO        ) # ntopo        ) # neighbor
+    FindStyleHeaders(${search_path} PAIR_CLASS         pair_         PAIR         ) # pair         ) # force
+    FindStyleHeaders(${search_path} READER_CLASS       reader_       READER       ) # reader       ) # read_dump
+    FindStyleHeaders(${search_path} REGION_CLASS       region_       REGION       ) # region       ) # domain
 endfunction(RegisterStyles)
 
 function(RegisterStylesExt search_path extension sources)
-    FindStyleHeadersExt(${search_path} ANGLE_CLASS     ${extension}  ANGLE     ${sources})
-    FindStyleHeadersExt(${search_path} ATOM_CLASS      ${extension}  ATOM_VEC  ${sources})
-    FindStyleHeadersExt(${search_path} BODY_CLASS      ${extension}  BODY      ${sources})
-    FindStyleHeadersExt(${search_path} BOND_CLASS      ${extension}  BOND      ${sources})
-    FindStyleHeadersExt(${search_path} COMMAND_CLASS   ${extension}  COMMAND   ${sources})
-    FindStyleHeadersExt(${search_path} COMPUTE_CLASS   ${extension}  COMPUTE   ${sources})
-    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS  ${extension}  DIHEDRAL  ${sources})
-    FindStyleHeadersExt(${search_path} DUMP_CLASS      ${extension}  DUMP      ${sources})
-    FindStyleHeadersExt(${search_path} FIX_CLASS       ${extension}  FIX       ${sources})
-    FindStyleHeadersExt(${search_path} IMPROPER_CLASS  ${extension}  IMPROPER  ${sources})
-    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS ${extension}  INTEGRATE ${sources})
-    FindStyleHeadersExt(${search_path} KSPACE_CLASS    ${extension}  KSPACE    ${sources})
-    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS  ${extension}  MINIMIZE  ${sources})
-    FindStyleHeadersExt(${search_path} NBIN_CLASS      ${extension}  NBIN      ${sources})
-    FindStyleHeadersExt(${search_path} NPAIR_CLASS     ${extension}  NPAIR     ${sources})
-    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS  ${extension}  NSTENCIL  ${sources})
-    FindStyleHeadersExt(${search_path} NTOPO_CLASS     ${extension}  NTOPO     ${sources})
-    FindStyleHeadersExt(${search_path} PAIR_CLASS      ${extension}  PAIR      ${sources})
-    FindStyleHeadersExt(${search_path} READER_CLASS    ${extension}  READER    ${sources})
-    FindStyleHeadersExt(${search_path} REGION_CLASS    ${extension}  REGION    ${sources})
+    FindStyleHeadersExt(${search_path} ANGLE_CLASS        ${extension}  ANGLE        ${sources})
+    FindStyleHeadersExt(${search_path} ATOM_CLASS         ${extension}  ATOM_VEC     ${sources})
+    FindStyleHeadersExt(${search_path} BODY_CLASS         ${extension}  BODY         ${sources})
+    FindStyleHeadersExt(${search_path} BOND_CLASS         ${extension}  BOND         ${sources})
+    FindStyleHeadersExt(${search_path} COMMAND_CLASS      ${extension}  COMMAND      ${sources})
+    FindStyleHeadersExt(${search_path} COMPUTE_CLASS      ${extension}  COMPUTE      ${sources})
+    FindStyleHeadersExt(${search_path} DIHEDRAL_CLASS     ${extension}  DIHEDRAL     ${sources})
+    FindStyleHeadersExt(${search_path} DUMP_CLASS         ${extension}  DUMP         ${sources})
+    FindStyleHeadersExt(${search_path} FIX_CLASS          ${extension}  FIX          ${sources})
+    FindStyleHeadersExt(${search_path} GRAN_SUB_MOD_CLASS ${extension}  GRAN_SUB_MOD ${sources})
+    FindStyleHeadersExt(${search_path} IMPROPER_CLASS     ${extension}  IMPROPER     ${sources})
+    FindStyleHeadersExt(${search_path} INTEGRATE_CLASS    ${extension}  INTEGRATE    ${sources})
+    FindStyleHeadersExt(${search_path} KSPACE_CLASS       ${extension}  KSPACE       ${sources})
+    FindStyleHeadersExt(${search_path} MINIMIZE_CLASS     ${extension}  MINIMIZE     ${sources})
+    FindStyleHeadersExt(${search_path} NBIN_CLASS         ${extension}  NBIN         ${sources})
+    FindStyleHeadersExt(${search_path} NPAIR_CLASS        ${extension}  NPAIR        ${sources})
+    FindStyleHeadersExt(${search_path} NSTENCIL_CLASS     ${extension}  NSTENCIL     ${sources})
+    FindStyleHeadersExt(${search_path} NTOPO_CLASS        ${extension}  NTOPO        ${sources})
+    FindStyleHeadersExt(${search_path} PAIR_CLASS         ${extension}  PAIR         ${sources})
+    FindStyleHeadersExt(${search_path} READER_CLASS       ${extension}  READER       ${sources})
+    FindStyleHeadersExt(${search_path} REGION_CLASS       ${extension}  REGION       ${sources})
 endfunction(RegisterStylesExt)
 
 function(GenerateStyleHeaders output_path)
     message(STATUS "Generating style headers...")
-    GenerateStyleHeader(${output_path} ANGLE      angle     ) # force
-    GenerateStyleHeader(${output_path} ATOM_VEC   atom      ) # atom      atom_vec_hybrid
-    GenerateStyleHeader(${output_path} BODY       body      ) # atom_vec_body
-    GenerateStyleHeader(${output_path} BOND       bond      ) # force
-    GenerateStyleHeader(${output_path} COMMAND    command   ) # input
-    GenerateStyleHeader(${output_path} COMPUTE    compute   ) # modify
-    GenerateStyleHeader(${output_path} DIHEDRAL   dihedral  ) # force
-    GenerateStyleHeader(${output_path} DUMP       dump      ) # output    write_dump
-    GenerateStyleHeader(${output_path} FIX        fix       ) # modify
-    GenerateStyleHeader(${output_path} IMPROPER   improper  ) # force
-    GenerateStyleHeader(${output_path} INTEGRATE  integrate ) # update
-    GenerateStyleHeader(${output_path} KSPACE     kspace    ) # force
-    GenerateStyleHeader(${output_path} MINIMIZE   minimize  ) # update
-    GenerateStyleHeader(${output_path} NBIN       nbin      ) # neighbor
-    GenerateStyleHeader(${output_path} NPAIR      npair     ) # neighbor
-    GenerateStyleHeader(${output_path} NSTENCIL   nstencil  ) # neighbor
-    GenerateStyleHeader(${output_path} NTOPO      ntopo     ) # neighbor
-    GenerateStyleHeader(${output_path} PAIR       pair      ) # force
-    GenerateStyleHeader(${output_path} READER     reader    ) # read_dump
-    GenerateStyleHeader(${output_path} REGION     region    ) # domain
+    GenerateStyleHeader(${output_path} ANGLE        angle        ) # force
+    GenerateStyleHeader(${output_path} ATOM_VEC     atom         ) # atom      atom_vec_hybrid
+    GenerateStyleHeader(${output_path} BODY         body         ) # atom_vec_body
+    GenerateStyleHeader(${output_path} BOND         bond         ) # force
+    GenerateStyleHeader(${output_path} COMMAND      command      ) # input
+    GenerateStyleHeader(${output_path} COMPUTE      compute      ) # modify
+    GenerateStyleHeader(${output_path} DIHEDRAL     dihedral     ) # force
+    GenerateStyleHeader(${output_path} DUMP         dump         ) # output    write_dump
+    GenerateStyleHeader(${output_path} FIX          fix          ) # modify
+    GenerateStyleHeader(${output_path} GRAN_SUB_MOD gran_sub_mod ) # granular_model
+    GenerateStyleHeader(${output_path} IMPROPER     improper     ) # force
+    GenerateStyleHeader(${output_path} INTEGRATE    integrate    ) # update
+    GenerateStyleHeader(${output_path} KSPACE       kspace       ) # force
+    GenerateStyleHeader(${output_path} MINIMIZE     minimize     ) # update
+    GenerateStyleHeader(${output_path} NBIN         nbin         ) # neighbor
+    GenerateStyleHeader(${output_path} NPAIR        npair        ) # neighbor
+    GenerateStyleHeader(${output_path} NSTENCIL     nstencil     ) # neighbor
+    GenerateStyleHeader(${output_path} NTOPO        ntopo        ) # neighbor
+    GenerateStyleHeader(${output_path} PAIR         pair         ) # force
+    GenerateStyleHeader(${output_path} READER       reader       ) # read_dump
+    GenerateStyleHeader(${output_path} REGION       region       ) # domain
 endfunction(GenerateStyleHeaders)
 
 function(DetectBuildSystemConflict lammps_src_dir)
@@ -184,7 +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}")
@@ -18,29 +18,33 @@ if(ENABLE_TESTING)
 
   # we need to build and link a LOT of tester executables, so it is worth checking if
   # a faster linker is available. requires GNU or Clang compiler, newer CMake.
-  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
-  if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-      AND ((CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-        OR (CMAKE_CXX_COMPILER_ID STREQUAL "Clang")))
-    if(((CMAKE_LINUX_DISTRO STREQUAL "Ubuntu") AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+  # 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_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)))
         OR ((CMAKE_LINUX_DISTRO STREQUAL "Fedora") AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
+      check_cxx_compiler_flag(-fuse-ld=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)
       check_cxx_compiler_flag(-fuse-ld=bfd HAVE_BFD_LINKER_FLAG)
+      find_program(HAVE_MOLD_LINKER_BIN ld.mold)
       find_program(HAVE_LLD_LINKER_BIN lld ld.lld)
       find_program(HAVE_GOLD_LINKER_BIN ld.gold)
       find_program(HAVE_BFD_LINKER_BIN ld.bfd)
-      if(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
+      if(HAVE_MOLD_LINKER_FLAG AND HAVE_MOLD_LINKER_BIN)
+        set(CMAKE_CUSTOM_LINKER_DEFAULT mold)
+      elseif(HAVE_LLD_LINKER_FLAG AND HAVE_LLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT lld)
       elseif(HAVE_GOLD_LINKER_FLAG AND HAVE_GOLD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT gold)
       elseif(HAVE_BFD_LINKER_FLAG AND HAVE_BFD_LINKER_BIN)
         set(CMAKE_CUSTOM_LINKER_DEFAULT bfd)
       endif()
-      set(CMAKE_CUSTOM_LINKER_VALUES lld gold bfd default)
-      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (lld, gold, bfd, default)")
+      set(CMAKE_CUSTOM_LINKER_VALUES mold lld gold bfd default)
+      set(CMAKE_CUSTOM_LINKER ${CMAKE_CUSTOM_LINKER_DEFAULT} CACHE STRING "Choose a custom linker for faster linking (mold, lld, gold, bfd, default)")
       validate_option(CMAKE_CUSTOM_LINKER CMAKE_CUSTOM_LINKER_VALUES)
       mark_as_advanced(CMAKE_CUSTOM_LINKER)
       if(NOT "${CMAKE_CUSTOM_LINKER}" STREQUAL "default")
@@ -62,16 +66,8 @@ 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()
 
@@ -106,24 +102,16 @@ 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

@@ -26,43 +26,19 @@ 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})
   endif()
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
+
+  add_subdirectory(${LAMMPS_TOOLS_DIR}/phonon ${CMAKE_BINARY_DIR}/phana_build)
 endif()
 
-if(BUILD_LAMMPS_SHELL)
-  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/)
+if(BUILD_LAMMPS_GUI)
+  get_filename_component(LAMMPS_GUI_DIR ${LAMMPS_SOURCE_DIR}/../tools/lammps-gui ABSOLUTE)
+  get_filename_component(LAMMPS_GUI_BIN ${CMAKE_BINARY_DIR}/lammps-gui-build ABSOLUTE)
+  add_subdirectory(${LAMMPS_GUI_DIR} ${LAMMPS_GUI_BIN})
 endif()
-
-

cmake/packaging/MacOSXBundleInfo.plist.in

@@ -0,0 +1,34 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE plist PUBLIC "-//Apple Computer//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
+<plist version="1.0">
+<dict>
+	<key>CFBundleDevelopmentRegion</key>
+	<string>en-US</string>
+	<key>CFBundleExecutable</key>
+	<string>${MACOSX_BUNDLE_EXECUTABLE_NAME}</string>
+        <key>CFBundleDisplayName</key>
+        <string>The LAMMPS Molecular Dynamics Software</string>
+	<key>CFBundleIconFile</key>
+	<string>lammps</string>
+	<key>CFBundleIdentifier</key>
+	<string>org.lammps.gui</string>
+	<key>CFBundleInfoDictionaryVersion</key>
+	<string>6.0</string>
+	<key>CFBundleLongVersionString</key>
+	<string>${MACOSX_BUNDLE_LONG_VERSION_STRING}</string>
+	<key>CFBundleName</key>
+	<string>LAMMPS_GUI</string>
+	<key>CFBundlePackageType</key>
+	<string>APPL</string>
+	<key>CFBundleShortVersionString</key>
+	<string>${MACOSX_BUNDLE_SHORT_VERSION_STRING}</string>
+	<key>CFBundleSignature</key>
+	<string>????</string>
+	<key>CFBundleVersion</key>
+	<string>${MACOSX_BUNDLE_BUNDLE_VERSION}</string>
+	<key>CSResourcesFileMapped</key>
+	<true/>
+	<key>NSHumanReadableCopyright</key>
+	<string>${MACOSX_BUNDLE_COPYRIGHT}</string>
+</dict>
+</plist>

cmake/packaging/README.macos

@@ -0,0 +1,69 @@
+LAMMPS and LAMMPS GUI universal binaries for macOS (arm64/x86_64)
+=================================================================
+
+This package provides universal binaries of LAMMPS and LAMMPS GUI that should
+run on macOS systems running running macOS version 11 (Big Sur) or newer.  Note
+the binaries are compiled without MPI support and contain a compatible subset
+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
+these steps:
+
+1. Open the Terminal app
+
+2. Type the following command and press ENTER:
+
+   open ~/.zprofile
+
+   This will open a text editor for modifying the .zprofile file in your home
+   directory.
+
+3. Add the following lines to the end of the file, save it, and close the editor
+
+   LAMMPS_INSTALL_DIR=/Applications/LAMMPS_GUI.app/Contents
+   LAMMPS_POTENTIALS=${LAMMPS_INSTALL_DIR}/share/lammps/potentials
+   LAMMPS_BENCH_DIR=${LAMMPS_INSTALL_DIR}/share/lammps/bench
+   MSI2LMP_LIBRARY=${LAMMPS_INSTALL_DIR}/share/lammps/frc_files
+   PATH=${LAMMPS_INSTALL_DIR}/bin:$PATH
+   export LAMMPS_POTENTIALS LAMMPS_BENCH_DIR PATH
+
+4. In your existing terminal, type the following command make the settings active
+
+   source ~/.zprofile
+
+   Note, you don't have to type this in new terminals, since they will apply
+   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.
+
+5. Try running LAMMPS (which might fail, see step 7)
+
+   lmp -in ${LAMMPS_BENCH_DIR}/in.lj
+
+6. Try running the LAMMPS GUI
+
+   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
+
+   export QT_FONT_DPI=96
+
+   and reload as shown above.
+
+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
+   "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

@@ -0,0 +1,80 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/../LAMMPS_GUI
+VERSION="$1"
+
+echo "Delete old files, if they exist"
+rm -rf ${DESTDIR} ../LAMMPS_GUI-Linux-amd64*.tar.gz
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+echo "Remove debug info"
+for s in ${DESTDIR}/bin/* ${DESTDIR}/lib/liblammps*
+do \
+        test -f $s && strip --strip-debug $s
+done
+
+echo "Remove libc, gcc, and X11 related shared libs"
+rm -f ${DESTDIR}/lib/ld*.so ${DESTDIR}/lib/ld*.so.[0-9]
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}.so.?
+rm -f ${DESTDIR}/lib/lib{c,dl,rt,m,pthread}-[0-9].[0-9]*.so
+rm -f ${DESTDIR}/lib/libX* ${DESTDIR}/lib/libxcb*
+rm -f ${DESTDIR}/lib/libgcc_s*
+rm -f ${DESTDIR}/lib/libstdc++*
+
+# get qt dir
+QTDIR=$(ldd ${DESTDIR}/bin/lammps-gui | grep libQt5Core | sed -e 's/^.*=> *//' -e 's/libQt5Core.so.*$/qt5/')
+cat > ${DESTDIR}/bin/qt.conf <<EOF
+[Paths]
+Plugins = ../qt5plugins
+EOF
+
+# platform plugin
+mkdir -p ${DESTDIR}/qt5plugins/platforms
+cp ${QTDIR}/plugins/platforms/libqxcb.so ${DESTDIR}/qt5plugins/platforms
+
+# get platform plugin dependencies
+QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd ${QTDIR}/plugins/platforms/libqxcb.so | grep -v ${DESTDIR} | grep libQt5 | sed -e 's/^.*=> *//' -e 's/\(libQt5.*.so.*\) .*$/\1/')
+for dep in ${QTDEPS}
+do \
+    cp ${dep} ${DESTDIR}/lib
+done
+
+echo "Add additional plugins for Qt"
+for dir in styles imageformats
+do \
+    cp -r  ${QTDIR}/plugins/${dir} ${DESTDIR}/qt5plugins/
+done
+
+# get imageplugin dependencies
+for s in ${DESTDIR}/qt5plugins/imageformats/*.so
+do \
+    QTDEPS=$(LD_LIBRARY_PATH=${DESTDIR}/lib ldd $s | grep -v ${DESTDIR} | grep -E '(libQt5|jpeg)' | sed -e 's/^.*=> *//' -e 's/\(lib.*.so.*\) .*$/\1/')
+    for dep in ${QTDEPS}
+    do \
+        cp ${dep} ${DESTDIR}/lib
+    done
+done
+
+echo "Set up wrapper script"
+MYDIR=$(dirname "$0")
+cp ${MYDIR}/xdg-open ${DESTDIR}/bin
+cp ${MYDIR}/linux_wrapper.sh ${DESTDIR}/bin
+for s in ${DESTDIR}/bin/*
+do \
+        EXE=$(basename $s)
+        test ${EXE} = linux_wrapper.sh && continue
+        test ${EXE} = qt.conf && continue
+        test ${EXE} = xdg-open && continue
+        ln -s bin/linux_wrapper.sh ${DESTDIR}/${EXE}
+done
+
+pushd ..
+tar -czvvf LAMMPS_GUI-Linux-amd64-${VERSION}.tar.gz LAMMPS_GUI
+popd
+
+echo "Cleanup dir"
+rm -r ${DESTDIR}
+exit 0

cmake/packaging/build_macos_dmg.sh

@@ -0,0 +1,112 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+VERSION="$1"
+
+echo "Delete old files, if they exist"
+rm -f ${APP_NAME}.dmg ${APP_NAME}-rw.dmg LAMMPS_GUI-macOS-multiarch*.dmg
+
+echo "Create initial dmg file with macdeployqt"
+macdeployqt  lammps-gui.app -dmg
+echo "Create writable dmg file"
+hdiutil convert ${APP_NAME}.dmg -format UDRW -o ${APP_NAME}-rw.dmg
+
+echo "Mount writeable DMG file in read-write mode. Keep track of device and volume names"
+DEVICE=$(hdiutil attach -readwrite -noverify ${APP_NAME}-rw.dmg | grep '^/dev/' | sed 1q | awk '{print $1}')
+VOLUME=$(df | grep ${DEVICE} | sed -e 's/^.*\(\/Volumes\/\)/\1/')
+sleep 2
+
+echo "Create link to Application folder and move README and background image files"
+
+pushd "${VOLUME}"
+ln -s /Applications .
+mv  ${APP_NAME}.app/Contents/Resources/README.txt .
+mkdir  .background
+mv ${APP_NAME}.app/Contents/Resources/LAMMPS_DMG_Background.png .background/background.png
+mv ${APP_NAME}.app LAMMPS_GUI.app
+cd LAMMPS_GUI.app/Contents
+
+echo "Attach icons to LAMMPS console and GUI executables"
+echo "read 'icns' (-16455) \"Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o bin/lmp
+SetFile -a C bin/lmp
+Rez -a icon.rsrc -o MacOS/lammps-gui
+SetFile -a C MacOS/lammps-gui
+rm icon.rsrc
+popd
+
+echo 'Tell the Finder to resize the window, set the background,'
+echo 'change the icon size, place the icons in the right position, etc.'
+echo '
+    tell application "Finder"
+    tell disk "'${APP_NAME}'"
+
+      -- wait for the image to finish mounting
+      set open_attempts to 0
+      repeat while open_attempts < 4
+        try
+          open
+            delay 1
+            set open_attempts to 5
+          close
+        on error errStr number errorNumber
+          set open_attempts to open_attempts + 1
+          delay 10
+        end try
+      end repeat
+      delay 5
+
+      -- open the image the first time and save a .DS_Store
+      -- just the background and icon setup
+      open
+        set current view of container window to icon view
+        set theViewOptions to the icon view options of container window
+        set background picture of theViewOptions to file ".background:background.png"
+        set arrangement of theViewOptions to not arranged
+        set icon size of theViewOptions to 64
+        delay 5
+      close
+
+      -- next set up the position of the app and Applications symlink
+      -- plus hide all window decorations
+      open
+        update without registering applications
+        tell container window
+          set sidebar width to 0
+          set statusbar visible to false
+          set toolbar visible to false
+          set the bounds to { 100, 40, 868, 640 }
+          set position of item "'LAMMPS_GUI'.app" to { 190, 216 }
+          set position of item "Applications" to { 576, 216 }
+          set position of item "README.txt" to { 190, 400 }
+        end tell
+        update without registering applications
+        delay 5
+      close
+
+      -- one last open and close to check the results
+      open
+        delay 5
+      close
+    end tell
+    delay 1
+  end tell
+' | osascript
+
+sync
+
+echo "Unmount modified disk image and convert to compressed read-only image"
+hdiutil detach "${DEVICE}"
+hdiutil convert "${APP_NAME}-rw.dmg" -format UDZO -o "LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg"
+
+echo "Attach icon to .dmg file"
+echo "read 'icns' (-16455) \"lammps-gui.app/Contents/Resources/lammps.icns\";" > icon.rsrc
+Rez -a icon.rsrc -o LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
+SetFile -a C LAMMPS_GUI-macOS-multiarch-${VERSION}.dmg
+rm icon.rsrc
+
+echo "Delete temporary disk images"
+rm -f "${APP_NAME}-rw.dmg"
+rm -f "${APP_NAME}.dmg"
+
+exit 0

cmake/packaging/build_windows_cross_zip.sh

@@ -0,0 +1,65 @@
+#!/bin/bash
+
+APP_NAME=lammps-gui
+DESTDIR=${PWD}/LAMMPS_GUI
+SYSROOT="$1"
+VERSION="$2"
+
+echo "Delete old files, if they exist"
+rm -rvf ${DESTDIR}/LAMMPS_GUI ${DESTDIR}/LAMMPS-Win10-amd64*.zip
+
+echo "Create staging area for deployment and populate"
+DESTDIR=${DESTDIR} cmake --install .  --prefix "/"
+
+# no static libs needed
+rm -rvf ${DESTDIR}/lib
+# but the LAMMPS lib
+
+echo "Copying required DLL files"
+for dll in $(objdump -p *.exe *.dll | sed -n -e '/DLL Name:/s/^.*DLL Name: *//p' | sort | uniq)
+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
+
+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

@@ -0,0 +1,35 @@
+# CMake script to be run post installation to build zipped package
+
+# clean up old zipfile and deployment tree
+file(REMOVE LAMMPS_GUI-Win10-amd64.zip)
+file(REMOVE_RECURSE LAMMPS_GUI)
+file(RENAME ${INSTNAME} LAMMPS_GUI)
+
+# move all executables and dlls to main folder and delete bin folder
+file(GLOB BINFILES LIST_DIRECTORIES FALSE LAMMPS_GUI/bin/*.exe LAMMPS_GUI/bin/*.dll)
+foreach(bin ${BINFILES})
+  get_filename_component(exe ${bin} NAME)
+  file(RENAME ${bin} LAMMPS_GUI/${exe})
+endforeach()
+file(REMOVE_RECURSE LAMMPS_GUI/bin)
+
+# create qt.conf so Qt will find its plugins
+file(WRITE LAMMPS_GUI/qt.conf "[Paths]\r\nPlugins = qt5plugins\r\n")
+
+# initialize environment and then run windeployqt to populate folder with missing dependencies and Qt plugins
+file(WRITE qtdeploy.bat "@ECHO OFF\r\nset VSCMD_DEBUG=0\r\nCALL ${VC_INIT} x64\r\nset PATH=${QT5_BIN_DIR};%PATH%\r\nwindeployqt --plugindir LAMMPS_GUI/qt5plugins --release  LAMMPS_GUI/lammps-gui.exe --no-quick-import --no-webkit2 --no-translations --no-system-d3d-compiler --no-angle --no-opengl-sw\r\n")
+execute_process(COMMAND cmd.exe /c qtdeploy.bat COMMAND_ECHO STDERR)
+file(REMOVE qtdeploy.bat)
+
+# download and uncompress static FFMpeg and gzip binaries
+file(DOWNLOAD "https://download.lammps.org/thirdparty/ffmpeg-gzip.zip" ffmpeg-gzip.zip)
+file(WRITE unpackzip.ps1 "Expand-Archive -Path ffmpeg-gzip.zip -DestinationPath LAMMPS_GUI")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File unpackzip.ps1)
+file(REMOVE unpackzip.ps1)
+file(REMOVE ffmpeg-gzip.zip)
+
+# create zip archive
+file(WRITE makearchive.ps1 "Compress-Archive -Path LAMMPS_GUI -CompressionLevel Optimal -DestinationPath LAMMPS_GUI-Win10-amd64.zip")
+execute_process(COMMAND powershell -ExecutionPolicy Bypass -File makearchive.ps1)
+file(REMOVE makearchive.ps1)
+file(REMOVE_RECURSE LAMMPS_GUI)

cmake/packaging/linux_wrapper.sh

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

cmake/packaging/png2iconset.sh

@@ -0,0 +1,30 @@
+#!/bin/sh
+
+if [ $# != 2 ]
+then
+   echo "usage: $0 <pngfile> <iconset name>"
+   exit 1
+fi
+
+png="$1"
+ico="$2"
+
+if [ ! -f ${png} ]
+then
+   echo "PNG Image $1 not found"
+fi
+
+rm -rf ${ico}.iconset
+mkdir ${ico}.iconset
+sips -z   16   16 ${png} --out ${ico}.iconset/icon_16x16.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_16x16@2x.png
+sips -z   32   32 ${png} --out ${ico}.iconset/icon_32x32.png
+sips -z   64   64 ${png} --out ${ico}.iconset/icon_32x32@2x.png
+sips -z  128  128 ${png} --out ${ico}.iconset/icon_128x128.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_128x128@2x.png
+sips -z  256  256 ${png} --out ${ico}.iconset/icon_256x256.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_256x256@2x.png
+sips -z  512  512 ${png} --out ${ico}.iconset/icon_512x512.png
+sips -z 1024 1024 ${png} --out ${ico}.iconset/icon_512x512@2x.png
+iconutil -c icns ${ico}.iconset
+rm -rf ${ico}.iconset

cmake/presets/all_off.cmake

@@ -26,8 +26,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -43,7 +44,6 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -61,11 +61,10 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT
@@ -83,6 +82,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SCAFACOS
   SHOCK

cmake/presets/all_on.cmake

@@ -28,8 +28,9 @@ set(ALL_PACKAGES
   DPD-REACT
   DPD-SMOOTH
   DRUDE
-  ELECTRODE
   EFF
+  ELECTRODE
+  EXTRA-COMMAND
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -45,7 +46,6 @@ set(ALL_PACKAGES
   KOKKOS
   KSPACE
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -63,11 +63,10 @@ set(ALL_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   OPENMP
   OPT
@@ -85,6 +84,7 @@ 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

@@ -1,16 +1,14 @@
 # Preset that turns on packages with automatic downloads of sources or potentials.
 # Compilation of libraries like Plumed or ScaFaCoS can take a considerable amount of time.
 
-set(ALL_PACKAGES KIM LATTE MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
+set(ALL_PACKAGES KIM MSCG VORONOI PLUMED SCAFACOS MACHDYN MESONT MDI ML-PACE)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)
 endforeach()
 
 set(DOWNLOAD_KIM ON CACHE BOOL "" FORCE)
-set(DOWNLOAD_LATTE ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_MDI ON CACHE BOOL "" FORCE)
-set(DOWNLOAD_MSCG ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_VORO ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_EIGEN3 ON CACHE BOOL "" FORCE)
 set(DOWNLOAD_PACE ON CACHE BOOL "" FORCE)

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/kokkos-cuda.cmake

@@ -1,11 +1,15 @@
 # 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
 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

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

cmake/presets/macos-multiarch.cmake

@@ -0,0 +1,12 @@
+# preset that will build portable multi-arch binaries on macOS without MPI
+
+set(CMAKE_OSX_ARCHITECTURES "arm64;x86_64" CACHE STRING "" FORCE)
+set(CMAKE_OSX_DEPLOYMENT_TARGET 11.0 CACHE STRING "" FORCE)
+set(CMAKE_BUILD_TYPE Release CACHE STRING "" FORCE)
+
+set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
+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)

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
@@ -32,10 +33,8 @@ set(WIN_PACKAGES
   FEP
   GPU
   GRANULAR
-  INTEL
   INTERLAYER
   KSPACE
-  LATTE
   LEPTON
   MACHDYN
   MANIFOLD
@@ -51,6 +50,7 @@ set(WIN_PACKAGES
   ML-POD
   ML-RANN
   ML-SNAP
+  ML-UF3
   MOFFF
   MOLECULE
   MOLFILE
@@ -84,7 +84,6 @@ endforeach()
 
 # these two packages require a full MPI implementation
 if(BUILD_MPI)
-  set(PKG_MPIIO ON CACHE BOOL "" FORCE)
   set(PKG_LATBOLTZ ON CACHE BOOL "" FORCE)
 endif()
 

cmake/presets/most.cmake

@@ -24,8 +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

cmake/presets/nolib.cmake

@@ -12,7 +12,6 @@ set(PACKAGES_WITH_LIB
   KIM
   KOKKOS
   LATBOLTZ
-  LATTE
   LEPTON
   MACHDYN
   MDI
@@ -20,8 +19,6 @@ set(PACKAGES_WITH_LIB
   ML-PACE
   ML-QUIP
   MOLFILE
-  MPIIO
-  MSCG
   NETCDF
   PLUMED
   PYTHON

cmake/presets/oneapi.cmake

@@ -18,11 +18,11 @@ 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_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_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_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" 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
@@ -41,15 +43,17 @@ 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

doc/Makefile

@@ -63,6 +63,7 @@ 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"
 
 # ------------------------------------------
@@ -94,10 +95,13 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -174,10 +178,13 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
+		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -208,14 +215,14 @@ anchor_check : $(ANCHORCHECK)
 style_check : $(VENV)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		python utils/check-styles.py -s ../src -d src ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \\
-		python utils/check-packages.py -s ../src -d src ;\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
@@ -224,6 +231,16 @@ char_check :
 
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+
+link_check : $(VENV) html
+	@(\
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		linkchecker -F html --check-extern html/Manual.html ;\
+		deactivate ;\
+	)
 
 xmlgen : doxygen/xml/index.xml
 

doc/github-development-workflow.md

@@ -1,12 +1,12 @@
 # Outline of the GitHub Development Workflow
 
-This purpose of this document is to provide a point of reference for the
+The purpose of this document is to provide a point of reference for the
 core LAMMPS developers and other LAMMPS contributors to understand the
 choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
-is likely to change as our experiences and needs change and we try to
-adapt accordingly. Last change 2021-09-02.
+is likely to change as our experiences and needs change, and we try to
+adapt it accordingly. Last change 2023-02-10.
 
 ## Table of Contents
 
@@ -22,47 +22,50 @@ adapt accordingly. Last change 2021-09-02.
 ## GitHub Merge Management
 
 In the interest of consistency, ONLY ONE of the core LAMMPS developers
-should doing the merging itself.  This is currently
+should do the merging.  This is currently
 [@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).  If this
 assignment needs to be changed, it shall be done right after a stable
 release.  If the currently assigned developer cannot merge outstanding
 pull requests in a timely manner, or in other extenuating circumstances,
-other core LAMMPS developers with merge rights can merge pull requests,
-when necessary.
+other core LAMMPS developers with merge permission may merge pull
+requests.
 
 ## Pull Requests
 
-ALL changes to the LAMMPS code and documentation, however trivial, 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 patch or stable releases with fast-forward merges based on the
-associated tags. Pull requests may also be submitted to (long-running)
-feature branches created by LAMMPS developers inside the LAMMPS project,
-if needed. Those are not subject to the merge and review restrictions
-discussed in this document, though, but get managed as needed on a
-case-by-case basis.
+*ALL* changes to the LAMMPS code and documentation, however trivial,
+MUST be submitted as a pull request to GitHub.  All changes to the
+"develop" branch must be made exclusively through merging pull requests.
+The "release" and "stable" branches, respectively, are only to be
+updated upon "feature releases" or "stable releases" based on the
+associated tags.  Updates to the stable release in between stable releases
+(for example, back-ported bug fixes) are first merged into the "maintenance"
+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
+are not subject to the merge and review restrictions discussed in this
+document, though, but get managed as needed on a case-by-case basis.
 
 ### Pull Request Assignments
 
 Pull requests can be "chaperoned" by one of the LAMMPS core developers.
-This is indicated by who the pull request is assigned to. LAMMPS core
-developers can self-assign or they can decide to assign a pull request
+This is indicated by whom the pull request is assigned to.  LAMMPS core
+developers can self-assign, or they can decide to assign a pull request
 to a different LAMMPS developer. Being assigned to a pull request means,
 that this pull request may need some work and the assignee is tasked to
-determine whether this might be needed or not, and may either implement
-the required changes or ask the submitter of the pull request to implement
-them.  Even though, all LAMMPS developers may have write access to pull
-requests (if enabled by the submitter, which is the default), only the
-submitter or the assignee of a pull request may do so.  During this
-period the `work_in_progress` label may be applied to the pull
-request.  The assignee gets to decide what happens to the pull request
-next, e.g. whether it should be assigned to a different developer for
-additional checks and changes, or is recommended to be merged.  Removing
-the `work_in_progress` label and assigning the pull request to the
-developer tasked with merging signals that a pull request is ready to be
-merged. In addition, a `ready_for_merge` label may also be assigned
-to signal urgency to merge this pull request quickly.
+determine whether this might be needed or not. The assignee may either
+choose to implement required changes or ask the submitter of the pull
+request to implement them.  Even though, all LAMMPS developers may have
+write access to pull requests (if enabled by the submitter, which is the
+default), only the submitter or the assignee of a pull request should do
+so.  During this period, the `work_in_progress` label may be applied to
+the pull request.  The assignee gets to decide what happens to the pull
+request next, e.g. whether it should be assigned to a different
+developer for additional checks and changes, or is recommended to be
+merged.  Removing the `work_in_progress` label and assigning the pull
+request to the developer tasked with merging signals that a pull request
+is ready to be merged. In addition, a `ready_for_merge` label may also
+be assigned to signal urgency to merge this pull request quickly.
 
 ### Pull Request Reviews
 
@@ -70,32 +73,33 @@ 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
-  * They can be automatically assigned, because a developers matches
-    a file pattern in the `.github/CODEOWNERS` file, which associates
-    developers with the code they contributed and maintain.
+  * 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
+    maintain.
 
 Reviewers are requested to state their appraisal of the proposed changes
 and either approve or request changes. People may unassign themselves
 from review, if they feel not competent about the changes proposed. At
-least two approvals from LAMMPS developers with write access are required
-before merging in addition to the automated compilation 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 feature, that reviews from code owners are "hard"
-reviews (i.e. they must all be approved before merging is allowed), is
-currently disabled and it is in the discretion of the merge maintainer to
-assess when a sufficient degree of approval, especially from external
-contributors, has been reached in these cases.  Reviews may be
-(automatically) dismissed, when the reviewed code has been changed,
-and then approval is required a second time.
+least two approvals from LAMMPS developers with write access are
+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
+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.
 
 ### Pull Request Discussions
 
 All discussions about a pull request should be kept as much as possible
 on the pull request discussion page on GitHub, so that other developers
 can later review the entire discussion after the fact and understand the
-rationale behind choices made.  Exceptions to this policy are technical
-discussions, that are centered on tools or policies themselves
+rationale behind choices that were made.  Exceptions to this policy are
+technical discussions, that are centered on tools or policies themselves
 (git, GitHub, c++) rather than on the content of the pull request.
 
 ## GitHub Issues
@@ -109,39 +113,47 @@ marker in the subject. This is automatically done when using the
 corresponding template for submitting an issue.  Issues may be assigned
 to one or more developers, if they are working on this feature or
 working to resolve an issue.  Issues that have nobody working
-on them at the moment or in the near future, have the label
+on them at the moment, or in the near future, have the label
 `volunteer needed` attached.
 
-When an issue, say `#125` is resolved by a specific pull request,
-the comment for the pull request shall contain the text `closes #125`
-or `fixes #125`, so that the issue is automatically deleted when
-the pull request is merged.  The template for pull requests includes
-a header where connections between pull requests and issues can be listed
-and thus were this comment should be placed.
+When an issue, say `#125` is resolved by a specific pull request, the
+comment for the pull request shall contain the text `closes #125` or
+`fixes #125`, so that the issue is automatically deleted when the pull
+request is merged.  The template for pull requests includes a header
+where connections between pull requests and issues can be listed, and
+thus where this comment should be placed.
 
-## Milestones and Release Planning
+## Release Planning
 
 LAMMPS uses a continuous release development model with incremental
-changes, i.e. significant effort is made - including automated pre-merge
-testing - that the code in the branch "develop" does not get easily
+changes, i.e. significant effort is made -- including automated pre-merge
+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 patch
-releases of LAMMPS every 3-5 weeks at a point, when the LAMMPS
-developers feel, that a sufficient amount of changes have happened, and
-the post-merge testing has been successful. These patch releases are
+extensive and time-consuming tests (including regression testing) are
+performed after code is merged to the "develop" branch.  There are feature
+releases of LAMMPS made about every 4-8 weeks at a point, when the LAMMPS
+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
-follows only these versions (and thus is always supposed to be of
-production quality, unlike "develop", which may be temporary broken, in
-the case of larger change sets or unexpected incompatibilities or side
-effects.
+follows only these versions with fast-forward merges.  While "develop" may
+be temporarily broken through issues only detected by the post-merge tests,
+The "release" branch is always supposed to be of production quality.
 
-About 1-2 times each year, there are going to be "stable" releases of
-LAMMPS.  These have seen additional, manual testing and review of
-results from testing with instrumented code and static code analysis.
-Also, the last 1-3 patch releases before a stable release are "release
-candidate" versions which only contain bugfixes and documentation
-updates.  For release planning and the information of code contributors,
-issues and pull requests being actively worked on are assigned a
-"milestone", which corresponds to the next stable release or the stable
-release after that, with a tentative release date.
+About once each year, there is a "stable" release of LAMMPS.  These have
+seen additional, manual testing and review of results from testing with
+instrumented code and static code analysis.  Also, the last few feature
+releases before a stable release are "release candidate" versions which
+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.
+
+## Project Management
+
+For release planning and the information of code contributors, issues
+and pull requests are being managed with GitHub Project Boards.  There
+are currently three boards: LAMMPS Feature Requests, LAMMPS Bug Reports,
+and LAMMPS Pull Requests.  Each board is organized in columns where
+submissions are categorized.  Within each column the entries are
+(manually) sorted according their priority.

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:"]
+        develop [label="'develop' branch" height=0.75];
+        maintenance [label="'maintenance' branch" height=0.75];
+    };
+    {
+        rank = "same";
+        upload [shape="none" label="Release branches:"]
+        release [label="'release' branch" height=0.75];
+        stable [label="'stable' branch" height=0.75];
+    };
+    develop -> release [label="Feature release\n(every 4-8 weeks)"];
+    release -> stable [label="Stable release\n(once per year)"];
+    stable -> maintenance [label="Reset on stable release" style="setlinewidth(2)"];
+    develop -> maintenance [label="Backports of bugfixes" style="dashed"];
+    maintenance -> stable [label="Updates to stable release"];
+    {
+        rank = "same";
+        tag [shape="none" label="Applied tags:"];
+        patchtag [shape="box" label="patch_<date>"];
+        stabletag [shape="box" label="stable_<date>"];
+        updatetag [shape="box" label="stable_<date>_update<num>"];
+    };
+    release -> patchtag [label="feature release" style="dotted"];
+    stable -> stabletag [label="stable release" style="dotted"];
+    stable -> updatetag [label="update release" style="dotted"];
+}
+

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "8 February 2023" "2023-02-08"
+.TH LAMMPS "1" "29 August 2024" "2024-08-29"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 8 February 2023
+\- Molecular Dynamics Simulator.  Version 29 August 2024
 
 .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--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/msi2lmp.1

@@ -1,11 +1,11 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
 
 .SH SYNOPSIS
 .B msi2lmp
-<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
 
 .SH DESCRIPTION
 .PP
@@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
 
 .SH OPTIONS
 .TP
+\fB\-h\fR, \fB\-help\fR,
+Print detailed help message to the screen and stop.
+.TP
 \fB\<ROOTNAME>\fR
 This has to be the first argument and is a
 .B mandatory

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
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    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)**
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-**(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)**
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@@ -58,7 +70,7 @@ Bibliography
 **(Babadi)**
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-**(Babadi)**
+**(Babadi2)**
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 **(Baczewski)**
@@ -73,23 +85,23 @@ Bibliography
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-**(Banna)**
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-
 **(Barrat)**
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 **(Barrett)**
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+**(Barros)**
+   Barros, Sinkovits, Luijten, J. Chem. Phys, 140, 064903 (2014)
+
 **(Bartok)**
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 **(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
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+**(Baskes2)**
+   Baskes, Phys Rev B, 75, 094113 (2007).
+
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+**(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.
+
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 **(Berardi)**
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-**(Berendsen)**
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-
 **(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)**
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 **(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
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 **(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)**
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+**(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)**
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 **(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).
@@ -203,7 +233,7 @@ Bibliography
    A Caro, DA Crowson, M Caro; Phys Rev Lett, 95, 075702 (2005)
 
 **(CasP)**
-   CasP webpage: https://www.helmholtz-berlin.de/people/gregor-schiwietz/casp_en.html
+   CasP webpage: http://www.casp-program.org/
 
 **(Cawkwell2012)**
    A.\  M. N. Niklasson, M. J. Cawkwell, Phys. Rev. B, 86 (17), 174308 (2012).
@@ -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)**
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@@ -268,6 +322,15 @@ Bibliography
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+**(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)**
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+**(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)**
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@@ -304,12 +382,21 @@ Bibliography
 **(Elliott)**
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+**(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)**
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 **(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]
+
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@@ -328,9 +415,18 @@ Bibliography
 **(Faken)**
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+**(Falk)**
+   Falk and Langer PRE, 57, 7192 (1998).
+
 **(Fath)**
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+**(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)**
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@@ -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)**
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@@ -412,6 +526,9 @@ Bibliography
 **(Guo)**
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+**(Gupta)**
+   Gupta ,Phys Rev. B, 23, 6265-6270 (1981).
+
 **(Hardy)**
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@@ -433,6 +550,9 @@ Bibliography
 **(Henrich)**
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+**(Herman)**
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+
 **(Hess)**
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@@ -454,24 +574,42 @@ Bibliography
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+**(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).
+
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 **(Hunt)**
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+**(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)**
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@@ -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)**
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+**(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_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::
@@ -129,13 +130,12 @@ 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. ``LATTE``, ``KSPACE``, and ``COLVARS``.  See the
-:doc:`Packages details <Packages_details>` page for more info on these
-packages, and the pages for their respective commands for OpenMP
-threading info.
+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
@@ -232,24 +232,32 @@ 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.
+      ``-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.
 
       Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts.
@@ -260,7 +268,7 @@ LAMMPS.
          When the cmake command completes, it prints a summary to the
          screen which compilers it is using and what flags and settings
          will be used for the compilation.  Note that if the top-level
-         compiler is mpicxx, it is simply a wrapper on a real compiler.
+         compiler is ``mpicxx``, it is simply a wrapper on a real compiler.
          The underlying compiler info is what CMake will try to
          determine and report.  You should check to confirm you are
          using the compiler and optimization flags you want.
@@ -279,19 +287,19 @@ 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::
 
@@ -317,10 +325,10 @@ LAMMPS.
          there may be specific compiler or linker flags that are either
          required or recommended to enable required features and to
          achieve optimal performance.  You need to include these in the
-         CCFLAGS and LINKFLAGS settings above.  For details, see the
+         ``CCFLAGS`` and ``LINKFLAGS`` settings above.  For details, see the
          documentation for the individual packages listed on the
          :doc:`Speed_packages` page.  Or examine these files in the
-         src/MAKE/OPTIONS directory.  They correspond to each of the 5
+         ``src/MAKE/OPTIONS`` directory.  They correspond to each of the 5
          accelerator packages and their hardware variants:
 
          .. code-block:: bash
@@ -389,7 +397,8 @@ 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 +460,7 @@ 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 +473,7 @@ 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 +498,12 @@ 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 +517,10 @@ 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

@@ -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 3.16 or later is available.
 
 .. warning::
 
@@ -34,19 +33,18 @@ 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
-software or for people that want to modify or extend LAMMPS.
+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.
+  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
@@ -133,20 +131,20 @@ 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 line.
 
 Generating files for alternate build tools (e.g. Ninja) and project files
-for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the *-G*
+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``.
 
@@ -173,19 +171,19 @@ 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

@@ -88,8 +88,8 @@ 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 +110,7 @@ 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 +123,44 @@ 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:
+
+- 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 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 regression testing
 are maintained in a
 `separate repository <https://github.com/lammps/lammps-testing>`_
-of the LAMMPS project on GitHub.
+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.
 
-The unit testing facility is integrated into the CMake build process
-of the LAMMPS source code distribution itself.  It can be enabled by
+The unit testing facility is integrated into the CMake build process of
+the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <https://pyyaml.org/>`_ library and 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 +168,7 @@ 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 +181,24 @@ 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 +213,25 @@ 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 +248,31 @@ 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 command lines 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 +288,18 @@ 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 +337,17 @@ 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 +361,10 @@ 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
@@ -416,15 +452,16 @@ 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
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -477,27 +514,51 @@ 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
 ----------------------
@@ -518,11 +579,15 @@ 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
 to some the coding style preferences of the LAMMPS developers.
 
+.. _clang-format:
+
 Clang-format support
 --------------------
 

doc/src/Build_link.rst

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

doc/src/Build_make.rst

@@ -25,7 +25,7 @@ additional tools to be available and functioning.
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
   * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
   * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * Python (optional, required for ``make lib-<pkg>`` in the src
+  * Python (optional, required for ``make lib-<pkg>`` in the ``src``
     folder).  Python scripts are currently tested with python 2.7 and
     3.6 to 3.11. The procedure for :doc:`building the documentation
     <Build_manual>` *requires* Python 3.5 or later.
@@ -117,8 +117,8 @@ their settings may become outdated, too:
 
 .. code-block:: bash
 
-   make mac             # build serial LAMMPS on a Mac
-   make mac_mpi         # build parallel LAMMPS on a Mac
+   make mac             # build serial LAMMPS on macOS
+   make mac_mpi         # build parallel LAMMPS on macOS
    make intel_cpu       # build with the INTEL package optimized for CPUs
    make knl             # build with the INTEL package optimized for KNLs
    make opt             # build with the OPT package optimized for CPUs

doc/src/Build_manual.rst

@@ -33,7 +33,7 @@ various tools and files.  Some of them have to be installed (see below).  For
 the rest the build process will attempt to download and install them into
 a python virtual environment and local folders.
 
-A current version of the manual (latest patch release, that is the state
+A current version of the manual (latest feature release, that is the state
 of the *release* branch) is is available online at:
 `https://docs.lammps.org/ <https://docs.lammps.org/>`_.
 A version of the manual corresponding to the ongoing development (that is
@@ -48,15 +48,15 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<https://sphinx-doc.org>`_ document generator tool.  It also
+<https://www.sphinx-doc.org/>`_ document generator tool.  It also
 incorporates programmer documentation extracted from the LAMMPS C++
-sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
+sources through the `Doxygen <https://doxygen.nl/>`_ program.  Currently
 the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
 and MOBI (for Amazon Kindle readers) are supported.  For that to work a
-Python 3 interpreter, the ``doxygen`` tools and internet access to
-download additional files and tools are required.  This download is
-usually only required once or after the documentation folder is returned
-to a pristine state with ``make clean-all``.
+Python interpreter version 3.8 or later, the ``doxygen`` tools and
+internet access to download additional files and tools are required.
+This download is usually only required once or after the documentation
+folder is returned to a pristine state with ``make clean-all``.
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -87,6 +87,7 @@ folder.  The following ``make`` commands are available:
    make anchor_check  # check for duplicate anchor labels
    make style_check   # check for complete and consistent style lists
    make package_check # check for complete and consistent package lists
+   make link_check    # check for broken or outdated URLs
    make spelling      # spell-check the manual
 
 ----------

doc/src/Build_package.rst

@@ -46,7 +46,6 @@ packages:
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
-   * :ref:`LATTE <latte>`
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
@@ -56,7 +55,6 @@ packages:
    * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
-   * :ref:`MSCG <mscg>`
    * :ref:`NETCDF <netcdf>`
    * :ref:`OPENMP <openmp>`
    * :ref:`OPT <opt>`
@@ -64,6 +62,7 @@ packages:
    * :ref:`POEMS <poems>`
    * :ref:`PYTHON <python>`
    * :ref:`QMMM <qmmm>`
+   * :ref:`RHEO <rheo>`
    * :ref:`SCAFACOS <scafacos>`
    * :ref:`VORONOI <voronoi>`
    * :ref:`VTK <vtk>`
@@ -101,10 +100,10 @@ versus make.
       .. code-block:: bash
 
          cd lammps/src
-         make ps                    # check which packages are currently installed
-         make yes-name              # install a package with name
-         make no-name               # uninstall a package with name
-         make mpi                   # build LAMMPS with whatever packages are now installed
+         make ps        # check which packages are currently installed
+         make yes-name  # install a package with name
+         make no-name   # uninstall a package with name
+         make mpi       # build LAMMPS with whatever packages are now installed
 
       Examples:
 
@@ -173,17 +172,41 @@ make a copy of one of them and modify it to suit your needs.
 
 .. code-block:: bash
 
-    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake  # enable just a few core packages
-    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake  # enable most packages
-    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake  # enable packages which download sources or potential files
-    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake  # disable packages that do require extra libraries or tools
-    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
-    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake  # change settings to use the GNU compilers by default
-    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
-    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
-    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
-    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
-    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross-compilers
+    # enable just a few core packages
+    cmake -C ../cmake/presets/basic.cmake    [OPTIONS] ../cmake
+
+    # enable most packages
+    cmake -C ../cmake/presets/most.cmake     [OPTIONS] ../cmake
+
+    # enable packages which download sources or potential files
+    cmake -C ../cmake/presets/download.cmake [OPTIONS] ../cmake
+
+    # disable packages that do require extra libraries or tools
+    cmake -C ../cmake/presets/nolib.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the Clang compilers by default
+    cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the GNU compilers by default
+    cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake
+
+    # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake
+
+    # change settings to use the PGI compilers by default
+    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake
+
+    # enable all packages
+    cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake
+
+    # disable all packages
+    cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake
+
+    #  compile with MinGW cross-compilers
+    mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake
+
+    # compile serial multi-arch binaries on macOS
+    cmake -C ../cmake/presets/macos-multiarch.cmake [OPTIONS] ../cmake
 
 Presets that have names starting with "windows" are specifically for
 compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
@@ -209,7 +232,8 @@ Example
    # GPU package and configure it for using CUDA. You can run.
    mkdir build
    cd build
-   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake -D PKG_GPU=on -D GPU_API=cuda ../cmake
+   cmake -C ../cmake/presets/most.cmake -C ../cmake/presets/nolib.cmake \
+         -D PKG_GPU=on -D GPU_API=cuda ../cmake
 
    # to add another package, say BODY to the previous configuration you can run:
    cmake -D PKG_BODY=on .

doc/src/Build_settings.rst

@@ -1,3 +1,7 @@
+.. raw:: latex
+
+    \clearpage
+
 Optional build settings
 =======================
 
@@ -8,7 +12,8 @@ explains how to do this for building both with CMake and make.
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
 * `Size of LAMMPS integer types and size limits`_
 * `Read or write compressed files`_
-* `Output of JPG, PNG, and move files` via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
+* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
+* `Support for downloading files`_
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
@@ -19,7 +24,7 @@ explains how to do this for building both with CMake and make.
 .. _cxx11:
 
 C++11 standard compliance
-------------------------------------------
+-------------------------
 
 A C++11 standard compatible compiler is a requirement for compiling LAMMPS.
 LAMMPS version 3 March 2020 is the last version compatible with the previous
@@ -31,12 +36,16 @@ flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
 
    CCFLAGS = -g -O3 -std=c++11
 
+Individual packages may require compliance with a later C++ standard
+like C++14 or C++17.  These requirements will be documented with the
+:doc:`individual packages <Packages_details>`.
+
 ----------
 
 .. _fft:
 
 FFT library
----------------------
+-----------
 
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
@@ -44,21 +53,36 @@ require use of an FFT library to compute 1d FFTs.  The KISS FFT
 library is included with LAMMPS, but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
+.. versionadded:: 7Feb2024
+
+Alternatively, LAMMPS can use the `heFFTe
+<https://icl-utk-edu.github.io/heffte/>`_ library for the MPI
+communication algorithms, which comes with many optimizations for
+special cases, e.g. leveraging available 2D and 3D FFTs in the back end
+libraries and better pipelining for packing and communication.
+
 .. tabs::
 
    .. tab:: CMake build
 
       .. code-block:: bash
 
-         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found, else KISS
+         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found,
+                                   # else KISS
+         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT,
+                                   # default is KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
+         -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
 
       .. note::
 
-         The values for the FFT variable must be in upper-case.  This is
-         an exception to the rule that all CMake variables can be specified
-         with lower-case values.
+         When the Kokkos variant of a package is compiled and selected at run time,
+         the FFT library selected by the ``FFT_KOKKOS`` variable applies. Otherwise,
+         the FFT library selected by the FFT variable applies.
+         The same FFT settings apply to both. ``FFT_KOKKOS`` must be compatible with the
+         Kokkos back end - for example, when using the CUDA back end of Kokkos,
+         you must use either ``CUFFT`` or ``KISS``.
 
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
@@ -76,6 +100,17 @@ LAMMPS can use them if they are available on your system.
          -D MKL_INCLUDE_DIR=path     # ditto for Intel MKL library
          -D FFT_MKL_THREADS=on       # enable using threaded FFTs with MKL libraries
          -D MKL_LIBRARY=path         # path to MKL libraries
+         -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
+                                     # heFFTe back end
+         -D Heffte_ROOT=path         # path to an existing heFFTe installation
+
+      .. note::
+
+         heFFTe comes with a builtin (= stock) back end for FFTs, i.e. a
+         default internal FFT implementation; however, this stock back
+         end is intended for testing purposes only and is not optimized
+         for production runs.
+
 
    .. tab:: Traditional make
 
@@ -85,32 +120,74 @@ LAMMPS can use them if they are available on your system.
 
       .. code-block:: make
 
-         FFT_INC = -DFFT_FFTW3         # -DFFT_FFTW3, -DFFT_FFTW (same as -DFFT_FFTW3), -DFFT_MKL, or -DFFT_KISS
-                                       # default is KISS if not specified
-         FFT_INC = -DFFT_SINGLE        # do not specify for double precision
-         FFT_INC = -DFFT_FFTW_THREADS  # enable using threaded FFTW3 libraries
-         FFT_INC = -DFFT_MKL_THREADS   # enable using threaded FFTs with MKL libraries
-         FFT_INC = -DFFT_PACK_ARRAY    # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
-                                       # default is FFT_PACK_ARRAY if not specified
+         FFT_INC = -DFFT_<NAME>        # where <NAME> is KISS (default), FFTW3,
+                                       # FFTW (same as FFTW3), or MKL
+         FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
+                                       # FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
+         FFT_INC = -DFFT_SINGLE       # do not specify for double precision
+         FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
+         FFT_INC = -DFFT_MKL_THREADS  # enable using threaded FFTs with MKL libraries
+         FFT_INC = -DFFT_PACK_ARRAY   # or -DFFT_PACK_POINTER or -DFFT_PACK_MEMCPY
+                                      # default is FFT_PACK_ARRAY if not specified
 
       .. code-block:: make
 
-         FFT_INC =       -I/usr/local/include
-         FFT_PATH =      -L/usr/local/lib
-         FFT_LIB =       -lfftw3             # FFTW3 double precision
-         FFT_LIB =       -lfftw3 -lfftw3_omp # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
-         FFT_LIB =       -lfftw3 -lfftw3f    # FFTW3 single precision
-         FFT_LIB =       -lmkl_intel_lp64 -lmkl_sequential -lmkl_core   # MKL with Intel compiler, serial interface
-         FFT_LIB =       -lmkl_gf_lp64 -lmkl_sequential -lmkl_core      # MKL with GNU compiler, serial interface
-         FFT_LIB =       -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core # MKL with Intel compiler, threaded interface
-         FFT_LIB =       -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core      # MKL with GNU compiler, threaded interface
-         FFT_LIB =       -lmkl_rt            # MKL with automatic runtime selection of interface libs
+         FFT_INC =  -I/usr/local/include
+         FFT_PATH = -L/usr/local/lib
+
+         # hipFFT either precision
+         FFT_LIB =  -lhipfft
+
+         # cuFFT either precision
+         FFT_LIB =  -lcufft
+
+         # FFTW3 double precision
+         FFT_LIB =  -lfftw3
+
+         # FFTW3 double precision with threads (needs -DFFT_FFTW_THREADS)
+         FFT_LIB =  -lfftw3 -lfftw3_omp
+
+         # FFTW3 single precision
+         FFT_LIB =  -lfftw3 -lfftw3f
+
+         # serial MKL with Intel compiler
+         FFT_LIB =  -lmkl_intel_lp64 -lmkl_sequential -lmkl_core
+
+         # serial MKL with GNU compiler
+         FFT_LIB =  -lmkl_gf_lp64 -lmkl_sequential -lmkl_core
+
+         # threaded MKL with Intel compiler
+         FFT_LIB =  -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core
+
+         # threaded MKL with GNU compiler
+         FFT_LIB =  -lmkl_gf_lp64 -lmkl_gnu_thread -lmkl_core
+
+         # MKL with automatic runtime selection of interface libs
+         FFT_LIB =  -lmkl_rt
 
       As with CMake, you do not need to set paths in ``FFT_INC`` or
       ``FFT_PATH``, if the compiler can find the FFT header and library
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
+      Traditional make can also link to heFFTe using an existing installation
+
+      .. code-block:: make
+
+         include <path-to-heffte-installation>/share/heffte/HeffteMakefile.in
+         FFT_INC = -DFFT_HEFFTE -DFFT_HEFFTE_FFTW $(heffte_include)
+         FFT_PATH =
+         FFT_LIB = $(heffte_link) $(heffte_libs)
+
+      The heFFTe install path will contain ``HeffteMakefile.in``.
+      which will define the ``heffte_`` include variables needed to link to heFFTe from
+      an external project using traditional make.
+      The ``-DFFT_HEFFTE`` is required to switch to using heFFTe, while the optional ``-DFFT_HEFFTE_FFTW``
+      selects the desired heFFTe back end, e.g., ``-DFFT_HEFFTE_FFTW`` or ``-DFFT_HEFFTE_MKL``,
+      omitting the variable will default to the `stock` back end.
+      The heFFTe `stock` back end is intended to be used for testing and debugging,
+      but is not performance optimized for large scale production runs.
+
 The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
 included in the LAMMPS distribution.  It is portable across all
 platforms.  Depending on the size of the FFTs and the number of
@@ -134,13 +211,18 @@ it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges
 (e.g. invoke it via sudo), unless you specify a local directory with
-the "--prefix" option of configure.  Type ``./configure --help`` to see
+the ``--prefix`` option of configure.  Type ``./configure --help`` to see
 various options.
 
 The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
+The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
+AMD's HIP installations, respectively. These FFT libraries require the
+Kokkos acceleration package to be enabled and the Kokkos back end to be
+GPU-resident (i.e., HIP or CUDA).
+
 Performing 3d FFTs in parallel can be time-consuming due to data access
 and required communication.  This cost can be reduced by performing
 single-precision FFTs instead of double precision.  Single precision
@@ -152,11 +234,11 @@ generally less than the difference in precision. Using the
 ``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
 use and parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
-library a second time with support for single-precision.
+When using ``-DFFT_SINGLE`` with FFTW3, you may need to ensure that
+the FFTW3 installation includes support for single-precision.
 
-For FFTW3, do the following, which should produce the additional
-library ``libfftw3f.a`` or ``libfftw3f.so``\ .
+When compiler FFTW3 from source, you can do the following, which should
+produce the additional libraries ``libfftw3f.a`` and/or ``libfftw3f.so``\ .
 
 .. code-block:: bash
 
@@ -165,13 +247,27 @@ library ``libfftw3f.a`` or ``libfftw3f.so``\ .
 
 Performing 3d FFTs requires communication to transpose the 3d FFT
 grid.  The data packing/unpacking for this can be done in one of 3
-modes (ARRAY, POINTER, MEMCPY) as set by the FFT_PACK syntax above.
+modes (ARRAY, POINTER, MEMCPY) as set by the ``FFT_PACK`` syntax above.
 Depending on the machine, the size of the FFT grid, the number of
 processors used, one option may be slightly faster.  The default is
 ARRAY mode.
 
+When using ``-DFFT_HEFFTE`` CMake will first look for an existing
+install with hints provided by ``-DHeffte_ROOT``, as recommended by the
+CMake standard and note that the name is case sensitive. If CMake cannot
+find a heFFTe installation with the correct back end (e.g., FFTW or
+MKL), it will attempt to download and build the library automatically.
+In this case, LAMMPS CMake will also accept all heFFTe specific
+variables listed in the `heFFTe documentation
+<https://mkstoyanov.bitbucket.io/heffte/md_doxygen_installation.html>`_
+and those variables will be passed into the heFFTe build.
+
 ----------
 
+.. raw:: latex
+
+    \clearpage
+
 .. _size:
 
 Size of LAMMPS integer types and size limits
@@ -212,7 +308,7 @@ LAMMPS system size restrictions
 
 .. list-table::
    :header-rows: 1
-   :widths: auto
+   :widths: 18 27 28 27
    :align: center
 
    * -
@@ -281,8 +377,8 @@ in whichever ``lib/gpu/Makefile`` is used must be the same as above.
 
 .. _graphics:
 
-Output of JPG, PNG, and movie files
---------------------------------------------------
+Output of JPEG, PNG, and movie files
+------------------------------------
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
 PNG image files.  Likewise, the :doc:`dump movie <dump_image>` command
@@ -295,12 +391,13 @@ requires the following settings:
 
       .. code-block:: bash
 
-         -D WITH_JPEG=value      # yes or no
-                                 # default = yes if CMake finds JPEG files, else no
-         -D WITH_PNG=value       # yes or no
-                                 # default = yes if CMake finds PNG and ZLIB files, else no
-         -D WITH_FFMPEG=value    # yes or no
-                                 # default = yes if CMake can find ffmpeg, else no
+         -D WITH_JPEG=value    # yes or no
+                               # default = yes if CMake finds JPEG development files, else no
+         -D WITH_PNG=value     # yes or no
+                               # default = yes if CMake finds PNG and ZLIB development files,
+                               # else no
+         -D WITH_FFMPEG=value  # yes or no
+                               # default = yes if CMake can find ffmpeg, else no
 
       Usually these settings are all that is needed.  If CMake cannot
       find the graphics header, library, executable files, you can set
@@ -322,8 +419,10 @@ requires the following settings:
 
          LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG  <other LMP_INC settings>
 
-         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
-         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
+         JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h headers
+                                          # if make cannot find them
+         JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so)
+                                          # files if make cannot find them
          JPG_LIB = -ljpeg -lpng -lz       # library names
 
       As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
@@ -354,8 +453,8 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Supported compression tools are currently
-``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
+:doc:`dump <dump>`.  Supported compression tools and algorithms are currently
+``gzip``, ``bzip2``, ``zstd``, ``xz``, ``lz4``, and ``lzma`` (via xz).
 
 .. tabs::
 
@@ -363,8 +462,8 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
 
       .. code-block:: bash
 
-         -D WITH_GZIP=value       # yes or no
-                                  # default is yes if CMake can find the gzip program, else no
+         -D WITH_GZIP=value  # yes or no
+                             # default is yes if CMake can find the gzip program
 
    .. tab:: Traditional make
 
@@ -386,18 +485,64 @@ during a run.
    available using a compression library instead, which is what the
    :ref:`COMPRESS package <PKG-COMPRESS>` enables.
 
+--------------------------------------------------
+
+.. _libcurl:
+
+Support for downloading files
+-----------------------------
+
+.. versionadded:: 29Aug2024
+
+The :doc:`geturl command <geturl>` command uses the `the libcurl library
+<https://curl.se/libcurl/>`_ to download files.  This requires that
+LAMMPS is compiled accordingly which needs the following settings:
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D WITH_CURL=value      # yes or no
+                                 # default = yes if CMake finds CURL development files, else no
+
+      Usually these settings are all that is needed.  If CMake cannot
+      find the graphics header, library, executable files, you can set
+      these variables:
+
+      .. code-block:: bash
+
+         -D CURL_INCLUDE_DIR=path    # path to folder which contains curl.h header file
+         -D CURL_LIBRARY=path        # path to libcurls.a (.so) file
+
+   .. tab:: Traditional make
+
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_CURL  <other LMP_INC settings>
+
+         CURL_INC = -I/usr/local/include   # path to curl folder with curl.h
+         CURL_PATH = -L/usr/lib            # paths to libcurl.a(.so) if make cannot find it
+         CURL_LIB = -lcurl                 # library names
+
+      As with CMake, you do not need to set ``CURL_INC`` or ``CURL_PATH``,
+      if make can find the libcurl header and library files in their
+      default system locations.  You must specify ``CURL_LIB`` with a
+      paths or linker flags to link to libcurl.
+
 ----------
 
 .. _align:
 
 Memory allocation alignment
----------------------------------------
+---------------------------
 
-This setting enables the use of the "posix_memalign()" call instead of
-"malloc()" when LAMMPS allocates large chunks of memory.  Vector
+This setting enables the use of the ``posix_memalign()`` call instead of
+``malloc()`` when LAMMPS allocates large chunks of memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
-current operating systems, the "malloc()" implementation returns
+current operating systems, the ``malloc()`` implementation returns
 pointers that are aligned to 16-byte boundaries. Using SSE vector
 instructions efficiently, however, requires memory blocks being aligned
 on 64-byte boundaries.
@@ -411,9 +556,9 @@ on 64-byte boundaries.
          -D LAMMPS_MEMALIGN=value            # 0, 8, 16, 32, 64 (default)
 
       Use a ``LAMMPS_MEMALIGN`` value of 0 to disable using
-      "posix_memalign()" and revert to using the "malloc()" C-library
+      ``posix_memalign()`` and revert to using the ``malloc()`` C-library
       function instead.  When compiling LAMMPS for Windows systems,
-      "malloc()" will always be used and this setting is ignored.
+      ``malloc()`` will always be used and this setting is ignored.
 
    .. tab:: Traditional make
 
@@ -422,7 +567,7 @@ on 64-byte boundaries.
          LMP_INC = -DLAMMPS_MEMALIGN=value   # 8, 16, 32, 64
 
       Do not set ``-DLAMMPS_MEMALIGN``, if you want to have memory
-      allocated with the "malloc()" function call
+      allocated with the ``malloc()`` function call
       instead. ``-DLAMMPS_MEMALIGN`` **cannot** be used on Windows, as
       Windows different function calls with different semantics for
       allocating aligned memory, that are not compatible with how LAMMPS
@@ -459,27 +604,13 @@ those systems:
 .. _exceptions:
 
 Exception handling when using LAMMPS as a library
-------------------------------------------------------------------
+-------------------------------------------------
 
-This setting is useful when external codes drive LAMMPS as a library.
-With this option enabled, LAMMPS errors do not kill the calling code.
-Instead, the call stack is unwound and control returns to the caller,
-e.g. to Python. Of course, the calling code has to be set up to
-*catch* exceptions thrown from within LAMMPS.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      .. code-block:: bash
-
-         -D LAMMPS_EXCEPTIONS=value        # yes or no (default)
-
-   .. tab:: Traditional make
-
-      .. code-block:: make
-
-         LMP_INC = -DLAMMPS_EXCEPTIONS   <other LMP_INC settings>
+LAMMPS errors do not kill the calling code, but throw an exception.  In
+the C-library interface, the call stack is unwound and control returns
+to the caller, e.g. to Python or a code that is coupled to LAMMPS. The
+error status can then be queried.  When using C++ directly, the calling
+code has to be set up to *catch* exceptions thrown from within LAMMPS.
 
 .. note::
 

doc/src/Commands_all.rst

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

doc/src/Commands_bond.rst

@@ -1,21 +1,7 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
 .. _bond:
 
-Bond_style potentials
-=====================
+Bond styles
+===========
 
 All LAMMPS :doc:`bond_style <bond_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -23,11 +9,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <bond_none>`
    * :doc:`zero <bond_zero>`
-   * :doc:`hybrid <bond_hybrid>`
+   * :doc:`hybrid (k) <bond_hybrid>`
+   *
+   *
    *
    *
    *
@@ -42,6 +30,7 @@ OPT.
    * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
+   * :doc:`harmonic/restrain <bond_harmonic_restrain>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
    * :doc:`lepton (o) <bond_lepton>`
@@ -53,13 +42,14 @@ OPT.
    * :doc:`oxdna2/fene <bond_oxdna>`
    * :doc:`oxrna2/fene <bond_oxdna>`
    * :doc:`quartic (o) <bond_quartic>`
+   * :doc:`rheo/shell <bond_rheo_shell>`
    * :doc:`special <bond_special>`
    * :doc:`table (o) <bond_table>`
 
 .. _angle:
 
-Angle_style potentials
-======================
+Angle styles
+============
 
 All LAMMPS :doc:`angle_style <angle_style>` commands.  Some styles have
 accelerated versions.  This is indicated by additional letters in
@@ -67,11 +57,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <angle_none>`
    * :doc:`zero <angle_zero>`
-   * :doc:`hybrid <angle_hybrid>`
+   * :doc:`hybrid (k) <angle_hybrid>`
+   *
+   *
    *
    *
    *
@@ -88,6 +80,7 @@ OPT.
    * :doc:`cosine/shift (o) <angle_cosine_shift>`
    * :doc:`cosine/shift/exp (o) <angle_cosine_shift_exp>`
    * :doc:`cosine/squared (o) <angle_cosine_squared>`
+   * :doc:`cosine/squared/restricted (o) <angle_cosine_squared_restricted>`
    * :doc:`cross <angle_cross>`
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
@@ -98,13 +91,13 @@ OPT.
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`spica (o) <angle_spica>`
+   * :doc:`spica (ko) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
 
-Dihedral_style potentials
-=========================
+Dihedral styles
+===============
 
 All LAMMPS :doc:`dihedral_style <dihedral_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -112,20 +105,23 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <dihedral_none>`
    * :doc:`zero <dihedral_zero>`
-   * :doc:`hybrid <dihedral_hybrid>`
+   * :doc:`hybrid (k) <dihedral_hybrid>`
+   *
+   *
    *
    *
    *
    *
    *
    * :doc:`charmm (iko) <dihedral_charmm>`
-   * :doc:`charmmfsw <dihedral_charmm>`
+   * :doc:`charmmfsw (k) <dihedral_charmm>`
    * :doc:`class2 (ko) <dihedral_class2>`
    * :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
+   * :doc:`cosine/squared/restricted <dihedral_cosine_squared_restricted>`
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
@@ -140,8 +136,8 @@ OPT.
 
 .. _improper:
 
-Improper_style potentials
-=========================
+Improper styles
+===============
 
 All LAMMPS :doc:`improper_style <improper_style>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -149,11 +145,13 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 4
+   :columns: 5
 
    * :doc:`none <improper_none>`
    * :doc:`zero <improper_zero>`
-   * :doc:`hybrid <improper_hybrid>`
+   * :doc:`hybrid (k) <improper_hybrid>`
+   *
+   *
    *
    *
    *

doc/src/Commands_category.rst

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

doc/src/Commands_compute.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Compute commands
-================
+Compute styles
+==============
 
 An alphabetic list of all LAMMPS :doc:`compute <compute>` commands.
 Some styles have accelerated versions.  This is indicated by
@@ -21,7 +7,7 @@ additional letters in parenthesis: g = GPU, i = INTEL, k =
 KOKKOS, o = OPENMP, t = OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`ackland/atom <compute_ackland_atom>`
    * :doc:`adf <compute_adf>`
@@ -46,12 +32,15 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`com/chunk <compute_com_chunk>`
    * :doc:`contact/atom <compute_contact_atom>`
    * :doc:`coord/atom (k) <compute_coord_atom>`
+   * :doc:`count/type <compute_count_type>`
    * :doc:`damage/atom <compute_damage_atom>`
    * :doc:`dihedral <compute_dihedral>`
    * :doc:`dihedral/local <compute_dihedral_local>`
    * :doc:`dilatation/atom <compute_dilatation_atom>`
    * :doc:`dipole <compute_dipole>`
    * :doc:`dipole/chunk <compute_dipole_chunk>`
+   * :doc:`dipole/tip4p <compute_dipole>`
+   * :doc:`dipole/tip4p/chunk <compute_dipole_chunk>`
    * :doc:`displace/atom <compute_displace_atom>`
    * :doc:`dpd <compute_dpd>`
    * :doc:`dpd/atom <compute_dpd_atom>`
@@ -61,7 +50,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
-   * :doc:`erotate/sphere <compute_erotate_sphere>`
+   * :doc:`erotate/sphere (k) <compute_erotate_sphere>`
    * :doc:`erotate/sphere/atom <compute_erotate_sphere_atom>`
    * :doc:`event/displace <compute_event_displace>`
    * :doc:`fabric <compute_fabric>`
@@ -88,6 +77,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`composition/atom (k) <compute_composition_atom>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -96,6 +86,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`nbond/atom <compute_nbond_atom>`
    * :doc:`omega/chunk <compute_omega_chunk>`
    * :doc:`orientorder/atom (k) <compute_orientorder_atom>`
+   * :doc:`pace <compute_pace>`
    * :doc:`pair <compute_pair>`
    * :doc:`pair/local <compute_pair_local>`
    * :doc:`pe <compute_pe>`
@@ -103,19 +94,28 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pe/mol/tally <compute_tally>`
    * :doc:`pe/tally <compute_tally>`
    * :doc:`plasticity/atom <compute_plasticity_atom>`
+   * :doc:`pod/atom <compute_pod_atom>`
+   * :doc:`podd/atom <compute_pod_atom>`
+   * :doc:`pod/local <compute_pod_atom>`
+   * :doc:`pod/global <compute_pod_atom>`
    * :doc:`pressure <compute_pressure>`
+   * :doc:`pressure/alchemy <compute_pressure_alchemy>`
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`
    * :doc:`property/chunk <compute_property_chunk>`
    * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
+   * :doc:`rattlers/atom <compute_rattlers_atom>`
    * :doc:`rdf <compute_rdf>`
+   * :doc:`reaxff/atom (k) <compute_reaxff_atom>`
    * :doc:`reduce <compute_reduce>`
    * :doc:`reduce/chunk <compute_reduce_chunk>`
    * :doc:`reduce/region <compute_reduce>`
+   * :doc:`rheo/property/atom <compute_rheo_property_atom>`
    * :doc:`rigid/local <compute_rigid_local>`
    * :doc:`saed <compute_saed>`
+   * :doc:`slcsa/atom <compute_slcsa_atom>`
    * :doc:`slice <compute_slice>`
    * :doc:`smd/contact/radius <compute_smd_contact_radius>`
    * :doc:`smd/damage <compute_smd_damage>`
@@ -149,11 +149,11 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`sph/t/atom <compute_sph_t_atom>`
    * :doc:`spin <compute_spin>`
    * :doc:`stress/atom <compute_stress_atom>`
-   * :doc:`stress/cartesian <compute_stress_profile>`
-   * :doc:`stress/cylinder <compute_stress_profile>`
+   * :doc:`stress/cartesian <compute_stress_cartesian>`
+   * :doc:`stress/cylinder <compute_stress_curvilinear>`
    * :doc:`stress/mop <compute_stress_mop>`
    * :doc:`stress/mop/profile <compute_stress_mop>`
-   * :doc:`stress/spherical <compute_stress_profile>`
+   * :doc:`stress/spherical <compute_stress_curvilinear>`
    * :doc:`stress/tally <compute_tally>`
    * :doc:`tdpd/cc/atom <compute_tdpd_cc_atom>`
    * :doc:`temp (k) <compute_temp>`

doc/src/Commands_dump.rst

@@ -1,39 +1,22 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Dump commands
-=============
+Dump styles
+===========
 
 An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 6
 
    * :doc:`atom <dump>`
    * :doc:`atom/adios <dump_adios>`
    * :doc:`atom/gz <dump>`
-   * :doc:`atom/mpiio <dump>`
    * :doc:`atom/zstd <dump>`
    * :doc:`cfg <dump>`
    * :doc:`cfg/gz <dump>`
-   * :doc:`cfg/mpiio <dump>`
    * :doc:`cfg/uef <dump_cfg_uef>`
    * :doc:`cfg/zstd <dump>`
    * :doc:`custom <dump>`
    * :doc:`custom/adios <dump_adios>`
    * :doc:`custom/gz <dump>`
-   * :doc:`custom/mpiio <dump>`
    * :doc:`custom/zstd <dump>`
    * :doc:`dcd <dump>`
    * :doc:`grid <dump>`
@@ -51,7 +34,6 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`xtc <dump>`
    * :doc:`xyz <dump>`
    * :doc:`xyz/gz <dump>`
-   * :doc:`xyz/mpiio <dump>`
    * :doc:`xyz/zstd <dump>`
    * :doc:`yaml <dump>`
 

doc/src/Commands_fix.rst

@@ -1,19 +1,5 @@
-.. table_from_list::
-   :columns: 3
-
-   * :doc:`General commands <Commands_all>`
-   * :doc:`Fix styles <Commands_fix>`
-   * :doc:`Compute styles <Commands_compute>`
-   * :doc:`Pair styles <Commands_pair>`
-   * :ref:`Bond styles <bond>`
-   * :ref:`Angle styles <angle>`
-   * :ref:`Dihedral styles <dihedral>`
-   * :ref:`Improper styles <improper>`
-   * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
-
-Fix commands
-============
+Fix styles
+==========
 
 An alphabetic list of all LAMMPS :doc:`fix <fix>` commands.  Some styles
 have accelerated versions.  This is indicated by additional letters in
@@ -21,14 +7,16 @@ parenthesis: g = GPU, i = INTEL, k = KOKKOS, o = OPENMP, t =
 OPT.
 
 .. table_from_list::
-   :columns: 5
+   :columns: 4
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
    * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
+   * :doc:`add/heat <fix_add_heat>`
    * :doc:`addtorque <fix_addtorque>`
+   * :doc:`alchemy <fix_alchemy>`
    * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
    * :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
    * :doc:`append/atoms <fix_append_atoms>`
@@ -60,6 +48,7 @@ OPT.
    * :doc:`controller <fix_controller>`
    * :doc:`damping/cundall <fix_damping_cundall>`
    * :doc:`deform (k) <fix_deform>`
+   * :doc:`deform/pressure <fix_deform_pressure>`
    * :doc:`deposit <fix_deposit>`
    * :doc:`dpd/energy (k) <fix_dpd_energy>`
    * :doc:`drag <fix_drag>`
@@ -68,7 +57,8 @@ OPT.
    * :doc:`drude/transform/inverse <fix_drude_transform>`
    * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
-   * :doc:`efield <fix_efield>`
+   * :doc:`efield (k) <fix_efield>`
+   * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electrode/conp (i) <fix_electrode>`
    * :doc:`electrode/conq (i) <fix_electrode>`
@@ -92,6 +82,7 @@ OPT.
    * :doc:`grem <fix_grem>`
    * :doc:`halt <fix_halt>`
    * :doc:`heat <fix_heat>`
+   * :doc:`heat/flow <fix_heat_flow>`
    * :doc:`hyper/global <fix_hyper_global>`
    * :doc:`hyper/local <fix_hyper_local>`
    * :doc:`imd <fix_imd>`
@@ -101,25 +92,25 @@ OPT.
    * :doc:`langevin/drude <fix_langevin_drude>`
    * :doc:`langevin/eff <fix_langevin_eff>`
    * :doc:`langevin/spin <fix_langevin_spin>`
-   * :doc:`latte <fix_latte>`
    * :doc:`lb/fluid <fix_lb_fluid>`
    * :doc:`lb/momentum <fix_lb_momentum>`
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`mdi/qm <fix_mdi_qm>`
+   * :doc:`mdi/qmmm <fix_mdi_qmmm>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`
-   * :doc:`mscg <fix_mscg>`
    * :doc:`msst <fix_msst>`
    * :doc:`mvv/dpd <fix_mvv_dpd>`
    * :doc:`mvv/edpd <fix_mvv_dpd>`
    * :doc:`mvv/tdpd <fix_mvv_dpd>`
    * :doc:`neb <fix_neb>`
    * :doc:`neb/spin <fix_neb_spin>`
+   * :doc:`nonaffine/displacement <fix_nonaffine_displacement>`
    * :doc:`nph (ko) <fix_nh>`
    * :doc:`nph/asphere (o) <fix_nph_asphere>`
    * :doc:`nph/body <fix_nph_body>`
@@ -168,7 +159,8 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
-   * :doc:`pimd <fix_pimd>`
+   * :doc:`pimd/langevin <fix_pimd>`
+   * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
@@ -178,6 +170,7 @@ OPT.
    * :doc:`pour <fix_pour>`
    * :doc:`precession/spin <fix_precession_spin>`
    * :doc:`press/berendsen <fix_press_berendsen>`
+   * :doc:`press/langevin <fix_press_langevin>`
    * :doc:`print <fix_print>`
    * :doc:`propel/self <fix_propel_self>`
    * :doc:`property/atom (k) <fix_property_atom>`
@@ -198,6 +191,11 @@ OPT.
    * :doc:`reaxff/species (k) <fix_reaxff_species>`
    * :doc:`recenter <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
+   * :doc:`rheo <fix_rheo>`
+   * :doc:`rheo/oxidation <fix_rheo_oxidation>`
+   * :doc:`rheo/pressure <fix_rheo_pressure>`
+   * :doc:`rheo/thermal <fix_rheo_thermal>`
+   * :doc:`rheo/viscosity <fix_rheo_viscosity>`
    * :doc:`rhok <fix_rhok>`
    * :doc:`rigid (o) <fix_rigid>`
    * :doc:`rigid/meso <fix_rigid_meso>`
@@ -229,15 +227,15 @@ OPT.
    * :doc:`spring <fix_spring>`
    * :doc:`spring/chunk <fix_spring_chunk>`
    * :doc:`spring/rg <fix_spring_rg>`
-   * :doc:`spring/self <fix_spring_self>`
+   * :doc:`spring/self (k) <fix_spring_self>`
    * :doc:`srd <fix_srd>`
    * :doc:`store/force <fix_store_force>`
    * :doc:`store/state <fix_store_state>`
    * :doc:`tdpd/source <fix_dpd_source>`
-   * :doc:`temp/berendsen <fix_temp_berendsen>`
+   * :doc:`temp/berendsen (k) <fix_temp_berendsen>`
    * :doc:`temp/csld <fix_temp_csvr>`
    * :doc:`temp/csvr <fix_temp_csvr>`
-   * :doc:`temp/rescale <fix_temp_rescale>`
+   * :doc:`temp/rescale (k) <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
    * :doc:`tgnpt/drude <fix_tgnh_drude>`
@@ -257,12 +255,14 @@ OPT.
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`
    * :doc:`wall/colloid <fix_wall>`
    * :doc:`wall/ees <fix_wall_ees>`
-   * :doc:`wall/gran <fix_wall_gran>`
+   * :doc:`wall/flow (k) <fix_wall_flow>`
+   * :doc:`wall/gran (k) <fix_wall_gran>`
    * :doc:`wall/gran/region <fix_wall_gran_region>`
    * :doc:`wall/harmonic <fix_wall>`
    * :doc:`wall/lj1043 <fix_wall>`
    * :doc:`wall/lj126 <fix_wall>`
    * :doc:`wall/lj93 (k) <fix_wall>`
+   * :doc:`wall/lepton <fix_wall>`
    * :doc:`wall/morse <fix_wall>`
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
@@ -270,4 +270,5 @@ OPT.
    * :doc:`wall/region <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
+   * :doc:`wall/table <fix_wall>`
    * :doc:`widom <fix_widom>`