Merge pull request #4524 from akohlmey/next_release

Step version strings for next feature release

.github/CODEOWNERS

@@ -71,7 +71,10 @@ src/EXTRA-COMMAND/group_ndx.*       @akohlmey
 src/EXTRA-COMMAND/ndx_group.*       @akohlmey
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
 src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
+src/EXTRA-DUMP/dump_extxyz.*          @fxcoudert
 src/EXTRA-FIX/fix_deform_pressure.* @jtclemm
+src/EXTRA-PAIR/pair_dispersion_d3.* @soniasolomoni @arthurfl
+src/EXTRA-PAIR/d3_parameters.h      @soniasolomoni @arthurfl
 src/MISC/*_tracker.*                @jtclemm
 src/MC/fix_gcmc.*                   @athomps
 src/MC/fix_sgcmc.*                  @athomps

.github/release_steps.md

@@ -1,58 +1,370 @@
 # LAMMPS Release Steps
 
-The following notes chronicle the current steps for preparing and publishing LAMMPS releases.
-For definition of what LAMMPS versions and the different kinds of releases mean, please
-refer to [the corresponding section in the LAMMPS manual](https://docs.lammps.org/Manual_version.html).
+The following notes chronicle the current steps for preparing and
+publishing LAMMPS releases.  For definitions of LAMMPS versions and
+releases, please refer to [the corresponding section in the LAMMPS
+manual](https://docs.lammps.org/Manual_version.html).
 
 ## LAMMPS Feature Release
 
-A LAMMPS feature release is currently prepared after about 500 to 750 commits to the
-'develop' branch or after a period of four weeks up to two months.
+A LAMMPS feature release is currently prepared after about 500 to 750
+commits to the 'develop' branch or after a period of four weeks up to
+two months.  This is not a fixed rule, though, since external
+circumstances can cause delays in preparing a release, or pull requests
+that are desired to be merged for the release are not yet completed.
 
 ### Preparing a 'next\_release' branch
 
 Create a 'next\_release' branch off 'develop' and make the following changes:
-- set the LAMMPS\_VERSION define to the planned release date in src/version.h in the format "D Mmm YYYY" or "DD Mmm YYYY"
+
+- set the LAMMPS\_VERSION define to the planned release date in
+  src/version.h in the format "D Mmm YYYY" or "DD Mmm YYYY"
 - remove the LAMMPS\_UPDATE define in src/version.h
 - update the release date in doc/lammps.1
-- update all TBD arguments for ..versionadded::, ..versionchanged:: ..deprecated:: to the
-  planned release date in the format "DMmmYYYY" or "DDMmmYYYY"
+- update all TBD arguments for ..versionadded::, ..versionchanged::
+  ..deprecated:: to the planned release date in the format "DMmmYYYY" or
+  "DDMmmYYYY"
+- check release notes for merged new features and check if
+  ..versionadded:: or ..versionchanged:: are missing and need to be
+  added
 
-Submit this pull request, rebase if needed. This is the last pull request merged for the release
-and should not contain any other changes. (Exceptions: this document, last minute trivial(!) changes).
-This PR shall not be merged before **all** pending tests have completed and cleared. If needed, a
-bugfix pull request should be created and merged to clear all tests.
+Submit this pull request.  This is the last pull request merged for the
+release and should not contain any other changes. (Exceptions: this
+document, last minute trivial(!) changes).
+
+This PR shall not be merged before **all** pending tests have completed
+and cleared.  We currently use a mix of automated tests running on
+either Temple's Jenkins cluster or GitHub workflows.  Those include time
+consuming tests not run on pull requests.  If needed, a bug-fix pull
+request should be created and merged to clear all tests.
+
+### Create release on GitHub
+
+When all pending pull requests for the release are merged and have
+cleared testing, the 'next\_release' branch is merged into 'develop'.
+
+Check out or update the 'develop' branch locally, pull the latest
+changes, merge them into 'release' with a fast forward(!) merge, and
+apply a suitable release tag (for historical reasons the tag starts with
+"patch_" followed by the date, and finally push everything back to
+GitHub.  There should be no commits made to 'release' but only
+fast forward merges.  Example:
+
+```
+git checkout develop
+git pull
+git checkout release
+git pull
+git merge --ff-only develop
+git tag -s -m "LAMMPS feature release 4 February 2025" patch_4Feb2025
+git push git@github.com:lammps/lammps.git --tags develop release
+```
+
+Applying this tag will trigger two actions on the Temple Jenkins cluster:
+- The online manual at https://docs.lammps.org/ will be updated to the
+  state of the 'release' branch.  Merges to the 'develop' branch will
+  trigger updating https://docs.lammps.org/latest/ so by reviewing the
+  version of the manual under the "latest" URL, it is possible to preview
+  what the updated release documentation will look like.
+- A downloadable tar archive of the LAMMPS distribution that includes the
+  html format documentation and a PDF of the manual will be created and
+  uploaded to the download server at https://download.lammps.org/tars
+  Note that the file is added, but the `index.html` file is not updated,
+  so it is not yet publicly visible.
+
+Go to https://github.com/lammps/lammps/releases and create a new (draft)
+release page with a summary of all the changes included and references
+to the pull requests they were merged from or check the existing draft
+for any necessary changes from pull requests that were merged but are
+not listed.  Then select the applied tag for the release in the "Choose
+a tag" drop-down list. Go to the bottom of the list and select the "Set
+as pre-release" checkbox.  The "Set as the latest release" button is
+reserved for stable releases and updates to them.
+
+If everything is in order, you can click on the "Publish release"
+button.  Otherwise, click on "Save draft" and finish pending tasks until
+you can return to edit the release page and publish it.
+
+### Prepare pre-compiled packages, update packages to GitHub
+
+A suitable build environment is provided with the
+https://download.lammps.org/static/fedora41_musl_mingw.sif container
+image.  The corresponding container build definition file is maintained
+in the tools/singularity folder of the LAMMPS source distribution.
+
+#### Fully portable static Linux x86_64 non-MPI binaries
+
+The following commands use the Fedora container to build a fully static
+LAMMPS installation using a musl-libc cross-compiler, install it into a
+`lammps-static` folder, and create a tarball called
+`lammps-linux-x86_64-4Feb2025.tar.gz` (or using a corresponding date
+with a future release) from the `lammps-static` folder.
+
+``` sh
+rm -rf release-packages
+mkdir release-packages
+cd release-packages
+wget https://download.lammps.org/static/fedora41_musl.sif
+apptainer shell fedora41_musl.sif
+git clone -b release --depth 10 https://github.com/lammps/lammps.git lammps-release
+cmake -S lammps-release/cmake -B build-release -G Ninja -D CMAKE_INSTALL_PREFIX=$PWD/lammps-static -D CMAKE_TOOLCHAIN_FILE=/usr/musl/share/cmake/linux-musl.cmake -C lammps-release/cmake/presets/most.cmake -C lammps-release/cmake/presets/kokkos-openmp.cmake -D DOWNLOAD_POTENTIALS=OFF -D BUILD_MPI=OFF -D BUILD_TESTING=OFF -D CMAKE_BUILD_TYPE=Release -D PKG_ATC=ON -D PKG_AWPMD=ON -D PKG_MANIFOLD=ON -D PKG_MESONT=ON -D PKG_MGPT=ON -D PKG_ML-PACE=ON -D PKG_ML-RANN=ON -D PKG_MOLFILE=ON -D PKG_PTM=ON -D PKG_QTB=ON -D PKG_SMTBQ=ON
+cmake --build build-release --target all
+cmake --build build-release --target install
+/usr/musl/bin/x86_64-linux-musl-strip lammps-static/bin/*
+tar -czvvf ../lammps-linux-x86_64-4Feb2025.tar.gz lammps-static
+exit # fedora 41 container
+cd ..
+```
+
+The resulting tar archive can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 lammps-linux-x86_64-4Feb2025.tar.gz
+```
+
+#### Linux x86_64 Flatpak bundle with GUI included
+
+Make sure you have the `flatpak` and `flatpak-builder` packages
+installed locally (they require binaries that run with elevated
+privileges and thus cannot be used from the container) and build a
+LAMMPS and LAMMPS-GUI flatpak bundle in the `release-packages` folder
+with:
+
+``` sh
+cd release-packages
+flatpak --user remote-add --if-not-exists flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+flatpak-builder  --force-clean --verbose --repo=$PWD/flatpak-repo --install-deps-from=flathub --state-dir=$PWD --user --ccache --default-branch=release flatpak-build lammps-release/tools/lammps-gui/org.lammps.lammps-gui.yml
+flatpak build-bundle --runtime-repo=https://flathub.org/repo/flathub.flatpakrepo --verbose $PWD/flatpak-repo ../LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak org.lammps.lammps-gui release
+cd ..
+```
+
+The resulting flatpak bundle file can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.flatpak
+```
+
+#### LAMMPS Source tarball
+
+The container for the static binary can also be used to prepare the source
+tarball including the HTML and PDF manual (this is currently done automatically
+when the releases is created and the tarball uploaded to https://download.lammps.org/tars/).
+The steps are as follows:
+
+``` sh
+cd release-packages
+apptainer shell fedora41_musl_mingw.sif
+cd lammps-release
+rm -f ../release.tar*
+git archive --output=../release.tar --prefix=lammps-4Feb2025/ HEAD
+cd doc
+make clean-all
+make html pdf
+tar -rf ../../release.tar --transform 's,^,lammps-4Feb2025/doc/,' html Manual.pdf
+gzip -9v ../../release.tar
+mv ../../release.tar.gz ../../lammps-src-4Feb2025.tar.gz
+exit # fedora41 container
+cd ..
+```
+
+The resulting source tarball can be uploaded to the GitHub release page with:
+
+``` sh
+gh release upload patch_4Feb2025 lammps-src-4Feb2025.tar.gz
+```
+
+#### Build Windows Installer Packages with MinGW Linux-to-Windows Cross-compiler
+
+The various Windows installer packages can also be built with
+apptainer container image.
+
+``` sh
+cd release-packages
+apptainer shell fedora41_musl_mingw.sif
+git clone --depth 10 https://github.com/lammps/lammps-packages.git lammps-packages
+cd lammps-packages/mingw-cross
+ln -sf ../../lammps-release lammps
+./buildall.sh release >& mk.log & less +F mk.log
+```
+
+The installer with the GUI included can be uploaded to the GitHub release page with:
+
+``` sh
+ln -sf LAMMPS-64bit-GUI-4Feb2025.exe LAMMPS-Win10-64bit-GUI-4Feb2025.exe
+gh release upload patch_4Feb2025 LAMMPS-Win10-64bit-GUI-4Feb2025.exe
+```
+
+The symbolic link is used to have a consistent naming scheme for the packages
+attached to the GitHub release page.
+
+#### Clean up:
+
+``` sh
+cd ..
+rm -r release-packages
+```
+
+#### Build Multi-arch App-bundle for macOS
+
+Building app-bundles for macOS is not as easily automated and portable
+as some of the other steps.  It requires a machine actually running
+macOS.  In that machine the Xcode compiler package needs to be
+installed. This also includes tools for building and manipulating disk
+images.  This compiler supports building executables for both, the
+x86_64 and the arm64 architectures.  This requires building with CMake
+and using the CMake settings:
+
+``` sh
+-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
+-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
+```
+
+This will add the compiler flags `-arch arm64 -arch x86_64
+-mmacosx-version-min=11.0` and thus produce object for both
+architectures and support for macOS versions back to version 11 (aka Big
+Sur).  With these settings the following libraries should be compiled
+and installed (e.g. to `$HOME/.local`) as static libraries only:
+- libomp taken from the LLVM/Clang source distribution (to support OpenMP)
+- jpeg
+- zlib
+- png
+- Qt (for LAMMPS-GUI)
+
+When configuring LAMMPS the `cmake/presets/clang.cmake` should be used
+and as many packages as possible enabled. For LAMMPS-GUI, MPI should be
+disabled with `-D BUILD_MPI=OFF` and LAMMPS-GUI enabled with 
+`-D BUILD_LAMMPS_GUI=ON`.  If the CMake configuration is successful,
+settings for building a macOS app-bundle are enabled and with `cmake
+--build build --target dmg` extra steps will be executed that will build
+a macOS application installer image under the name
+`LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg`
+
+The application image can be uploaded to the GitHub release page with:
+
+``` sh
+ln -sf LAMMPS_GUI-macOS-multiarch-4Feb2025.dmg LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
+gh release upload patch_4Feb2025 LAMMPS-macOS-multiarch-GUI-4Feb2025.dmg
+```
+
+The symbolic link is used to have a consistent naming scheme for the packages
+attached to the GitHub release page.
+
+We are currently building the application images on macOS 12 (aka Monterey).
+
+#### Build Linux x86_64 binary tarball on Ubuntu 20.04LTS
+
+While the flatpak Linux version uses portable runtime libraries provided
+by the flatpak environment, we also build regular Linux executables that
+use a wrapper script and matching shared libraries in a tarball.  To be
+compatible with many Linux distributions, one has to build this on a
+very old Linux distribution, since most Linux system libraries are
+usually backward compatible but not forward compatible.  This is
+currently done on an Ubuntu 20.04LTS system. Once LAMMPS moves to
+require CMake 3.20 and C++17, we will have to move to Ubuntu 22.04LTS.
+This installation (either on a real or a virtual machine) should have
+the packages installed that are indicated in
+`tools/singularity/ubuntu20.04.def` plus Qt version 5.x with development
+headers, so that LAMMPS-GUI can be compiled.
+
+Also the building of the binary tarball and setup of the bundled
+libraries and wrapper scripts is automated and can executed with `cmake
+--build build --target tgz`.  This should produce a file
+`LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz` which can be uploaded to the
+GitHub release page with:
+
+``` sh
+ln -sf LAMMPS_GUI-Linux-amd64-4Feb2025.tar.gz LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
+gh release upload patch_4Feb2025 LAMMPS-Linux-x86_64-GUI-4Feb2025.tar.gz
+```
+
+### Update download page on LAMMPS website
+
+Check out the LAMMPS website repo
+https://github.com/lammps/lammps-website.git and edit the file
+`src/download.txt` for the new release.  Test translation with `make
+html` and review `html/download.html` Then add and commit to git and
+push the changes to GitHub.  The Temple Jenkis cluster will
+automatically update https://www.lammps.org/download.html accordingly.
+
+Also notify Steve of the release so he can update `src/bug.txt` on the
+website from the available release notes.
 
 ## LAMMPS Stable Release
 
-A LAMMPS stable release is prepared about once per year in the months July, August, or September.
-One (or two, if needed) feature releases before the stable release shall contain only bug fixes
-or minor feature updates in optional packages.  Also substantial changes to the core of the code
-shall be applied rather toward the beginning of a development cycle between two stable releases
-than toward the end.  The intention is to stablilize significant change to the core and have
-outside users and developers try them out during the development cycle; the sooner the changes
-are included, the better chances for spotting peripheral bugs and issues.
+A LAMMPS stable release is prepared about once per year in the months
+July, August, or September.  One (or two, if needed) feature releases
+before the stable release shall contain only bug fixes or minor feature
+updates in optional packages.  Also substantial changes to the core of
+the code shall be applied rather toward the beginning of a development
+cycle between two stable releases than toward the end.  The intention is
+to stablilize significant change to the core and have outside users and
+developers try them out during the development cycle; the sooner the
+changes are included, the better chances for spotting peripheral bugs
+and issues.
 
 ### Prerequesites
 
-Before making a stable release all remaining backported bugfixes shall be released as a (final)
-stable update release (see below).
+Before making a stable release all remaining backported bugfixes shall
+be released as a (final) stable update release (see below).
 
-A LAMMPS stable release process starts like a feature release (see above), only that this feature
-release is called a "Stable Release Candidate" and no assets are uploaded to GitHub.
+A LAMMPS stable release process starts like a feature release (see
+above), only that this feature release is called a "Stable Release
+Candidate" and no assets are uploaded to GitHub.
 
 ### Synchronize 'maintenance' branch with 'release'
 
-The state of the 'release' branch is then transferred to the 'maintenance' branch (which will
-have diverged significantly from 'release' due to the selectively backported bug fixes).
+The state of the 'release' branch is then transferred to the
+'maintenance' branch (which will have diverged significantly from
+'release' due to the selectively backported bug fixes).
 
 ### Fast-forward merge of 'maintenance' into 'stable' and apply tag
 
-At this point it should be possible to do a fast-forward merge of 'maintenance' to 'stable'
-and then apply the stable\_DMmmYYYY tag.
+At this point it should be possible to do a fast-forward merge of
+'maintenance' to 'stable' and then apply the stable\_DMmmYYYY tag.
 
 ### Push branches and tags
 
-
-
 ## LAMMPS Stable Update Release
+
+After making a stable release, bugfixes from the 'develop' branch
+are selectively backported to the 'maintenance' branch.  This is
+done with "git cherry-pick \<commit hash\>' wherever possible.
+The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
+
+### Prerequesites
+
+When a sufficient number of bugfixes has accumulated or an urgent
+or important bugfix needs to be distributed a new stable update
+release is made.  To make this publicly visible a pull request
+is submitted that will merge 'maintenance' into 'stable'.  Before
+merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
+"#" indicating the update count (1, 2, and so on).
+Also draft suitable release notes under https://github.com/lammps/lammps/releases
+
+### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
+
+Do a fast-forward merge of 'maintenance' to 'stable' and then
+apply the stable\_DMmmYYYY\_update# tag and push branch and tag
+to GitHub. The corresponding pull request will be automatically
+closed.   Example:
+
+```
+git checkout maintenance
+git pull
+git checkout stable
+git pull
+git merge --ff-only maintenance
+git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
+git push git@github.com:lammps/lammps.git --tags maintenance stable
+```
+
+Associate draft release notes with new tag and publish as "latest release".
+
+On https://ci.lammps.org/ go to "dev", "stable" and manually execute
+the "update\_release" task. This will update https://docs.lammps.org/stable
+and prepare a stable tarball.
+
+### Build and upload binary packages and source tarball to GitHub
+
+The build procedure is the same as for the feature releases, only
+that packages are built from the 'stable' branch.

.github/workflows/check-vla.yml

@@ -77,7 +77,7 @@ jobs:
               -D PKG_MDI=on \
               -D PKG_MANIFOLD=on \
               -D PKG_ML-PACE=on \
-              -D PKG_ML-RANN=off \
+              -D PKG_ML-RANN=on \
               -D PKG_MOLFILE=on \
               -D PKG_RHEO=on \
               -D PKG_PTM=on \

.github/workflows/coverity.yml

@@ -67,7 +67,6 @@ jobs:
         -D PKG_MANIFOLD=on \
         -D PKG_MDI=on \
         -D PKG_MGPT=on \
-        -D PKG_ML-PACE=on \
         -D PKG_ML-RANN=on \
         -D PKG_MOLFILE=on \
         -D PKG_NETCDF=on \

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

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

.github/workflows/style-check.yml

@@ -35,3 +35,4 @@ jobs:
          make check-permissions
          make check-homepage
          make check-errordocs
+         make check-fmtlib

.github/workflows/unittest-arm64.yml

@@ -0,0 +1,81 @@
+# GitHub action to build LAMMPS on Linux with ARM64 and run standard unit tests
+name: "Unittest for Linux on ARM64"
+
+on:
+  push:
+    branches: [develop]
+
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
+jobs:
+  build:
+    name: Linux ARM64 Unit Test
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-22.04-arm
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 2
+
+    - name: Install extra packages
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y ccache \
+                                libeigen3-dev \
+                                libcurl4-openssl-dev \
+                                mold \
+                                ninja-build \
+                                python3-dev
+
+    - name: Create Build Environment
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: linux-unit-ccache-${{ github.sha }}
+        restore-keys: linux-unit-ccache-
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      run: |
+        ccache -z
+        python3 -m venv linuxenv
+        source linuxenv/bin/activate
+        python3 -m pip install numpy
+        python3 -m pip install pyyaml
+        cmake -S cmake -B build \
+              -C cmake/presets/gcc.cmake \
+              -C cmake/presets/most.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D BUILD_SHARED_LIBS=on \
+              -D DOWNLOAD_POTENTIALS=off \
+              -D ENABLE_TESTING=on \
+              -D MLIAP_ENABLE_ACE=on \
+              -D MLIAP_ENABLE_PYTHON=off \
+              -D PKG_MANIFOLD=on \
+              -D PKG_ML-PACE=on \
+              -D PKG_ML-RANN=on \
+              -D PKG_RHEO=on \
+              -D PKG_PTM=on \
+              -D PKG_PYTHON=on \
+              -D PKG_QTB=on \
+              -D PKG_SMTBQ=on \
+              -G Ninja
+        cmake --build build
+        ccache -s
+
+    - name: Run Tests
+      working-directory: build
+      shell: bash
+      run: ctest -V -LE unstable

README

@@ -23,17 +23,20 @@ more information about the code and its uses.
 The LAMMPS distribution includes the following files and directories:
 
 README                     this file
-LICENSE                    the GNU General Public License (GPL)
-bench                      benchmark problems
+LICENSE                    the GNU General Public License (GPLv2)
+CITATION.cff               Citation information for LAMMPS in CFF format
+bench                      benchmark inputs
 cmake                      CMake build files
 doc                        documentation
-examples                   simple test problems
-fortran                    Fortran wrapper for LAMMPS
+examples                   example inputs for many LAMMPS commands
+fortran                    Fortran 2003 module for LAMMPS
 lib                        additional provided or external libraries
 potentials                 interatomic potential files
-python                     Python wrappers for LAMMPS
+python                     Python module for LAMMPS
 src                        source files
 tools                      pre- and post-processing tools
+unittest                   test programs for use with CTest
+.github                    Git and GitHub related files and tools
 
 Point your browser at any of these files to get started:
 
@@ -42,6 +45,8 @@ https://docs.lammps.org/Intro.html          hi-level introduction
 https://docs.lammps.org/Build.html          how to build LAMMPS
 https://docs.lammps.org/Run_head.html       how to run LAMMPS
 https://docs.lammps.org/Commands_all.html   Table of available commands
+https://docs.lammps.org/Howto.html          Short tutorials and HowTo discussions
+https://docs.lammps.org/Errors.html         How to interpret and debug errors
 https://docs.lammps.org/Library.html        LAMMPS library interfaces
 https://docs.lammps.org/Modify.html         how to modify and extend LAMMPS
 https://docs.lammps.org/Developer.html      LAMMPS developer info

cmake/CMakeLists.txt

@@ -3,6 +3,9 @@
 # CMake build system
 # This file is part of LAMMPS
 cmake_minimum_required(VERSION 3.16)
+if(CMAKE_VERSION VERSION_LESS 3.20)
+  message(WARNING "LAMMPS is planning to require at least CMake version 3.20 by Summer 2025. Please upgrade!")
+endif()
 ########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
@@ -144,16 +147,28 @@ if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT}" "-Xcudafe --diag_suppress=unrecognized_pragma,--diag_suppress=128")
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++17 (currently)
+# we *require* C++11 without extensions but prefer C++17.
+# Kokkos requires at least C++17 (currently)
 if(NOT CMAKE_CXX_STANDARD)
-  set(CMAKE_CXX_STANDARD 11)
+  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
+    set(CMAKE_CXX_STANDARD 17)
+  else()
+    set(CMAKE_CXX_STANDARD 11)
+  endif()
 endif()
 if(CMAKE_CXX_STANDARD LESS 11)
   message(FATAL_ERROR "C++ standard must be set to at least 11")
 endif()
+if(CMAKE_CXX_STANDARD LESS 17)
+  message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
+endif()
 if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
   set(CMAKE_CXX_STANDARD 17)
 endif()
+# turn off C++17 check in lmptype.h
+if(LAMMPS_CXX11)
+  add_compile_definitions(LAMMPS_CXX11)
+endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
@@ -194,7 +209,7 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# backward compatibility with CMake before 3.12 and older LAMMPS documentation
+# backward compatibility with older LAMMPS documentation
 if (PYTHON_EXECUTABLE)
   set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
 endif()
@@ -210,6 +225,12 @@ if(DEFINED ENV{VIRTUAL_ENV} AND NOT Python_EXECUTABLE)
     "   Setting Python interpreter to: ${Python_EXECUTABLE}")
 endif()
 
+find_package(Python COMPONENTS Interpreter QUIET)
+# NOTE: RHEL 8.0 and Ubuntu 18.04LTS ship with Python 3.6, Python 3.8 was EOL in 2024
+if(Python_VERSION VERSION_LESS 3.6)
+  message(FATAL_ERROR "LAMMPS requires Python 3.6 or later")
+endif()
+
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
 mark_as_advanced(LAMMPS_MACHINE)
 if(LAMMPS_MACHINE)
@@ -347,6 +368,17 @@ foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
 
+set(DEPRECATED_PACKAGES AWPMD ATC POEMS)
+foreach(PKG ${DEPRECATED_PACKAGES})
+  if(PKG_${PKG})
+    message(WARNING
+          "The ${PKG} package will be removed from LAMMPS in Summer 2025 due to lack of "
+          "maintenance and use of code constructs that conflict with modern C++ compilers "
+          "and standards.  Please contact developers@lammps.org if you have any concerns "
+          "about this step.")
+  endif()
+endforeach()
+
 ######################################################
 # packages with special compiler needs or external libs
 ######################################################
@@ -399,8 +431,8 @@ else()
   target_link_libraries(lammps PUBLIC mpi_stubs)
 endif()
 
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
@@ -579,6 +611,16 @@ foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE
   endif()
 endforeach()
 
+# settings for misc packages and styles
+if(PKG_MISC)
+  option(LAMMPS_ASYNC_IMD "Asynchronous IMD processing" OFF)
+  mark_as_advanced(LAMMPS_ASYNC_IMD)
+  if(LAMMPS_ASYNC_IMD)
+    target_compile_definitions(lammps PRIVATE -DLAMMPS_ASYNC_IMD)
+    message(STATUS "Using IMD in asynchronous mode")
+  endif()
+endif()
+
 # optionally enable building script wrappers using swig
 option(WITH_SWIG "Build scripting language wrappers with SWIG" OFF)
 if(WITH_SWIG)
@@ -894,7 +936,7 @@ endif()
 include(Testing)
 include(CodeCoverage)
 include(CodingStandard)
-find_package(ClangFormat 11.0)
+find_package(ClangFormat 11.0 QUIET)
 
 if(ClangFormat_FOUND)
   add_custom_target(format-src
@@ -1078,12 +1120,15 @@ if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
 if(BUILD_LAMMPS_GUI)
-  message(STATUS "<<< Building LAMMPS GUI >>>")
+  message(STATUS "<<< Building LAMMPS-GUI >>>")
   if(LAMMPS_GUI_USE_PLUGIN)
     message(STATUS "Loading LAMMPS library as plugin at run time")
   else()
     message(STATUS "Linking LAMMPS library at compile time")
   endif()
+  if(BUILD_WHAM)
+    message(STATUS "<<< Building WHAM >>>")
+  endif()
 endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")

cmake/Modules/CodeCoverage.cmake

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

cmake/Modules/CodingStandard.cmake

@@ -1,40 +1,39 @@
-# use default (or custom) Python executable, if version is sufficient
-if(Python_VERSION VERSION_GREATER_EQUAL 3.6)
+# use default (or custom) Python executable.
+# Python version check is in main CMakeLists.txt file
+if(Python_EXECUTABLE)
   set(Python3_EXECUTABLE ${Python_EXECUTABLE})
 endif()
 find_package(Python3 COMPONENTS Interpreter)
 
 if(Python3_EXECUTABLE)
-    if(Python3_VERSION VERSION_GREATER_EQUAL 3.6)
-        add_custom_target(
-          check-whitespace
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for whitespace errors")
-        add_custom_target(
-          check-homepage
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for homepage URL errors")
-        add_custom_target(
-          check-permissions
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Check for permission errors")
-        add_custom_target(
-          fix-whitespace
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix whitespace errors")
-        add_custom_target(
-          fix-homepage
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix homepage URL errors")
-        add_custom_target(
-          fix-permissions
-          ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
-          WORKING_DIRECTORY  ${LAMMPS_DIR}
-          COMMENT "Fix permission errors")
-    endif()
+  add_custom_target(
+    check-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for whitespace errors")
+  add_custom_target(
+    check-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for homepage URL errors")
+  add_custom_target(
+    check-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Check for permission errors")
+  add_custom_target(
+    fix-whitespace
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/whitespace.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix whitespace errors")
+  add_custom_target(
+    fix-homepage
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/homepage.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix homepage URL errors")
+  add_custom_target(
+    fix-permissions
+    ${Python3_EXECUTABLE} ${LAMMPS_TOOLS_DIR}/coding_standard/permissions.py -f .
+    WORKING_DIRECTORY  ${LAMMPS_DIR}
+    COMMENT "Fix permission errors")
 endif()

cmake/Modules/Documentation.cmake

@@ -13,7 +13,7 @@ if(BUILD_DOC)
   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")
+    message(FATAL_ERROR "Python 3.8 and up is required to build the LAMMPS HTML documentation")
   endif()
   set(VIRTUALENV ${Python3_EXECUTABLE} -m venv)
 
@@ -65,8 +65,8 @@ if(BUILD_DOC)
     find_package(Sphinx)
   endif()
 
-  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.2.2.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "08dd6ef33ca08870220d9aade2a62845" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
   GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
 

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -34,8 +34,26 @@ if(MSVC)
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
-# C++11 is required
-set(CMAKE_CXX_STANDARD 11)
+if(NOT CMAKE_CXX_STANDARD)
+  if(cxx_std_17 IN_LIST CMAKE_CXX_COMPILE_FEATURES)
+    set(CMAKE_CXX_STANDARD 17)
+  else()
+    set(CMAKE_CXX_STANDARD 11)
+  endif()
+endif()
+if(CMAKE_CXX_STANDARD LESS 11)
+  message(FATAL_ERROR "C++ standard must be set to at least 11")
+endif()
+if(CMAKE_CXX_STANDARD LESS 17)
+  message(WARNING "Selecting C++17 standard is preferred over C++${CMAKE_CXX_STANDARD}")
+endif()
+if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 17))
+  set(CMAKE_CXX_STANDARD 17)
+endif()
+# turn off C++17 check in lmptype.h
+if(LAMMPS_CXX11)
+  add_compile_definitions(LAMMPS_CXX11)
+endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
 # Need -restrict with Intel compilers
@@ -242,8 +260,8 @@ endif()
 
 ################
 # integer size selection
-set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
-set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig)
 set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
 validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
 string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)

cmake/Modules/Packages/INTEL.cmake

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

cmake/Modules/Packages/KOKKOS.cmake

@@ -7,26 +7,13 @@ endif()
 
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
-if(Kokkos_ENABLE_CUDA)
-  option(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC "CUDA asynchronous malloc support" OFF)
-  mark_as_advanced(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
-  if(Kokkos_ENABLE_IMPL_CUDA_MALLOC_ASYNC)
-    message(STATUS "KOKKOS: CUDA malloc async support enabled")
-  else()
-    message(STATUS "KOKKOS: CUDA malloc async support disabled")
-  endif()
-endif()
 if(Kokkos_ENABLE_HIP)
   option(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS "Enable multiple kernel instantiations with HIP" ON)
   mark_as_advanced(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS)
   option(Kokkos_ENABLE_ROCTHRUST "Use RoCThrust library" ON)
   mark_as_advanced(Kokkos_ENABLE_ROCTHRUST)
-
-  if(Kokkos_ARCH_AMD_GFX942 OR Kokkos_ARCH_AMD_GFX940)
-    option(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY "Enable unified memory with HIP" ON)
-    mark_as_advanced(Kokkos_ENABLE_IMPL_HIP_UNIFIED_MEMORY)
-  endif()
 endif()
+
 # Adding OpenMP compiler flags without the checks done for
 # BUILD_OMP can result in compile failures. Enforce consistency.
 if(Kokkos_ENABLE_OPENMP)
@@ -70,8 +57,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.4.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "de6ee80d00b6212b02bfb7f1e71a8392" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/4.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "61b2b69ae50d83eedcc7d47a3fa3d6cb" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -96,7 +83,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.4.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.6.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -130,7 +117,6 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/atom_vec_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/comm_tiled_kokkos.cpp
-                       ${KOKKOS_PKG_SOURCES_DIR}/group_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/min_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/min_linesearch_kokkos.cpp
                        ${KOKKOS_PKG_SOURCES_DIR}/neighbor_kokkos.cpp

cmake/Modules/Packages/ML-IAP.cmake

@@ -24,9 +24,7 @@ if(MLIAP_ENABLE_PYTHON)
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
-  if(Python_VERSION VERSION_LESS 3.6)
-    message(FATAL_ERROR "Python support in ML-IAP requires Python 3.6 or later")
-  endif()
+  # Python version check is in main CMakeLists.txt file
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
   file(GLOB MLIAP_CYTHON_SRC CONFIGURE_DEPENDS ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,50 +1,62 @@
 # PACE library support for ML-PACE package
+find_package(pace QUIET)
 
-# 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)
-
-# 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}")
+if(pace_FOUND)
+    find_package(pace)
+    target_link_libraries(lammps PRIVATE pace::pace)
 else()
-  # download library sources to build folder
-  if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  endif()
-  if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-    message(STATUS "Downloading ${PACELIB_URL}")
-    file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-    file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-      message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-      file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+    # 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()
-  else()
-    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-  endif()
+
+    set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.11.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+    set(PACELIB_MD5 "a53bd87cfee8b07d9f44bc17aad69c3f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+    mark_as_advanced(PACELIB_URL)
+    mark_as_advanced(PACELIB_MD5)
+    GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
+
+    # LOCAL_ML-PACE points to top-level dir with local lammps-user-pace repo,
+    # to make it easier to check local build without going through the public github releases
+    if(LOCAL_ML-PACE)
+     set(lib-pace "${LOCAL_ML-PACE}")
+    else()
+      # download library sources to build folder
+      if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
+        file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+      endif()
+      if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
+        message(STATUS "Downloading ${PACELIB_URL}")
+        file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
+        file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
+        if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
+          message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
+          file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
+        endif()
+      else()
+        message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
+      endif()
 
 
-  # uncompress downloaded sources
-  execute_process(
-    COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
-    COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
-    WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-  )
-  get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
-endif()
-
-add_subdirectory(${lib-pace} build-pace)
-set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-
-if(CMAKE_PROJECT_NAME STREQUAL "lammps")
-  target_link_libraries(lammps PRIVATE pace)
+      # uncompress downloaded sources
+      execute_process(
+        COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+        COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+        WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+      )
+      get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
+    endif()
+
+    # some preinstalled yaml-cpp versions don't provide a namespaced target
+    find_package(yaml-cpp QUIET)
+    if(TARGET yaml-cpp AND NOT TARGET yaml-cpp::yaml-cpp)
+      add_library(yaml-cpp::yaml-cpp ALIAS yaml-cpp)
+    endif()
+
+    add_subdirectory(${lib-pace} build-pace)
+    set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+
+    if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+      target_link_libraries(lammps PRIVATE pace)
+    endif()
 endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -37,7 +37,7 @@ if(DOWNLOAD_QUIP)
   endforeach()
   # Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
   set(temp "${temp} -L/_DUMMY_PATH_\n")
-  set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
+  set(temp "${temp}PYTHON=${Python_EXECUTABLE}\nPIP=pip\nEXTRA_LINKOPTS=\n")
   set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
   set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
   set(temp "${temp}HAVE_TURBOGAP=0\nHAVE_QR=1\nHAVE_THIRDPARTY=0\nHAVE_FX=0\nHAVE_SCME=0\nHAVE_MTP=0\n")

cmake/Modules/Packages/PLUMED.cmake

@@ -32,14 +32,21 @@ endif()
 
 # Note: must also adjust check for supported API versions in
 # fix_plumed.cpp when version changes from v2.n.x to v2.n+1.y
-set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.3/plumed-src-2.9.3.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "ee1249805fe94bccee17d10610d3f6f1" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)
 GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
 
+# adjust C++ standard support for self-compiled Plumed2
+if(CMAKE_CXX_STANDARD GREATER 11)
+  set(PLUMED_CXX_STANDARD 14)
+else()
+  set(PLUMED_CXX_STANDARD 11)
+endif()
+
 if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
   if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
     set(CROSS_CONFIGURE mingw64-configure)
@@ -55,7 +62,7 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND (CMAKE_CROSSCOMPILING))
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND ${CROSS_CONFIGURE} --disable-shared --disable-bsymbolic
-                                         --disable-python --enable-cxx=11
+                                         --disable-python --enable-cxx=${PLUMED_CXX_STANDARD}
                                          --enable-modules=-adjmat:+crystallization:-dimred:+drr:+eds:-fisst:+funnel:+logmfd:+manyrestraints:+maze:+opes:+multicolvar:-pamm:-piv:+s2cm:-sasa:-ves
                                          ${PLUMED_CONFIG_OMP}
                                          ${PLUMED_CONFIG_MPI}
@@ -142,7 +149,7 @@ else()
       CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}
                                              --enable-modules=all
-                                             --enable-cxx=11
+                                             --enable-cxx=${PLUMED_CXX_STANDARD}
                                              --disable-python
                                              ${PLUMED_CONFIG_MPI}
                                              ${PLUMED_CONFIG_OMP}

cmake/Modules/Packages/PYTHON.cmake

@@ -1,6 +1,6 @@
 
 if(NOT Python_INTERPRETER)
-  # backward compatibility with CMake before 3.12 and older LAMMPS documentation
+  # backward compatibility with older LAMMPS documentation
   if(PYTHON_EXECUTABLE)
     set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
   endif()

cmake/Modules/Packages/VTK.cmake

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

cmake/presets/kokkos-cuda.cmake

@@ -1,6 +1,5 @@
 # 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)

doc/Makefile

@@ -17,9 +17,11 @@ MATHJAXTAG     = 3.2.2
 
 PYTHON         = $(word 3,$(shell type python3))
 DOXYGEN        = $(word 3,$(shell type doxygen))
+PANDOC         = $(word 3,$(shell type pandoc))
 HAS_PYTHON3    = NO
 HAS_DOXYGEN    = NO
 HAS_PDFLATEX   = NO
+HAS_PANDOC     = NO
 
 ifeq ($(shell type python3 >/dev/null 2>&1; echo $$?), 0)
 HAS_PYTHON3    = YES
@@ -31,10 +33,14 @@ endif
 
 ifeq ($(shell type pdflatex >/dev/null 2>&1; echo $$?), 0)
 ifeq ($(shell type latexmk >/dev/null 2>&1; echo $$?), 0)
-HAS_PDFLATEX = YES
+HAS_PDFLATEX   = YES
 endif
 endif
 
+ifeq ($(shell type pandoc >/dev/null 2>&1; echo $$?), 0)
+HAS_PANDOC     = YES
+endif
+
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
@@ -45,8 +51,9 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml fasthtml-init 
 
+FASTHTMLFILES = $(patsubst $(RSTDIR)/%.rst,fasthtml/%.html,$(wildcard $(RSTDIR)/*rst))
 # ------------------------------------------
 
 help:
@@ -105,6 +112,8 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -116,25 +125,23 @@ html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJ
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
-	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
-	@$(MAKE) $(MFLAGS) -C graphviz all
-	@mkdir -p fasthtml
-	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		deactivate ;\
-	)
-	@rm -rf fasthtml/_sources
-	@rm -rf fasthtml/PDF
-	@rm -rf fasthtml/USER
-	@rm -rf fasthtml/JPG
-	@cp -r src/PDF fasthtml/PDF
-	@rm -rf fasthtml/PDF/.[sg]*
+fasthtml: fasthtml-init $(FASTHTMLFILES)
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
+fasthtml-init:
+	@mkdir -p fasthtml/JPG
+	@cp src/JPG/*.* fasthtml/JPG
+	@cp $(RSTDIR)/accel_styles.rst $(RSTDIR)/lepton_expression.rst fasthtml/
+	@cp $(BUILDDIR)/utils/pandoc.css fasthtml/
+
+fasthtml/%.html: $(RSTDIR)/%.rst
+	@if [ "$(HAS_PANDOC)" == "NO" ] ; then echo "Make 'fasthtml' requires the 'pandoc' software" 1>&2; exit 1; fi
+	@mkdir -p fasthtml
+	@echo converting $< to $@
+	@sed -e 's/\\AA/\\mathring{\\mathrm{A}}/g' $< > fasthtml/$*.temp.rst
+	@pandoc -s --mathml --css="pandoc.css" --template=$(BUILDDIR)/utils/pandoc.html --metadata title="$@" -o $@ fasthtml/$*.temp.rst
+	@rm -f fasthtml/$*.temp.rst
+
 spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
@@ -188,6 +195,8 @@ pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
 		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                         $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -237,6 +246,8 @@ role_check :
 	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
 	@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n -E '^ *\.\. [a-z0-9]+:(\s+.*|)$$' \
+                        $(RSTDIR)/*.rst ../src/*.{cpp,h} ../src/*/*.{cpp,h} && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/README

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

doc/doxygen/Doxyfile.in

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

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "19 November 2024" "2024-11-19"
+.TH LAMMPS "1" "2 April 2025" "2025-04-02"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 19 November 2024
+\- Molecular Dynamics Simulator.  Version 2 April 2025
 
 .SH SYNOPSIS
 .B lmp
@@ -311,7 +311,7 @@ the chapter on errors in the
 manual gives some additional information about error messages, if possible.
 
 .SH COPYRIGHT
-© 2003--2024 Sandia Corporation
+© 2003--2025 Sandia Corporation
 
 This package is free software; you can redistribute it and/or modify
 it under the terms of the GNU General Public License version 2 as

doc/src/Build.rst

@@ -1,15 +1,42 @@
 Build LAMMPS
 ============
 
-LAMMPS is built as a library and an executable from source code using
-either traditional makefiles for use with GNU make (which may require
-manual editing), or using a build environment generated by CMake (Unix
-Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
+LAMMPS is built as a library and an executable from source code using a
+build environment generated by CMake (Unix Makefiles, Ninja, Xcode,
+Visual Studio, KDevelop, CodeBlocks and more depending on the platform).
+Using CMake is the preferred way to build LAMMPS.  In addition, LAMMPS
+can be compiled using the legacy build system based on traditional
+makefiles for use with GNU make (which may require manual editing).
+Support for the legacy build system is slowly being phased out and may
+not be available for all optional features.
 
 As an alternative, you can download a package with pre-built executables
 or automated build trees, as described in the :doc:`Install <Install>`
 section of the manual.
 
+Prerequisites
+-------------
+
+Which software you need to compile and use LAMMPS strongly depends on
+which :doc:`features and settings <Build_settings>` and which
+:doc:`optional packages <Packages_list>` you are trying to include.
+Common to all is that you need a C++ and C compiler, where the C++
+compiler has to support at least the C++11 standard (note that some
+compilers require command-line flag to activate C++11 support).
+Furthermore, if you are building with CMake, you need at least CMake
+version 3.20 and a compatible build tool (make or ninja-build); if you
+are building the the legacy GNU make based build system you need GNU
+make (other make variants are not going to work since the build system
+uses features unique to GNU make) and a Unix-like build environment with
+a Bourne shell, and shell tools like "sed", "grep", "touch", "test",
+"tr", "cp", "mv", "rm", "ln", "diff" and so on. Parts of LAMMPS
+interface with or use Python version 3.6 or later.
+
+The LAMMPS developers aim to keep LAMMPS very portable and usable -
+at least in parts - on most operating systems commonly used for
+running MD simulations.  Please see the :doc:`section on portablility
+<Intro_portability>` for more details.
+
 .. toctree::
    :maxdepth: 1
 

doc/src/Build_basics.rst

@@ -160,7 +160,7 @@ with the OpenMP 3.1 semantics used in LAMMPS for maximal compatibility
 with compiler versions in use.  If compilation with OpenMP enabled fails
 because of your compiler requiring strict OpenMP 4.0 semantics, you can
 change the behavior by adding ``-D LAMMPS_OMP_COMPAT=4`` to the
-``LMP_INC`` variable in your makefile, or add it to the command line
+``LMP_INC`` variable in your makefile, or add it to the command-line flags
 while configuring with CMake.  LAMMPS will auto-detect a suitable setting
 for most GNU, Clang, and Intel compilers.
 
@@ -196,13 +196,18 @@ LAMMPS.
 
    .. tab:: CMake build
 
-      By default CMake will use the compiler it finds according to
+      By default CMake will use the compiler it finds according to its
       internal preferences, and it will add optimization flags
       appropriate to that compiler and any :doc:`accelerator packages
       <Speed_packages>` you have included in the build.  CMake will
       check if the detected or selected compiler is compatible with the
       C++ support requirements of LAMMPS and stop with an error, if this
-      is not the case.
+      is not the case.  A C++11 compatible compiler is currently
+      required, but a transition to require C++17 is in progress and
+      planned to be completed in Summer 2025. Currently, setting
+      ``-DLAMMPS_CXX11=yes`` is required when configuring with CMake while
+      using a C++11 compatible compiler that does not support C++17,
+      otherwise setting ``-DCMAKE_CXX_STANDARD=17`` is preferred.
 
       You can tell CMake to look for a specific compiler with setting
       CMake variables (listed below) during configuration.  For a few
@@ -223,6 +228,8 @@ LAMMPS.
          -D CMAKE_C_COMPILER=name              # name of C compiler
          -D CMAKE_Fortran_COMPILER=name        # name of Fortran compiler
 
+         -D CMAKE_CXX_STANDARD=17              # put compiler in C++17 mode
+         -D LAMMPS_CXX11=yes                   # enforce compilation in C++11 mode
          -D CMAKE_CXX_FLAGS=string             # flags to use with C++ compiler
          -D CMAKE_C_FLAGS=string               # flags to use with C compiler
          -D CMAKE_Fortran_FLAGS=string         # flags to use with Fortran compiler
@@ -321,15 +328,23 @@ LAMMPS.
          you would have to install a newer compiler that supports C++11;
          either as a binary package or through compiling from source.
 
-         If you build LAMMPS with any :doc:`Speed_packages` included,
-         there may be specific compiler or linker flags that are either
-         required or recommended to enable required features and to
-         achieve optimal performance.  You need to include these in the
-         ``CCFLAGS`` and ``LINKFLAGS`` settings above.  For details, see the
-         documentation for the individual packages listed on the
-         :doc:`Speed_packages` page.  Or examine these files in the
-         ``src/MAKE/OPTIONS`` directory.  They correspond to each of the 5
-         accelerator packages and their hardware variants:
+      While a C++11 compatible compiler is currently sufficient to compile
+      LAMMPS, a transition to require C++17 is in progress and planned to
+      be completed in Summer 2025. Currently, setting ``-DLAMMPS_CXX11``
+      in the ``LMP_INC =`` line in the machine makefile is required when
+      using a C++11 compatible compiler that does not support C++17.
+      Otherwise, to enable C++17 support (if not enabled by default) using
+      a compiler flag like ``-std=c++17`` in CCFLAGS may needed.
+
+      If you build LAMMPS with any :doc:`Speed_packages` included,
+      there may be specific compiler or linker flags that are either
+      required or recommended to enable required features and to
+      achieve optimal performance.  You need to include these in the
+      ``CCFLAGS`` and ``LINKFLAGS`` settings above.  For details, see the
+      documentation for the individual packages listed on the
+      :doc:`Speed_packages` page.  Or examine these files in the
+      ``src/MAKE/OPTIONS`` directory.  They correspond to each of the 5
+      accelerator packages and their hardware variants:
 
          .. code-block:: bash
 
@@ -502,6 +517,8 @@ using CMake or Make.
                                       # 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).

doc/src/Build_cmake.rst

@@ -8,7 +8,7 @@ packages.  Links to those pages on the :doc:`Build overview <Build>`
 page.
 
 The following text assumes some familiarity with CMake and focuses on
-using the command line tool ``cmake`` and what settings are supported
+using the command-line tool ``cmake`` and what settings are supported
 for building LAMMPS.  A more detailed tutorial on how to use CMake
 itself, the text mode or graphical user interface, to change the
 generated output files for different build tools and development
@@ -16,7 +16,7 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
-   LAMMPS currently requires that CMake version 3.16 or later is available.
+   LAMMPS currently requires that CMake version 3.20 or later is available.
 
 .. warning::
 
@@ -32,29 +32,29 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 Advantages of using CMake
 ^^^^^^^^^^^^^^^^^^^^^^^^^
 
-CMake is an alternative to compiling LAMMPS in the traditional way
-through :doc:`(manually customized) makefiles <Build_make>`.  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 is the preferred way of compiling LAMMPS in contrast to the legacy
+build system based on GNU make and through :doc:`(manually customized)
+makefiles <Build_make>`.  Using CMake has multiple advantages that are
+specifically helpful for people with limited experience in compiling
+software or for people that want to modify or extend LAMMPS.
 
 - CMake can detect available hardware, tools, features, and libraries
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
-- CMake supports customization of settings with a command line, text
+- CMake supports customization of settings with a command-line, text
   mode, or graphical user interface.  No manual editing of files,
-  knowledge of file formats or complex command line syntax is required.
+  knowledge of file formats or complex command-line syntax is required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
-- Support for true out-of-source compilation. Multiple configurations
+- Support for true out-of-source compilation.  Multiple configurations
   and settings with different choices of LAMMPS packages, settings, or
   compilers can be configured and built concurrently from the same
   source tree.
 - Simplified packaging of LAMMPS for Linux distributions, environment
-  modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
-- Integration of automated unit and regression testing (the LAMMPS side
-  of this is still under active development).
+  modules, or automated build tools like `Spack <https://spack.io>`_
+  or `Homebrew <https://brew.sh/>`_.
+- Integration of automated unit and regression testing.
 
 .. _cmake_build:
 
@@ -68,7 +68,7 @@ that purpose you can use either the command-line utility ``cmake`` (or
 graphical utility ``cmake-gui``, or use them interchangeably.  The
 second step is then the compilation and linking of all objects,
 libraries, and executables using the selected build tool.  Here is a
-minimal example using the command line version of CMake to build LAMMPS
+minimal example using the command-line version of CMake to build LAMMPS
 with no add-on packages enabled and no customization:
 
 .. code-block:: bash
@@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
 potential and force field files.  The location of the installation tree
 defaults to ``${HOME}/.local``.
 
+.. note::
+
+   If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
+   system location on a Linux machine , you may also have to run (as
+   root) the `ldconfig` program to update the cache file for fast lookup
+   of system shared libraries.
+
 .. _cmake_options:
 
 Configuration and build options
@@ -131,7 +138,7 @@ 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.
 
@@ -141,11 +148,11 @@ a different compiler tool chain.  Those are loaded with the ``-C`` flag
 (``-C ../cmake/presets/basic.cmake``).  This step would only be needed
 once, as the settings from the preset files are stored in the
 ``CMakeCache.txt`` file. It is also possible to customize the build
-by adding one or more ``-D`` flags to the CMake command line.
+by adding one or more ``-D`` flags to the CMake command.
 
 Generating files for alternate build tools (e.g. Ninja) and project files
 for IDEs like Eclipse, CodeBlocks, or Kate can be selected using the ``-G``
-command line flag.  A list of available generator settings for your
+command-line flag.  A list of available generator settings for your
 specific CMake version is given when running ``cmake --help``.
 
 .. _cmake_multiconfig:

doc/src/Build_development.rst

@@ -263,9 +263,9 @@ will be skipped if prerequisite features are not available in LAMMPS.
    time.  Preference is given to parts of the code base that are easy to
    test or commonly used.
 
-Tests as shown by the ``ctest`` program are command lines defined in the
+Tests as shown by the ``ctest`` program are commands defined in the
 ``CMakeLists.txt`` files in the ``unittest`` directory tree.  A few
-tests simply execute LAMMPS with specific command line flags and check
+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
@@ -420,7 +420,7 @@ during MD timestepping and manipulate per-atom properties like
 positions, velocities, and forces.  For those fix styles, testing can be
 done in a very similar fashion as for force fields and thus there is a
 test program `test_fix_timestep` that shares a lot of code, properties,
-and command line flags with the force field style testers described in
+and command-line flags with the force field style testers described in
 the previous section.
 
 This tester will set up a small molecular system run with verlet run
@@ -642,10 +642,10 @@ The following target are available for both, GNU make and CMake:
 
 .. _gh-cli:
 
-GitHub command line interface
+GitHub command-line interface
 -----------------------------
 
-GitHub has developed a `command line tool <https://cli.github.com>`_
+GitHub has developed a `command-line tool <https://cli.github.com>`_
 to interact with the GitHub website via a command called ``gh``.
 This is extremely convenient when working with a Git repository hosted
 on GitHub (like LAMMPS).  It is thus highly recommended to install it

doc/src/Build_extras.rst

@@ -48,6 +48,7 @@ This is the list of packages that may require additional steps.
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
+   * :ref:`MISC <misc>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
@@ -209,7 +210,7 @@ necessary for ``hipcc`` and the linker to work correctly.
 Using the CHIP-SPV implementation of HIP is supported. It allows one to
 run HIP code on Intel GPUs via the OpenCL or Level Zero back ends. To use
 CHIP-SPV, you must set ``-DHIP_USE_DEVICE_SORT=OFF`` in your CMake
-command line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
+command-line as CHIP-SPV does not yet support hipCUB. As of Summer 2022,
 the use of HIP for Intel GPUs is experimental. You should only use this
 option in preparations to run on Aurora system at Argonne.
 
@@ -232,7 +233,7 @@ option in preparations to run on Aurora system at Argonne.
 
 .. code:: bash
 
-   # CUDA target (not recommended, use GPU_ARCH=cuda)
+   # CUDA target (not recommended, use GPU_API=cuda)
    # !!! DO NOT set CMAKE_CXX_COMPILER !!!
    export HIP_PLATFORM=nvcc
    export HIP_PATH=/path/to/HIP/install
@@ -254,11 +255,10 @@ Traditional make
 
 Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
 You can do this manually if you prefer; follow the instructions in
-``lib/gpu/README``.  Note that the GPU library uses MPI calls, so you must
-use the same MPI library (or the STUBS library) settings as the main
-LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG``\ ,
-``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever
-Makefile you use.
+``lib/gpu/README``.  Note that the GPU library uses MPI calls, so you
+must use the same MPI library (or the STUBS library) settings as the
+main LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG`` or
+``-DLAMMPS_SMALLBIG`` settings in whichever Makefile you use.
 
 You can also build the library in one step from the ``lammps/src`` dir,
 using a command like these, which simply invokes the ``lib/gpu/Install.py``
@@ -421,9 +421,10 @@ minutes to hours) to build.  Of course you only need to do that once.)
       cmake build system.  The ``lib/kim/Install.py`` script supports a
       ``CMAKE`` environment variable if the cmake executable is named other
       than ``cmake`` on your system.  Additional environment variables may be
-      provided on the command line for use by cmake.  For example, to use the
-      ``cmake3`` executable and tell it to use the gnu version 11 compilers
-      to build KIM, one could use the following command line.
+      set with the ``make`` command for use by cmake.  For example, to use the
+      ``cmake3`` executable and tell it to use the GNU version 11 compilers
+      called ``g++-11``, ``gcc-11`` and ``gfortran-11`` to build KIM, one
+      could use the following command.
 
       .. code-block:: bash
 
@@ -546,16 +547,7 @@ They must be specified in uppercase.
       - Local machine
    *  - AMDAVX
       - HOST
-      - AMD 64-bit x86 CPU (AVX 1)
-   *  - ZEN
-      - HOST
-      - AMD Zen class CPU (AVX 2)
-   *  - ZEN2
-      - HOST
-      - AMD Zen2 class CPU (AVX 2)
-   *  - ZEN3
-      - HOST
-      - AMD Zen3 class CPU (AVX 2)
+      - AMD chip
    *  - ARMV80
       - HOST
       - ARMv8.0 Compatible CPU
@@ -571,105 +563,129 @@ They must be specified in uppercase.
    *  - A64FX
       - HOST
       - ARMv8.2 with SVE Support
+   *  - ARMV9_GRACE
+      - HOST
+      - ARMv9 NVIDIA Grace CPU
    *  - SNB
       - HOST
-      - Intel Sandy/Ivy Bridge CPU (AVX 1)
+      - Intel Sandy/Ivy Bridge CPUs
    *  - HSW
       - HOST
-      - Intel Haswell CPU (AVX 2)
+      - Intel Haswell CPUs
    *  - BDW
       - HOST
-      - Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
-   *  - SKL
-      - HOST
-      - Intel Skylake Client CPU
-   *  - SKX
-      - HOST
-      - Intel Skylake Xeon Server CPU (AVX512)
+      - Intel Broadwell Xeon E-class CPUs
    *  - ICL
       - HOST
-      - Intel Ice Lake Client CPU (AVX512)
+      - Intel Ice Lake Client CPUs (AVX512)
    *  - ICX
       - HOST
-      - Intel Ice Lake Xeon Server CPU (AVX512)
-   *  - SPR
+      - Intel Ice Lake Xeon Server CPUs (AVX512)
+   *  - SKL
       - HOST
-      - Intel Sapphire Rapids Xeon Server CPU (AVX512)
+      - Intel Skylake Client CPUs
+   *  - SKX
+      - HOST
+      - Intel Skylake Xeon Server CPUs (AVX512)
    *  - KNC
       - HOST
       - Intel Knights Corner Xeon Phi
    *  - KNL
       - HOST
       - Intel Knights Landing Xeon Phi
+   *  - SPR
+      - HOST
+      - Intel Sapphire Rapids Xeon Server CPUs (AVX512)
    *  - POWER8
       - HOST
-      - IBM POWER8 CPU
+      - IBM POWER8 CPUs
    *  - POWER9
       - HOST
-      - IBM POWER9 CPU
+      - IBM POWER9 CPUs
+   *  - ZEN
+      - HOST
+      - AMD Zen architecture
+   *  - ZEN2
+      - HOST
+      - AMD Zen2 architecture
+   *  - ZEN3
+      - HOST
+      - AMD Zen3 architecture
+   *  - ZEN4
+      - HOST
+      - AMD Zen4 architecture
    *  - RISCV_SG2042
       - HOST
-      - SG2042 (RISC-V) CPU
+      - SG2042 (RISC-V) CPUs
+   *  - RISCV_RVA22V
+      - HOST
+      - RVA22V (RISC-V) CPUs
    *  - KEPLER30
       - GPU
-      - NVIDIA Kepler generation CC 3.0 GPU
+      - NVIDIA Kepler generation CC 3.0
    *  - KEPLER32
       - GPU
-      - NVIDIA Kepler generation CC 3.2 GPU
+      - NVIDIA Kepler generation CC 3.2
    *  - KEPLER35
       - GPU
-      - NVIDIA Kepler generation CC 3.5 GPU
+      - NVIDIA Kepler generation CC 3.5
    *  - KEPLER37
       - GPU
-      - NVIDIA Kepler generation CC 3.7 GPU
+      - NVIDIA Kepler generation CC 3.7
    *  - MAXWELL50
       - GPU
-      - NVIDIA Maxwell generation CC 5.0 GPU
+      - NVIDIA Maxwell generation CC 5.0
    *  - MAXWELL52
       - GPU
-      - NVIDIA Maxwell generation CC 5.2 GPU
+      - NVIDIA Maxwell generation CC 5.2
    *  - MAXWELL53
       - GPU
-      - NVIDIA Maxwell generation CC 5.3 GPU
+      - NVIDIA Maxwell generation CC 5.3
    *  - PASCAL60
       - GPU
-      - NVIDIA Pascal generation CC 6.0 GPU
+      - NVIDIA Pascal generation CC 6.0
    *  - PASCAL61
       - GPU
-      - NVIDIA Pascal generation CC 6.1 GPU
+      - NVIDIA Pascal generation CC 6.1
    *  - VOLTA70
       - GPU
-      - NVIDIA Volta generation CC 7.0 GPU
+      - NVIDIA Volta generation CC 7.0
    *  - VOLTA72
       - GPU
-      - NVIDIA Volta generation CC 7.2 GPU
+      - NVIDIA Volta generation CC 7.2
    *  - TURING75
       - GPU
-      - NVIDIA Turing generation CC 7.5 GPU
+      - NVIDIA Turing generation CC 7.5
    *  - AMPERE80
       - GPU
-      - NVIDIA Ampere generation CC 8.0 GPU
+      - NVIDIA Ampere generation CC 8.0
    *  - AMPERE86
       - GPU
-      - NVIDIA Ampere generation CC 8.6 GPU
+      - NVIDIA Ampere generation CC 8.6
    *  - ADA89
       - GPU
-      - NVIDIA Ada Lovelace generation CC 8.9 GPU
+      - NVIDIA Ada generation CC 8.9
    *  - HOPPER90
       - GPU
-      - NVIDIA Hopper generation CC 9.0 GPU
+      - NVIDIA Hopper generation CC 9.0
    *  - AMD_GFX906
       - GPU
-      - AMD GPU MI50/MI60
+      - AMD GPU MI50/60
    *  - AMD_GFX908
       - GPU
       - AMD GPU MI100
    *  - AMD_GFX90A
       - GPU
       - AMD GPU MI200
+   *  - AMD_GFX940
+      - GPU
+      - AMD GPU MI300
    *  - AMD_GFX942
       - GPU
       - AMD GPU MI300
+   *  - AMD_GFX942_APU
+      - GPU
+      - AMD APU MI300A
    *  - AMD_GFX1030
       - GPU
       - AMD GPU V620/W6800
@@ -678,7 +694,7 @@ They must be specified in uppercase.
       - AMD GPU RX7900XTX
    *  - AMD_GFX1103
       - GPU
-      - AMD Phoenix APU with Radeon 740M/760M/780M/880M/890M
+      - AMD APU Phoenix
    *  - INTEL_GEN
       - GPU
       - SPIR64-based devices, e.g. Intel GPUs, using JIT
@@ -701,7 +717,7 @@ They must be specified in uppercase.
       - GPU
       - Intel GPU Ponte Vecchio
 
-This list was last updated for version 4.3.0 of the Kokkos library.
+This list was last updated for version 4.6.0 of the Kokkos library.
 
 .. tabs::
 
@@ -1125,11 +1141,10 @@ POEMS package
 PYTHON package
 ---------------------------
 
-Building with the PYTHON package requires you have a the Python development
-headers and library available on your system, which needs to be a Python 2.7
-version or a Python 3.x version.  Since support for Python 2.x has ended,
-using Python 3.x is strongly recommended. See ``lib/python/README`` for
-additional details.
+Building with the PYTHON package requires you have a the Python
+development headers and library available on your system, which
+needs to be Python version 3.6 or later.  See ``lib/python/README``
+for additional details.
 
 .. tabs::
 
@@ -1145,7 +1160,7 @@ additional details.
       set the Python_EXECUTABLE variable to specify which Python
       interpreter should be used.  Note note that you will also need to
       have the development headers installed for this version,
-      e.g. python2-devel.
+      e.g. python3-devel.
 
    .. tab:: Traditional make
 
@@ -2018,7 +2033,7 @@ TBB and MKL.
 .. _mdi:
 
 MDI package
------------------------------
+-----------
 
 .. tabs::
 
@@ -2045,6 +2060,37 @@ MDI package
 
 ----------
 
+.. _misc:
+
+MISC package
+------------
+
+The :doc:`fix imd <fix_imd>` style in this package can be run either
+synchronously (communication with IMD clients is done in the main
+process) or asynchronously (the fix spawns a separate thread that can
+communicate with IMD clients concurrently to the LAMMPS execution).
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D LAMMPS_ASYNC_IMD=value  # Run IMD server asynchronously
+                                    # value = no (default) or yes
+
+   .. tab:: Traditional make
+
+      To enable asynchronous mode the ``-DLAMMPS_ASYNC_IMD`` define
+      needs to be added to the ``LMP_INC`` variable in the
+      ``Makefile.machine`` you are using.  For example:
+
+      .. code-block:: make
+
+         LMP_INC = -DLAMMPS_ASYNC_IMD -DLAMMPS_MEMALIGN=64
+
+----------
+
 .. _molfile:
 
 MOLFILE package
@@ -2191,7 +2237,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       from the sources in the *lib* folder (including the essential
       libqmmm.a) are not included in the static LAMMPS library and
       (currently) not installed, while their code is included in the
-      shared LAMMPS library.  Thus a typical command line to configure
+      shared LAMMPS library.  Thus a typical command to configure
       building LAMMPS for QMMM would be:
 
       .. code-block:: bash

doc/src/Build_make.rst

@@ -8,6 +8,10 @@ Building LAMMPS with traditional makefiles requires that you have a
 for customizing your LAMMPS build with a number of global compilation
 options and features.
 
+This build system is slowly being phased out and may not support all
+optional features and packages in LAMMPS.  It is recommended to switch
+to the :doc:`CMake based build system <Build_cmake>`.
+
 Requirements
 ^^^^^^^^^^^^
 
@@ -26,9 +30,9 @@ additional tools to be available and functioning.
   * 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``
-    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.
+    folder).  Python scripts are currently tested with 3.6 to 3.11.
+    The procedure for :doc:`building the documentation <Build_manual>`
+    *requires* Python 3.8 or later.
 
 Getting started
 ^^^^^^^^^^^^^^^

doc/src/Build_manual.rst

@@ -78,8 +78,7 @@ folder.  The following ``make`` commands are available:
    make epub          # generate LAMMPS.epub in ePUB format using Sphinx
    make mobi          # generate LAMMPS.mobi in MOBI format using ebook-convert
 
-   make fasthtml      # generate approximate HTML in fasthtml dir using Sphinx
-                      # some Sphinx extensions do not work correctly with this
+   make fasthtml      # generate approximate HTML in fasthtml dir using pandoc
 
    make clean         # remove intermediate RST files created by HTML build
    make clean-all     # remove entire build folder and any cached data
@@ -116,9 +115,9 @@ environment variable.
 Prerequisites for HTML
 ----------------------
 
-To run the HTML documentation build toolchain, python 3, git, doxygen,
-and virtualenv have to be installed locally.  Here are instructions for
-common setups:
+To run the HTML documentation build toolchain, Python 3.8 or later, git,
+doxygen, and virtualenv have to be installed locally.  Here are
+instructions for common setups:
 
 .. tabs::
 
@@ -128,13 +127,7 @@ common setups:
 
          sudo apt-get install git doxygen
 
-   .. tab:: RHEL or CentOS (Version 7.x)
-
-      .. code-block:: bash
-
-         sudo yum install git doxygen
-
-   .. tab:: Fedora or RHEL/CentOS (8.x or later)
+   .. tab:: Fedora or RHEL/AlmaLinux/RockyLinux (8.x or later)
 
       .. code-block:: bash
 
@@ -154,7 +147,36 @@ Prerequisites for PDF
 
 In addition to the tools needed for building the HTML format manual,
 a working LaTeX installation with support for PDFLaTeX and a selection
-of LaTeX styles/packages are required.  To run the PDFLaTeX translation
+of LaTeX styles/packages are required.  Apart from LaTeX packages that
+are usually installed by default, the following packages are required:
+
+.. table_from_list::
+   :columns: 11
+
+   - amsmath
+   - anysize
+   - babel
+   - capt-of
+   - cmap
+   - dvipng
+   - ellipse
+   - fncychap
+   - fontawesome
+   - framed
+   - geometry
+   - gyre
+   - hyperref
+   - hypcap
+   - needspace
+   - pict2e
+   - times
+   - tabulary
+   - titlesec
+   - upquote
+   - wrapfig
+   - xindy
+
+To run the PDFLaTeX translation
 the ``latexmk`` script needs to be installed as well.
 
 Prerequisites for ePUB and MOBI
@@ -182,12 +204,42 @@ documentation is required and either existing files in the ``src``
 folder need to be updated or new files added. These files are written in
 `reStructuredText <rst_>`_ markup for translation with the Sphinx tool.
 
+Testing your contribution
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
 Before contributing any documentation, please check that both the HTML
-and the PDF format documentation can translate without errors.  During
-testing the html translation, you may use the ``make fasthtml`` command
-which does an approximate translation (i.e. not all Sphinx features and
-extensions will work), but runs very fast because it will only translate
-files that have been changed since the last ``make fasthtml`` command.
+and the PDF format documentation can translate without errors and that
+there are no spelling issues.  This is done with ``make html``, ``make pdf``,
+and ``make spelling``, respectively.
+
+Fast and approximate translation to HTML
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Translating the full manual to HTML or PDF can take a long time.  Thus
+there is a fast and approximate way to translate the reStructuredText to
+HTML as a quick-n-dirty way of checking your manual page.
+
+This translation uses `Pandoc <https://pandoc.org>`_ instead of Sphinx
+and thus all special Sphinx features (cross-references, advanced tables,
+embedding of Python docstrings or doxygen documentation, and so on) will
+not render correctly.  Most embedded math should render correctly.  This
+is a **very fast** way to check the syntax and layout of a documentation
+file translated to HTML while writing or updating it.
+
+To translate **all** manual pages, you can type ``make fasthtml`` at the
+command line.  The translated HTML files are then in the ``fasthtml``
+folder. All subsequent ``make fasthtml`` commands will only translate
+``.rst`` files that have been changed.  The ``make fasthtml`` command
+can be parallelized with make using the `-j` flag.  You can also
+directly translate only individual pages: e.g. to translate only the
+``doc/src/pair_lj.rst`` page type ``make fasthtml/pair_lj.html``
+
+After writing the documentation is completed, you will still need
+to verify with ``make html`` and ``make pdf`` that it translates
+correctly in both formats.
+
+Tests for consistency, completeness, and other known issues
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Please also check the output to the console for any warnings or problems.  There will
 be multiple tests run automatically:

doc/src/Build_package.rst

@@ -49,6 +49,7 @@ packages:
    * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
+   * :ref:`MISC <misc>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`

doc/src/Build_settings.rst

@@ -8,12 +8,13 @@ Optional build settings
 LAMMPS can be built with several optional settings.  Each subsection
 explains how to do this for building both with CMake and make.
 
-* `C++11 standard compliance`_ when building all of LAMMPS
+* `C++11 and C++17 standard compliance`_ when building all of LAMMPS
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
 * `Size of LAMMPS integer types and size limits`_
 * `Read or write compressed files`_
 * `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
-* `Support for downloading files`_
+* `Support for downloading files from the input`_
+* `Prevent download of large potential files`_
 * `Memory allocation alignment`_
 * `Workaround for long long integers`_
 * `Exception handling when using LAMMPS as a library`_ to capture errors
@@ -23,14 +24,15 @@ explains how to do this for building both with CMake and make.
 
 .. _cxx11:
 
-C++11 standard compliance
--------------------------
+C++11 and C++17 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
-C++98 standard for the core code and most packages. Most currently used
-C++ compilers are compatible with C++11, but some older ones may need extra
-flags to enable C++11 compliance.  Example for GNU c++ 4.8.x:
+A C++11 standard compatible compiler is currently the minimum
+requirement for compiling LAMMPS.  LAMMPS version 3 March 2020 is the
+last version compatible with the previous C++98 standard for the core
+code and most packages. Most currently used C++ compilers are compatible
+with C++11, but some older ones may need extra flags to enable C++11
+compliance.  Example for GNU c++ 4.8.x:
 
 .. code-block:: make
 
@@ -40,6 +42,17 @@ 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>`.
 
+.. versionchanged:: 4Feb2025
+
+Starting with LAMMPS version 4 February 2025 we are starting a
+transition to require the C++17 standard.  Most current compilers are
+compatible and if the C++17 standard is available by default, LAMMPS
+will enable C++17 and will compile normally.  If the chosen compiler is
+not compatible with C++17, but only supports C++11, then the define
+-DLAMMPS_CXX11 is required to fall back to compiling with a C++11
+compiler.  After the next stable release of LAMMPS in summer 2025, the
+LAMMPS development branch and future releases will require C++17.
+
 ----------
 
 .. _fft:
@@ -303,7 +316,7 @@ large counters can become before "rolling over".  The default setting of
 
       .. code-block:: bash
 
-         -D LAMMPS_SIZES=value   # smallbig (default) or bigbig or smallsmall
+         -D LAMMPS_SIZES=value   # smallbig (default) or bigbig
 
       If the variable is not set explicitly, "smallbig" is used.
 
@@ -314,7 +327,7 @@ large counters can become before "rolling over".  The default setting of
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
+         LMP_INC = -DLAMMPS_SMALLBIG    # or -DLAMMPS_BIGBIG
 
       The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
 
@@ -323,34 +336,27 @@ LAMMPS system size restrictions
 
 .. list-table::
    :header-rows: 1
-   :widths: 18 27 28 27
+   :widths: 27 36 37
    :align: center
 
    * -
      - smallbig
      - bigbig
-     - smallsmall
    * - Total atom count
      - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
      - :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
-     - :math:`2^{31}` atoms (= :math:`2.147 \cdot 10^9`)
    * - Total timesteps
      - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
      - :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
-     - :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`)
    * - Atom ID values
      - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
      - :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})`
-     - :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
    * - Image flag values
      - :math:`-512 \le i \le 511`
      - :math:`- 1\,048\,576 \le i \le 1\,048\,575`
-     - :math:`-512 \le i \le 511`
 
 The "bigbig" setting increases the size of image flags and atom IDs over
-"smallbig" and the "smallsmall" setting is only needed if your machine
-does not support 64-bit integers or incurs performance penalties when
-using them.
+the default "smallbig" setting.
 
 These are limits for the core of the LAMMPS code, specific features or
 some styles may impose additional limits.  The :ref:`ATC
@@ -504,8 +510,8 @@ during a run.
 
 .. _libcurl:
 
-Support for downloading files
------------------------------
+Support for downloading files from the input
+--------------------------------------------
 
 .. versionadded:: 29Aug2024
 
@@ -548,6 +554,25 @@ LAMMPS is compiled accordingly which needs the following settings:
 
 ----------
 
+.. _download_pot:
+
+Prevent download of large potential files
+-----------------------------------------
+
+.. versionadded:: 8Feb2023
+
+LAMMPS bundles a selection of potential files in the ``potentials``
+folder as examples of how those kinds of potential files look like and
+for use with the provided input examples in the ``examples`` tree.  To
+keep the size of the distributed LAMMPS source package small, very large
+potential files (> 5 MBytes) are not bundled, but only downloaded on
+demand when the :doc:`corresponding package <Packages_list>` is
+installed.  This automatic download can be prevented when :doc:`building
+LAMMPS with CMake <Build_cmake>` by adding the setting `-D
+DOWNLOAD_POTENTIALS=off` when configuring.
+
+----------
+
 .. _align:
 
 Memory allocation alignment

doc/src/Build_windows.rst

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

doc/src/Classes_lammps.rst

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

doc/src/Commands_all.rst

@@ -140,6 +140,7 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`plugin <plugin>`
    * :doc:`prd <prd>`
    * :doc:`python <python>`
+   * :doc:`region2vmd <region2vmd>`
    * :doc:`tad <tad>`
    * :doc:`temper <temper>`
    * :doc:`temper/grem <temper_grem>`

doc/src/Commands_bond.rst

@@ -23,6 +23,7 @@ OPT.
    *
    * :doc:`bpm/rotational <bond_bpm_rotational>`
    * :doc:`bpm/spring <bond_bpm_spring>`
+   * :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>`
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (o) <bond_fene_expand>`
@@ -90,6 +91,7 @@ OPT.
    * :doc:`lepton (o) <angle_lepton>`
    * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
+   * :doc:`mwlc <angle_mwlc>`
    * :doc:`quartic (o) <angle_quartic>`
    * :doc:`spica (ko) <angle_spica>`
    * :doc:`table (o) <angle_table>`
@@ -126,7 +128,7 @@ OPT.
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
    * :doc:`lepton (o) <dihedral_lepton>`
-   * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
+   * :doc:`multi/harmonic (ko) <dihedral_multi_harmonic>`
    * :doc:`nharmonic (o) <dihedral_nharmonic>`
    * :doc:`opls (iko) <dihedral_opls>`
    * :doc:`quadratic (o) <dihedral_quadratic>`

doc/src/Commands_compute.rst

@@ -58,6 +58,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`fep/ta <compute_fep_ta>`
    * :doc:`force/tally <compute_tally>`
    * :doc:`fragment/atom <compute_cluster_atom>`
+   * :doc:`gaussian/grid/local (k) <compute_gaussian_grid_local>`
    * :doc:`global/atom <compute_global_atom>`
    * :doc:`group/group <compute_group_group>`
    * :doc:`gyration <compute_gyration>`
@@ -140,8 +141,8 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`smd/vol <compute_smd_vol>`
    * :doc:`snap <compute_sna_atom>`
    * :doc:`sna/atom <compute_sna_atom>`
-   * :doc:`sna/grid <compute_sna_atom>`
-   * :doc:`sna/grid/local <compute_sna_atom>`
+   * :doc:`sna/grid (k) <compute_sna_atom>`
+   * :doc:`sna/grid/local (k) <compute_sna_atom>`
    * :doc:`snad/atom <compute_sna_atom>`
    * :doc:`snav/atom <compute_sna_atom>`
    * :doc:`sph/e/atom <compute_sph_e_atom>`
@@ -177,6 +178,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ti <compute_ti>`
    * :doc:`torque/chunk <compute_torque_chunk>`
    * :doc:`vacf <compute_vacf>`
+   * :doc:`vacf/chunk <compute_vacf_chunk>`
    * :doc:`vcm/chunk <compute_vcm_chunk>`
    * :doc:`viscosity/cos <compute_viscosity_cos>`
    * :doc:`voronoi/atom <compute_voronoi_atom>`

doc/src/Commands_dump.rst

@@ -19,6 +19,7 @@ An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
    * :doc:`custom/gz <dump>`
    * :doc:`custom/zstd <dump>`
    * :doc:`dcd <dump>`
+   * :doc:`extxyz <dump>`
    * :doc:`grid <dump>`
    * :doc:`grid/vtk <dump>`
    * :doc:`h5md <dump_h5md>`

doc/src/Commands_fix.rst

@@ -58,6 +58,7 @@ OPT.
    * :doc:`dt/reset (k) <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield (k) <fix_efield>`
+   * :doc:`efield/lepton <fix_efield_lepton>`
    * :doc:`efield/tip4p <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electrode/conp (i) <fix_electrode>`
@@ -161,6 +162,8 @@ OPT.
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
+   * :doc:`pimd/langevin/bosonic <fix_pimd>`
+   * :doc:`pimd/nvt/bosonic <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`
    * :doc:`poems <fix_poems>`
@@ -183,6 +186,7 @@ OPT.
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
    * :doc:`qeq/reaxff (ko) <fix_qeq_reaxff>`
+   * :doc:`qeq/rel/reaxff <fix_qeq_rel_reaxff>`
    * :doc:`qeq/shielded <fix_qeq>`
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`

doc/src/Commands_input.rst

@@ -69,7 +69,7 @@ WARNING message is printed.  The :doc:`Errors <Errors>` page gives
 more information on what errors mean.  The documentation for each
 command lists restrictions on how the command can be used.
 
-You can use the :ref:`-skiprun <skiprun>` command line flag
+You can use the :ref:`-skiprun <skiprun>` command-line flag
 to have LAMMPS skip the execution of any ``run``, ``minimize``, or similar
 commands to check the entire input for correct syntax to avoid crashes
 on typos or syntax errors in long runs.

doc/src/Commands_pair.rst

@@ -80,6 +80,7 @@ OPT.
    * :doc:`coul/tt <pair_coul_tt>`
    * :doc:`coul/wolf (ko) <pair_coul>`
    * :doc:`coul/wolf/cs <pair_cs>`
+   * :doc:`dispersion/d3 <pair_dispersion_d3>`
    * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/coul/slater/long (g) <pair_dpd_coul_slater_long>`
    * :doc:`dpd/ext (ko) <pair_dpd_ext>`
@@ -114,7 +115,9 @@ OPT.
    * :doc:`gw/zbl <pair_gw>`
    * :doc:`harmonic/cut (o) <pair_harmonic_cut>`
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
+   * :doc:`hbond/dreiding/lj/angleoffset (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
+   * :doc:`hbond/dreiding/morse/angleoffset (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
    * :doc:`hippo (g) <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`

doc/src/Commands_removed.rst

@@ -1,6 +1,10 @@
 Removed commands and packages
 =============================
 
+.. contents:: \
+
+------
+
 This page lists LAMMPS commands and packages that have been removed from
 the distribution and provides suggestions for alternatives or
 replacements.  LAMMPS has special dummy styles implemented, that will
@@ -8,94 +12,32 @@ stop LAMMPS and print a suitable error message in most cases, when a
 style/command is used that has been removed or will replace the command
 with the direct alternative (if available) and print a warning.
 
-restart2data tool
------------------
-
-.. versionchanged:: 23Nov2013
-
-The functionality of the restart2data tool has been folded into the
-LAMMPS executable directly instead of having a separate tool.  A
-combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For
-added convenience this conversion can also be triggered by
-:doc:`command line flags <Run_options>`
-
-Fix ave/spatial and fix ave/spatial/sphere
-------------------------------------------
-
-.. deprecated:: 11Dec2015
-
-The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
-since they were superseded by the more general and extensible "chunk
-infrastructure".  Here the system is partitioned in one of many possible
-ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
-and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
-Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
-
-Box command
------------
-
-.. deprecated:: 22Dec2022
-
-The *box* command has been removed and the LAMMPS code changed so it won't
-be needed.  If present, LAMMPS will ignore the command and print a warning.
-
-Reset_ids, reset_atom_ids, reset_mol_ids commands
--------------------------------------------------
-
-.. deprecated:: 22Dec2022
-
-The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
-been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
-present, LAMMPS will replace the commands accordingly and print a
-warning.
-
-LATTE package
--------------
-
-.. deprecated:: 15Jun2023
-
-The LATTE package with the fix latte command was removed from LAMMPS.
-This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
-and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
-<PKG-MDI>`.  These fixes are compatible with several quantum software
-packages, including LATTE.  See the ``examples/QUANTUM`` dir and the
-:doc:`MDI coupling HOWTO <Howto_mdi>` page.  MDI supports running LAMMPS
-with LATTE as a plugin library (similar to the way fix latte worked), as
-well as on a different set of MPI processors.
-
-MEAM package
+LAMMPS shell
 ------------
 
-The MEAM package in Fortran has been replaced by a C++ implementation.
-The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
-Fortran code of MEAM into C++, which removes several restrictions
-(e.g. there can be multiple instances in hybrid pair styles) and allows
-for some optimizations leading to better performance.  The pair style
-:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
-period the C++ version of MEAM was called USER-MEAMC so it could
-coexist with the Fortran version.
+.. versionchanged:: 29Aug2024
 
-Minimize style fire/old
------------------------
+The LAMMPS shell has been removed from the LAMMPS distribution. Users
+are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
 
-.. deprecated:: 8Feb2023
+i-PI tool
+---------
 
-Minimize style *fire/old* has been removed. Its functionality can be
-reproduced with *fire* with specific options. Please see the
-:doc:`min_modify command <min_modify>` documentation for details.
+.. versionchanged:: 27Jun2024
 
-Pair style mesont/tpm, compute style mesont, atom style mesont
---------------------------------------------------------------
+The i-PI tool has been removed from the LAMMPS distribution.  Instead,
+instructions to install i-PI from PyPI via pip are provided.
 
-.. deprecated:: 8Feb2023
+USER-REAXC package
+------------------
 
-Pair style *mesont/tpm*, compute style *mesont*, and atom style
-*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
-The same functionality is available through
-:doc:`pair style mesocnt <pair_mesocnt>`,
-:doc:`bond style mesocnt <bond_mesocnt>` and
-:doc:`angle style mesocnt <angle_mesocnt>`.
+.. deprecated:: 7Feb2024
+
+The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
+In the process also the pair style and related fixes were renamed to use
+the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
+backward compatibility by providing aliases for the styles.  These have
+been removed, so using "reaxff" is now *required*.
 
 MPIIO package
 -------------
@@ -115,7 +57,6 @@ Similarly, the "nfile" and "fileper" keywords exist for restarts:
 see :doc:`restart <restart>`, :doc:`read_restart <read_restart>`,
 :doc:`write_restart <write_restart>`.
 
-
 MSCG package
 ------------
 
@@ -126,9 +67,73 @@ for many years and instead superseded by the `OpenMSCG software
 <https://software.rcc.uchicago.edu/mscg/>`_ of the Voth group at the
 University of Chicago, which can be used independent from LAMMPS.
 
+LATTE package
+-------------
+
+.. deprecated:: 15Jun2023
+
+The LATTE package with the fix latte command was removed from LAMMPS.
+This functionality has been superseded by :doc:`fix mdi/qm <fix_mdi_qm>`
+and :doc:`fix mdi/qmmm <fix_mdi_qmmm>` from the :ref:`MDI package
+<PKG-MDI>`.  These fixes are compatible with several quantum software
+packages, including LATTE.  See the ``examples/QUANTUM`` dir and the
+:doc:`MDI coupling HOWTO <Howto_mdi>` page.  MDI supports running LAMMPS
+with LATTE as a plugin library (similar to the way fix latte worked), as
+well as on a different set of MPI processors.
+
+Minimize style fire/old
+-----------------------
+
+.. deprecated:: 8Feb2023
+
+Minimize style *fire/old* has been removed. Its functionality can be
+reproduced with style *fire* with specific options. Please see the
+:doc:`min_modify command <min_modify>` documentation for details.
+
+Pair style mesont/tpm, compute style mesont, atom style mesont
+--------------------------------------------------------------
+
+.. deprecated:: 8Feb2023
+
+Pair style *mesont/tpm*, compute style *mesont*, and atom style
+*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
+The same functionality is available through
+:doc:`pair style mesocnt <pair_mesocnt>`,
+:doc:`bond style mesocnt <bond_mesocnt>` and
+:doc:`angle style mesocnt <angle_mesocnt>`.
+
+Box command
+-----------
+
+.. deprecated:: 22Dec2022
+
+The *box* command has been removed and the LAMMPS code changed so it won't
+be needed.  If present, LAMMPS will ignore the command and print a warning.
+
+Reset_ids, reset_atom_ids, reset_mol_ids commands
+-------------------------------------------------
+
+.. deprecated:: 22Dec2022
+
+The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
+been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
+present, LAMMPS will replace the commands accordingly and print a
+warning.
+
+MESSAGE package
+---------------
+
+.. deprecated:: 4May2022
+
+The MESSAGE package has been removed since it was superseded by the
+:ref:`MDI package <PKG-MDI>`. MDI implements the same functionality
+and in a more general way with direct support for more applications.
+
 REAX package
 ------------
 
+.. deprecated:: 4Jan2019
+
 The REAX package has been removed since it was superseded by the
 :ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF package has been tested
 to yield equivalent results to the REAX package, offers better
@@ -138,20 +143,25 @@ syntax compatible with the removed reax pair style, so input files will
 have to be adapted.  The REAXFF package was originally called
 USER-REAXC.
 
-USER-REAXC package
-------------------
+MEAM package
+------------
 
-.. deprecated:: 7Feb2024
+.. deprecated:: 4Jan2019
 
-The USER-REAXC package has been renamed to :ref:`REAXFF <PKG-REAXFF>`.
-In the process also the pair style and related fixes were renamed to use
-the "reaxff" string instead of "reax/c". For a while LAMMPS was maintaining
-backward compatibility by providing aliases for the styles.  These have
-been removed, so using "reaxff" is now *required*.
+The MEAM package in Fortran has been replaced by a C++ implementation.
+The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
+Fortran code of MEAM into C++, which removes several restrictions
+(e.g. there can be multiple instances in hybrid pair styles) and allows
+for some optimizations leading to better performance.  The pair style
+:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
+period the C++ version of MEAM was called USER-MEAMC so it could
+coexist with the Fortran version.
 
 USER-CUDA package
 -----------------
 
+.. deprecated:: 31May2016
+
 The USER-CUDA package had been removed, since it had been unmaintained
 for a long time and had known bugs and problems.  Significant parts of
 the design were transferred to the
@@ -160,19 +170,39 @@ performance characteristics on NVIDIA GPUs. Both, the KOKKOS
 and the :ref:`GPU package <PKG-GPU>` are maintained
 and allow running LAMMPS with GPU acceleration.
 
-i-PI tool
----------
+Compute atom/molecule
+---------------------
 
-.. versionchanged:: 27Jun2024
+.. deprecated:: 11 Dec2015
 
-The i-PI tool has been removed from the LAMMPS distribution.  Instead,
-instructions to install i-PI from PyPI via pip are provided.
+The atom/molecule command has been removed from LAMMPS since it was superseded
+by the more general and extensible "chunk infrastructure".  Here the system is
+partitioned in one of many possible ways - including using molecule IDs -
+through the :doc:`compute chunk/atom <compute_chunk_atom>` command and then
+summing is done using :doc:`compute reduce/chunk <compute_reduce_chunk>` Please
+refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
-LAMMPS shell
-------------
+Fix ave/spatial and fix ave/spatial/sphere
+------------------------------------------
 
-.. versionchanged:: 29Aug2024
+.. deprecated:: 11Dec2015
 
-The LAMMPS shell has been removed from the LAMMPS distribution. Users
-are encouraged to use the :ref:`LAMMPS-GUI <lammps_gui>` tool instead.
+The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
+since they were superseded by the more general and extensible "chunk
+infrastructure".  Here the system is partitioned in one of many possible
+ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
+and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
+Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
+
+restart2data tool
+-----------------
+
+.. deprecated:: 23Nov2013
+
+The functionality of the restart2data tool has been folded into the
+LAMMPS executable directly instead of having a separate tool.  A
+combination of the commands :doc:`read_restart <read_restart>` and
+:doc:`write_data <write_data>` can be used to the same effect.  For
+added convenience this conversion can also be triggered by
+:doc:`command-line flags <Run_options>`
 

doc/src/Developer.rst

@@ -24,4 +24,5 @@ of time and requests from the LAMMPS user community.
    Classes
    Developer_platform
    Developer_utils
+   Developer_internal
    Developer_grid

doc/src/Developer_code_design.rst

@@ -203,6 +203,7 @@ processed in the expected order before types are removed from dynamic
 dispatch.
 
 .. admonition:: Important Notes
+   :class: note
 
    In order to be able to detect incompatibilities at compile time and
    to avoid unexpected behavior, it is crucial that all member functions
@@ -300,18 +301,24 @@ Formatting with the {fmt} library
 
 The LAMMPS source code includes a copy of the `{fmt} library
 <https://fmt.dev>`_, which is preferred over formatting with the
-"printf()" family of functions.  The primary reason is that it allows
-a typesafe default format for any type of supported data.  This is
+"printf()" family of functions.  The primary reason is that it allows a
+typesafe default format for any type of supported data.  This is
 particularly useful for formatting integers of a given size (32-bit or
-64-bit) which may require different format strings depending on
-compile time settings or compilers/operating systems.  Furthermore,
-{fmt} gives better performance, has more functionality, a familiar
-formatting syntax that has similarities to ``format()`` in Python, and
-provides a facility that can be used to integrate format strings and a
-variable number of arguments into custom functions in a much simpler
-way than the varargs mechanism of the C library.  Finally, {fmt} has
-been included into the C++20 language standard, so changes to adopt it
-are future-proof.
+64-bit) which may require different format strings depending on compile
+time settings or compilers/operating systems.  Furthermore, {fmt} gives
+better performance, has more functionality, a familiar formatting syntax
+that has similarities to ``format()`` in Python, and provides a facility
+that can be used to integrate format strings and a variable number of
+arguments into custom functions in a much simpler way than the varargs
+mechanism of the C library.  Finally, {fmt} has been included into the
+C++20 language standard as ``std::format()``, so changes to adopt it are
+future-proof, for as long as they are not using any extensions that are
+not (yet) included into C++.
+
+The long-term plan is to switch to using ``std::format()`` instead of
+``fmt::format()`` when the minimum C++ standard required for LAMMPS will
+be set to C++20. See the :ref:`basic build instructions <compile>` for
+more details.
 
 Formatted strings are frequently created by calling the
 ``fmt::format()`` function, which will return a string as a
@@ -319,11 +326,13 @@ Formatted strings are frequently created by calling the
 ``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
 In the simplest case, no additional characters are needed, as {fmt} will
 choose the default format based on the data type of the argument.
-Otherwise, the ``fmt::print()`` function may be used instead of
-``printf()`` or ``fprintf()``.  In addition, several LAMMPS output
-functions, that originally accepted a single string as argument have
-been overloaded to accept a format string with optional arguments as
-well (e.g., ``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
+Otherwise, the :cpp:func:`utils::print() <LAMMPS_NS::utils::print>`
+function may be used instead of ``printf()`` or ``fprintf()``.  In
+addition, several LAMMPS output functions, that originally accepted a
+single string as argument have been overloaded to accept a format string
+with optional arguments as well (e.g., ``Error::all()``,
+``Error::one()``, :cpp:func:`utils::logmesg()
+<LAMMPS_NS::utils::logmesg>`).
 
 Summary of the {fmt} format syntax
 ==================================

doc/src/Developer_comm_ops.rst

@@ -79,19 +79,19 @@ containing ``double`` values.  To correctly store integers that may be
 64-bit (bigint, tagint, imageint) in the buffer, you need to use the
 :ref:`ubuf union <communication_buffer_coding_with_ubuf>` construct.
 
-The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
-of forward and reverse communication operations using the same *Comm*
-class methods.  Likewise, the same pack/unpack methods and
+The *Fix*, *Bond*, *Compute*, and *Dump* classes can also invoke the
+same kind of forward and reverse communication operations using the
+same *Comm* class methods.  Likewise, the same pack/unpack methods and
 comm_forward/comm_reverse variables must be defined by the calling
-*Fix*, *Compute*, or *Dump* class.
+*Fix*, *Bond*, *Compute*, or *Dump* class.
 
-For *Fix* classes, there is an optional second argument to the
+For all of these classes, there is an optional second argument to the
 *forward_comm()* and *reverse_comm()* call which can be used when the
-fix performs multiple modes of communication, with different numbers
-of values per atom.  The fix should set the *comm_forward* and
+class performs multiple modes of communication, with different numbers
+of values per atom.  The class should set the *comm_forward* and
 *comm_reverse* variables to the maximum value, but can invoke the
 communication for a particular mode with a smaller value.  For this
-to work, the *pack_forward_comm()*, etc methods typically use a class
+to work, the *pack_forward_comm()*, etc. methods typically use a class
 member variable to choose which values to pack/unpack into/from the
 buffer.
 

doc/src/Developer_flow.rst

@@ -209,7 +209,7 @@ nve, nvt, npt.
 
 At the end of the timestep, fixes that contain an ``end_of_step()``
 method are invoked.  These typically perform a diagnostic calculation,
-e.g. the ave/time and ave/spatial fixes.  The final operation of the
+e.g. the ave/time and ave/chunk fixes.  The final operation of the
 timestep is to perform any requested output, via the ``write()`` method
 of the Output class.  There are 3 kinds of LAMMPS output: thermodynamic
 output to the screen and log file, snapshots of atom data to a dump

doc/src/Developer_internal.rst

@@ -0,0 +1,120 @@
+Internal Styles
+---------------
+
+LAMMPS has a number of styles that are not meant to be used in an input
+file and thus are not documented in the :doc:`LAMMPS command
+documentation <Commands_all>`.  The differentiation between user
+commands and internal commands is through the case of the command name:
+user commands and styles are all lower case, internal styles are all
+upper case.  Internal styles are not called from the input file, but
+their classes are instantiated by other styles.  Often they are
+created by other styles to store internal data or to perform actions
+regularly at specific steps of the simulation.
+
+The paragraphs below document some of those styles that have general
+utility and may be used to avoid redundant implementation.
+
+DEPRECATED Styles
+^^^^^^^^^^^^^^^^^
+
+The styles called DEPRECATED (e.g. pair, bond, fix, compute, region, etc.)
+have the purpose to inform users that a specific style has been removed
+or renamed.  This is achieved by creating an alias for the deprecated
+style to the corresponding class.  For example, the fix style DEPRECATED
+is aliased to fix style ave/spatial and fix style ave/spatial/sphere with
+the following code:
+
+.. code-block:: c++
+
+   FixStyle(DEPRECATED,FixDeprecated);
+   FixStyle(ave/spatial,FixDeprecated);
+   FixStyle(ave/spatial/sphere,FixDeprecated);
+
+The individual class will then determine based on the style name
+what action to perform:
+
+- inform that the style has been removed and what style replaces it, if any, and then error out
+- inform that the style has been renamed and then either execute the replacement or error out
+- inform that the style is no longer required, and it is thus ignored and continue
+
+There is also a section in the user's guide for :doc:`removed commands
+and packages <Commands_removed>` with additional explanations.
+
+Internal fix styles
+^^^^^^^^^^^^^^^^^^^
+
+These provide an implementation of features that would otherwise have
+been replicated across multiple styles.  The used fix ID is generally
+derived from the compute or fix ID creating the fix with some string
+appended.  When needed, the fix can be looked up with
+``Modify::get_fix_by_id()``, which returns a pointer to the fix
+instance.  The data managed by the fix can be accessed just as for other
+fixes that can be used in input files.
+
+fix DUMMY
+"""""""""
+
+Most fix classes cannot be instantiated before the simulation box has
+been created since they access data that is only available then.
+However, in some cases it is required that a fix must be at or close to
+the top of the list of all fixes.  In those cases an instance of the
+DUMMY fix style may be created by calling ``Modify::add_fix()`` and then
+later replaced by the intended fix through calling ``Modify::replace_fix()``.
+
+fix STORE/ATOM
+""""""""""""""
+
+Fix STORE/ATOM can be used as persistent storage of per-atom data.
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/ATOM N1 N2 gflag rflag
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/ATOM = style name of this fix command
+* N1 = 1, N2 = 0 : data is per-atom vector = single value per atom
+* N1 > 1, N2 = 0 : data is per-atom array = N1 values per atom
+* N1 > 0, N2 > 0 : data is per-atom tensor = N1xN2 values per atom
+* gflag = 1 communicate per-atom values with ghost atoms, 0 do not update ghost atom data
+* rflag = 1 store per-atom value in restart file, 0 do not store data in restart
+
+Similar functionality is also available through using custom per-atom
+properties with :doc:`fix property/atom <fix_property_atom>`.  The
+choice between the two fixes should be based on whether the user should
+be able to access this per-atom data: if yes, then fix property/atom is
+preferred, otherwise fix STORE/ATOM.
+
+fix STORE/GLOBAL
+""""""""""""""""
+
+Fix STORE/GLOBAL can be used as persistent storage of global data with support for restarts
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/GLOBAL N1 N2
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/GLOBAL = style name of this fix command
+* N1 >=1 : number of global items to store
+* N2 = 1 : data is global vector of length N1
+* N2 > 1 : data is global N1xN2 array
+
+fix STORE/LOCAL
+"""""""""""""""
+
+Fix STORE/LOCAL can be used as persistent storage for local data
+
+**Syntax**
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID STORE/LOCAL Nreset Nvalues
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* STORE/LOCAL = style name of this fix command
+* Nreset = frequency at which local data is available
+* Nvalues = number of values per local item, that is the number of columns

doc/src/Developer_notes.rst

@@ -7,13 +7,7 @@ typically document what a variable stores, what a small section of
 code does, or what a function does and its input/outputs.  The topics
 on this page are intended to document code functionality at a higher level.
 
-Available topics are:
-
-- `Reading and parsing of text and text files`_
-- `Requesting and accessing neighbor lists`_
-- `Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM`_
-- `Fix contributions to instantaneous energy, virial, and cumulative energy`_
-- `KSpace PPPM FFT grids`_
+.. contents:: Available notes
 
 ----
 
@@ -218,6 +212,149 @@ command:
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
+
+Errors, warnings, and informational messages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+LAMMPS has specialized functionality to handle errors (which should
+terminate LAMMPS), warning messages (which should indicate possible
+problems *without* terminating LAMMPS), and informational text for
+messages about the progress and chosen settings.  We *strongly*
+encourage using these facilities and to *stay away* from using
+``printf()`` or ``fprintf()`` or ``std::cout`` or ``std::cerr`` and
+calling ``MPI_Abort()`` or ``exit()`` directly.  Warnings and
+informational messages should be printed only on MPI rank 0 to avoid
+flooding the output when running in parallel with many MPI processes.
+
+**Errors**
+
+When LAMMPS encounters an error, for example a syntax error in the
+input, then a suitable error message should be printed giving a brief,
+one line remark about the reason and then call either ``Error::all()``
+or ``Error::one()``.  ``Error::all()`` must be called when the failing
+code path is executed by *all* MPI processes and the error condition
+will appear for *all* MPI processes the same.  If desired, each MPI
+process may set a flag to either 0 or 1 and then MPI_Allreduce()
+searching for the maximum can be used to determine if there was an error
+on *any* of the MPI processes and make this information available to
+*all*.  ``Error::one()`` in contrast needs to be called when only one or
+a few MPI processes execute the code path or can have the error
+condition.  ``Error::all()`` is generally the preferred option.
+
+Calling these functions does not abort LAMMPS directly, but rather
+throws either a ``LAMMPSException`` (from ``Error::all()``) or a
+``LAMMPSAbortException`` (from ``Error::one()``).  These exceptions are
+caught by the LAMMPS ``main()`` program and then handled accordingly.
+The reason for this approach is to support applications, especially
+graphical applications like :ref:`LAMMPS-GUI <lammps_gui>`, that are
+linked to the LAMMPS library and have a mechanism to avoid that an error
+in LAMMPS terminates the application. By catching the exceptions, the
+application can delete the failing LAMMPS class instance and create a
+new one to try again.  In a similar fashion, the :doc:`LAMMPS Python
+module <Python_module>` checks for this and then re-throws corresponding
+Python exception, which in turn can be caught by the calling Python
+code.
+
+There are multiple "signatures" that can be called:
+
+- ``Error::all(FLERR, "Error message")``: this will abort LAMMPS with
+  the error message "Error message", followed by the last line of input
+  that was read and processed before the error condition happened.
+
+- ``Error::all(FLERR, Error::NOLASTLINE, "Error message")``: this is the
+  same as before but without the last line of input.  This is preferred
+  for errors that would happen *during* a :doc:`run <run>` or
+  :doc:`minimization <minimize>`, since showing the "run" or "minimize"
+  command would be the last line, but is unrelated to the error.
+
+- ``Error::all(FLERR, idx, "Error message")``: this is for argument
+  parsing where "idx" is the index (starting at 0) of the argument for a
+  LAMMPS command that is causing the failure (use -1 for the command
+  itself).  For index 0, you need to use the constant ``Error::ARGZERO``
+  to work around the inability of some compilers to disambiguate between
+  a NULL pointer and an integer constant 0, even with an added type cast.
+  The output may also include the last input line *before* and
+  *after*, if they differ due to substituting variables.  A textual
+  indicator is pointing to the specific word that failed.  Using the
+  constant ``Error::NOPOINTER`` in place of the *idx* argument will
+  suppress the marker and then the behavior is like the *idx* argument
+  is not provided.
+
+FLERR is a macro containing the filename and line where the Error class
+is called and that information is appended to the error message.  This
+allows to quickly find the relevant source code causing the error.  For
+all three signatures, the single string "Error message" may be replaced
+with a format string using '{}' placeholders and followed by a variable
+number of arguments, one for each placeholder. This format string and
+the arguments are then handed for formatting to the `{fmt} library
+<https://fmt.dev>`_ (which is bundled with LAMMPS) and thus allow
+processing similar to the "format()" functionality in Python.
+
+.. note::
+
+   For commands like :doc:`fix ave/time <fix_ave_time>` that accept
+   wildcard arguments, the :cpp:func:`utils::expand_args` function
+   may be passed as an optional argument where the function will provide
+   a map to the original arguments from the expanded argument indices.
+
+For complex errors, that can have multiple causes and which cannot be
+explained in a single line, you can append to the error message, the
+string created by :cpp:func:`utils::errorurl`, which then provides a
+URL pointing to a paragraph of the :doc:`Errors_details` that
+corresponds to the number provided. Example:
+
+.. code-block:: c++
+
+   error->all(FLERR, "Unknown identifier in data file: {}{}", keyword, utils::errorurl(1));
+
+This will output something like this:
+
+.. parsed-literal::
+
+   ERROR: Unknown identifier in data file: Massess
+   For more information see https://docs.lammps.org/err0001 (src/read_data.cpp:1482)
+   Last input line: read_data       data.peptide
+
+Where the URL points to the first paragraph with explanations on
+the :doc:`Errors_details` page in the manual.
+
+**Warnings**
+
+To print warnings, the ``Errors::warning()`` function should be used.
+It also requires the FLERR macros as first argument to easily identify
+the location of the warning in the source code.  Same as with the error
+functions above, the function has two variants: one just taking a single
+string as final argument and a second that uses the `{fmt} library
+<https://fmt.dev>`_ to make it similar to, say, ``fprintf()``.  One
+motivation to use this function is that it will output warnings with
+always the same capitalization of the leading "WARNING" string.  A
+second is that it has a built in rate limiter.  After a given number (by
+default 100), that can be set via the :doc:`thermo_modify command
+<thermo_modify>` no more warnings are printed.  Also, warnings are
+written consistently to both screen and logfile or not, depending on the
+settings for :ref:`screen <screen>` or :doc:`logfile <log>` output.
+
+.. note::
+
+   Unlike ``Error::all()``, the warning function will produce output on
+   *every* MPI process, so it typically would be prefixed with an if
+   statement testing for ``comm->me == 0``, i.e. limiting output to MPI
+   rank 0.
+
+**Informational messages**
+
+Finally, for informational message LAMMPS has the
+:cpp:func:`utils::logmesg() convenience function
+<LAMMPS_NS::utils::logmesg>`.  It also uses the `{fmt} library
+<https://fmt.dev>`_ to support using a format string followed by a
+matching number of arguments.  It will output the resulting formatted
+text to both, the screen and the logfile and will honor the
+corresponding settings about whether this output is active and to which
+file it should be send.  Same as for ``Error::warning()``, it would
+produce output for every MPI process and thus should usually be called
+only on MPI rank 0 to avoid flooding the output when running with many
+parallel processes.
+
 Choosing between a custom atom style, fix property/atom, and fix STORE/ATOM
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_org.rst

@@ -94,12 +94,12 @@ represents what is generally referred to as an "instance of LAMMPS".  It
 is a composite holding pointers to instances of other core classes
 providing the core functionality of the MD engine in LAMMPS and through
 them abstractions of the required operations.  The constructor of the
-LAMMPS class will instantiate those instances, process the command line
+LAMMPS class will instantiate those instances, process the command-line
 flags, initialize MPI (if not already done) and set up file pointers for
 input and output.  The destructor will shut everything down and free all
 associated memory.  Thus code for the standalone LAMMPS executable in
 ``main.cpp`` simply initializes MPI, instantiates a single instance of
-LAMMPS while passing it the command line flags and input script. It
+LAMMPS while passing it the command-line flags and input script. It
 deletes the LAMMPS instance after the method reading the input returns
 and shuts down the MPI environment before it exits the executable.
 

doc/src/Developer_unittest.rst

@@ -227,12 +227,12 @@ Tests for the C-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Tests for validating the LAMMPS C-style library interface are in the
-``unittest/c-library`` folder.  They are implemented either to be used
-for utility functions or for LAMMPS commands, but use the functions
-implemented in the ``src/library.cpp`` file as much as possible.  There
-may be some overlap with other tests, but only in as much as is required
-to test the C-style library API.  The tests are distributed over
-multiple test programs which try to match the grouping of the
+``unittest/c-library`` folder.  They text either utility functions or
+LAMMPS commands, but use the functions implemented in
+``src/library.cpp`` as much as possible.  There may be some overlap with
+other tests as far as the LAMMPS functionality is concerned, but the
+focus is on testing the C-style library API.  The tests are distributed
+over multiple test programs which try to match the grouping of the
 functions in the source code and :ref:`in the manual <lammps_c_api>`.
 
 This group of tests also includes tests invoking LAMMPS in parallel
@@ -258,7 +258,7 @@ Tests for the Python module and package
 
 The ``unittest/python`` folder contains primarily tests for classes and
 functions in the LAMMPS python module but also for commands in the
-PYTHON package.  These tests are only enabled if the necessary
+PYTHON package.  These tests are only enabled, if the necessary
 prerequisites are detected or enabled during configuration and
 compilation of LAMMPS (shared library build enabled, Python interpreter
 found, Python development files found).
@@ -272,29 +272,30 @@ Tests for the Fortran interface
 
 Tests for using the Fortran module are in the ``unittest/fortran``
 folder.  Since they are also using the GoogleTest library, they require
-implementing test wrappers in C++ that will call fortran functions
-which provide a C function interface through ISO_C_BINDINGS that will in
-turn call the functions in the LAMMPS Fortran module.
+test wrappers written in C++ that will call fortran functions with a C
+function interface through ISO_C_BINDINGS which will in turn call the
+functions in the LAMMPS Fortran module.
 
 Tests for the C++-style library interface
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The tests in the ``unittest/cplusplus`` folder are somewhat similar to
 the tests for the C-style library interface, but do not need to test the
-several convenience and utility functions that are only available through
-the C-style interface.  Instead it can focus on the more generic features
-that are used internally.  This part of the unit tests is currently still
-mostly in the planning stage.
+convenience and utility functions that are only available through the
+C-style library interface.  Instead they focus on the more generic
+features that are used in LAMMPS internally.  This part of the unit
+tests is currently still mostly in the planning stage.
 
 Tests for reading and writing file formats
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``unittest/formats`` folder contains test programs for reading and
-writing files like data files, restart files, potential files or dump files.
-This covers simple things like the file i/o convenience functions in the
-``utils::`` namespace to complex tests of atom styles where creating and
-deleting atoms with different properties is tested in different ways
-and through script commands or reading and writing of data or restart files.
+writing files like data files, restart files, potential files or dump
+files.  This covers simple things like the file i/o convenience
+functions in the ``utils::`` namespace to complex tests of atom styles
+where creating and deleting of atoms with different properties is tested
+in different ways and through script commands or reading and writing of
+data or restart files.
 
 Tests for styles computing or modifying forces
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -443,7 +444,7 @@ file for a style that is similar to one to be tested.  The file name should
 follow the naming conventions described above and after copying the file,
 the first step is to replace the style names where needed.  The coefficient
 values do not have to be meaningful, just in a reasonable range for the
-given system.  It does not matter if some forces are large, as long as
+given system.  It does not matter if some forces are large, for as long as
 they do not diverge.
 
 The template input files define a large number of index variables at the top
@@ -476,7 +477,7 @@ the tabulated coulomb, to test both code paths.  The reference results in the YA
 files then should be compared manually, if they agree well enough within the limits
 of those two approximations.
 
-The ``test_pair_style`` and equivalent programs have special command line options
+The ``test_pair_style`` and equivalent programs have special command-line options
 to update the YAML files. Running a command like
 
 .. code-block:: bash
@@ -531,19 +532,20 @@ Python module.
 Troubleshooting failed unit tests
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-The are by default no unit tests for newly added features (e.g. pair, fix,
-or compute styles) unless your pull request also includes tests for the
-added features.  If you are modifying some features, you may see failures
-for existing tests, if your modifications have some unexpected side effects
-or your changes render the existing test invalid.  If you are adding an
-accelerated version of an existing style, then only tests for INTEL,
-KOKKOS (with OpenMP only), OPENMP, and OPT will be run automatically.
-Tests for the GPU package are time consuming and thus are only run
-*after* a merge, or when a special label, ``gpu_unit_tests`` is added
-to the pull request.  After the test has started, it is often best to
-remove the label since every PR activity will re-trigger the test (that
-is a limitation of triggering a test with a label).  Support for unit
-tests when using KOKKOS with GPU acceleration is currently not supported.
+There are by default no unit tests for newly added features (e.g. pair,
+fix, or compute styles) unless your pull request also includes tests for
+these added features.  If you are modifying some existing LAMMPS
+features, you may see failures for existing tests, if your modifications
+have some unexpected side effects or your changes render the existing
+test invalid.  If you are adding an accelerated version of an existing
+style, then only tests for INTEL, KOKKOS (with OpenMP only), OPENMP, and
+OPT will be run automatically.  Tests for the GPU package are time
+consuming and thus are only run *after* a merge, or when a special
+label, ``gpu_unit_tests`` is added to the pull request.  After the test
+has started, it is often best to remove the label since every PR
+activity will re-trigger the test (that is a limitation of triggering a
+test with a label).  Support for unit tests using KOKKOS with GPU
+acceleration is currently not supported.
 
 When you see a failed build on GitHub, click on ``Details`` to be taken
 to the corresponding LAMMPS Jenkins CI web page.  Click on the "Exit"
@@ -588,7 +590,7 @@ While the epsilon (relative precision) for a single, `IEEE 754 compliant
 <https://en.wikipedia.org/wiki/IEEE_754>`_, double precision floating
 point operation is at about 2.2e-16, the achievable precision for the
 tests is lower due to most numbers being sums over intermediate results
-and the non-associativity of floating point math leading to larger
+for which the non-associativity of floating point math leads to larger
 errors.  As a rule of thumb, the test epsilon can often be in the range
 5.0e-14 to 1.0e-13.  But for "noisy" force kernels, e.g. those a larger
 amount of arithmetic operations involving `exp()`, `log()` or `sin()`
@@ -602,14 +604,14 @@ of floating point operations or that some or most intermediate operations
 may be done using approximations or with single precision floating point
 math.
 
-To rerun the failed unit test individually, change to the ``build`` directory
+To rerun a failed unit test individually, change to the ``build`` directory
 and run the test with verbose output. For example,
 
 .. code-block:: bash
 
     env TEST_ARGS=-v ctest -R ^MolPairStyle:lj_cut_coul_long -V
 
-``ctest`` with the ``-V`` flag also shows the exact command line
+``ctest`` with the ``-V`` flag also shows the exact command
 of the test. One can then use ``gdb --args`` to further debug and
 catch exceptions with the test command, for example,
 

doc/src/Developer_utils.rst

@@ -133,6 +133,9 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_comment
    :project: progguide
 
+.. doxygenfunction:: strcompress
+   :project: progguide
+
 .. doxygenfunction:: strip_style_suffix
    :project: progguide
 
@@ -166,6 +169,9 @@ and parsing files or arguments.
 .. doxygenfunction:: split_lines
    :project: progguide
 
+.. doxygenfunction:: strsame
+   :project: progguide
+
 .. doxygenfunction:: strmatch
    :project: progguide
 
@@ -232,12 +238,21 @@ Convenience functions
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
+.. doxygenfunction:: print(FILE *fp, const std::string &format, Args&&... args)
+   :project: progguide
+
+.. doxygenfunction:: print(FILE *fp, const std::string &mesg)
+   :project: progguide
+
 .. doxygenfunction:: errorurl
    :project: progguide
 
 .. doxygenfunction:: missing_cmd_args
    :project: progguide
 
+.. doxygenfunction:: point_to_error
+   :project: progguide
+
 .. doxygenfunction:: flush_buffers(LAMMPS *lmp)
    :project: progguide
 

doc/src/Developer_write_fix.rst

@@ -96,8 +96,8 @@ Here the we specify which methods of the fix should be called during
      MPI_Allreduce(localAvgVel, globalAvgVel, 4, MPI_DOUBLE, MPI_SUM, world);
      scale3(1.0 / globalAvgVel[3], globalAvgVel);
      if ((comm->me == 0) && screen) {
-       fmt::print(screen,"{}, {}, {}\n",
-                  globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
+       utils::print(screen, "{}, {}, {}\n",
+                    globalAvgVel[0], globalAvgVel[1], globalAvgVel[2]);
      }
    }
 

doc/src/Developer_write_pair.rst

@@ -310,7 +310,7 @@ the constructor and the destructor.
 
 Pair styles are different from most classes in LAMMPS that define a
 "style", as their constructor only uses the LAMMPS class instance
-pointer as an argument, but **not** the command line arguments of the
+pointer as an argument, but **not** the arguments of the
 :doc:`pair_style command <pair_style>`.  Instead, those arguments are
 processed in the ``Pair::settings()`` function (or rather the version in
 the derived class).  The constructor is the place where global defaults
@@ -891,7 +891,7 @@ originally created from mixing or not).
 These data file output functions are only useful for true pair-wise
 additive potentials, where the potential parameters can be entered
 through *multiple* :doc:`pair_coeff commands <pair_coeff>`.  Pair styles
-that require a single "pair_coeff \* \*" command line are not compatible
+that require a single "pair_coeff \* \*" command are not compatible
 with reading their parameters from data files.  For pair styles like
 *born/gauss* that do support writing to data files, the potential
 parameters will be read from the data file, if present, and
@@ -1122,7 +1122,7 @@ once.  Thus, the ``coeff()`` function has to do three tasks, each of
 which is delegated to a function in the ``PairTersoff`` class:
 
 #. map elements to atom types.  Those follow the potential file name in the
-   command line arguments and are processed by the ``map_element2type()`` function.
+   command arguments and are processed by the ``map_element2type()`` function.
 #. read and parse the potential parameter file in the ``read_file()`` function.
 #. Build data structures where the original and derived parameters are
    indexed by all possible triples of atom types and thus can be looked
@@ -1356,8 +1356,8 @@ either 0 or 1.
 
 The ``morseflag`` variable defaults to 0 and is set to 1 in the
 ``PairAIREBOMorse::settings()`` function which is called by the
-:doc:`pair_style <pair_style>` command.  This function delegates
-all command line processing and setting of other parameters to the
+:doc:`pair_style <pair_style>` command.  This function delegates all
+command argument processing and setting of other parameters to the
 ``PairAIREBO::settings()`` function of the base class.
 
 .. code-block:: c++

doc/src/Errors_debug.rst

@@ -83,7 +83,7 @@ Run LAMMPS from within the debugger
 Running LAMMPS under the control of the debugger as shown below only
 works for a single MPI rank (for debugging a program running in parallel
 you usually need a parallel debugger program).  A simple way to launch
-GDB is to prefix the LAMMPS command line with ``gdb --args`` and then
+GDB is to prefix the LAMMPS command-line with ``gdb --args`` and then
 type the command "run" at the GDB prompt.  This will launch the
 debugger, load the LAMMPS executable and its debug info, and then run
 it.  When it reaches the code causing the segmentation fault, it will
@@ -180,7 +180,7 @@ inspect the behavior of a compiled program by essentially emulating a
 CPU and instrumenting the program while running.  This slows down
 execution quite significantly, but can also report issues that are not
 resulting in a crash.  The default valgrind tool is a memory checker and
-you can use it by prefixing the normal command line with ``valgrind``.
+you can use it by prefixing the normal command-line with ``valgrind``.
 Unlike GDB, this will also work for parallel execution, but it is
 recommended to redirect the valgrind output to a file (e.g. with
 ``--log-file=crash-%p.txt``, the %p will be substituted with the
@@ -235,3 +235,53 @@ from GDB. In addition you get a more specific hint about what cause the
 segmentation fault, i.e. that it is a NULL pointer dereference.  To find
 out which pointer exactly was NULL, you need to use the debugger, though.
 
+Debugging when LAMMPS appears to be stuck
+=========================================
+
+Sometimes the LAMMPS calculation appears to be stuck, that is the LAMMPS
+process or processes are active, but there is no visible progress.  This
+can have multiple reasons:
+
+- The selected styles are slow and require a lot of CPU time and the
+  system is large. When extrapolating the expected speed from smaller
+  systems, one has to factor in that not all models scale linearly with
+  system size, e.g. :doc:`kspace styles like ewald or pppm
+  <kspace_style>`. There is very little that can be done in this case.
+- The output interval is not set or set to a large value with the
+  :doc:`thermo <thermo>` command. I the first case, there will be output
+  only at the first and last step.
+- The output is block-buffered and instead of line-buffered. The output
+  will only be written to the screen after 4096 or 8192 characters of
+  output have accumulated.  This most often happens for files but also
+  with MPI parallel executables for output to the screen, since the
+  output to the screen is handled by the MPI library so that output from
+  all processes can be shown.  This can be suppressed by using the
+  ``-nonblock`` or ``-nb`` command-line flag, which turns off buffering
+  for screen and logfile output.
+- An MPI parallel calculation has a bug where a collective MPI function
+  is called (e.g. ``MPI_Barrier()``, ``MPI_Bcast()``,
+  ``MPI_Allreduce()`` and so on) before pending point-to-point
+  communications are completed or when the collective function is only
+  called from a subset of the MPI processes.  This also applies to some
+  internal LAMMPS functions like ``Error::all()`` which uses
+  ``MPI_Barrier()`` and thus ``Error::one()`` must be called, if the
+  error condition does not happen on all MPI processes simultaneously.
+- Some function in LAMMPS has a bug where a ``for`` or ``while`` loop
+  does not trigger the exit condition and thus will loop forever.  This
+  can happen when the wrong variable is incremented or when one value in
+  a comparison becomes ``NaN`` due to an overflow.
+
+In the latter two cases, further information and stack traces (see above)
+can be obtain by attaching a debugger to a running process.  For that the
+process ID (PID) is needed; this can be found on Linux machines with the
+``top``, ``htop``, ``ps``, or ``pstree`` commands.
+
+Then running the (GNU) debugger ``gdb`` with the ``-p`` flag followed by
+the process id will attach the process to the debugger and stop
+execution of that specific process.  From there on it is possible to
+issue all debugger commands in the same way as when LAMMPS was started
+from the debugger (see above).  Most importantly it is possible to
+obtain a stack trace with the ``where`` command and thus determine where
+in the execution of a timestep this process is.  Also internal data can
+be printed and execution single stepped or continued.  When the debugger
+is exited, the calculation will resume normally.

doc/src/Errors_details.rst

@@ -1,12 +1,246 @@
-Error and warning details
-=========================
+Errors and warnings details
+===========================
 
-Many errors or warnings are self-explanatory and thus straightforward to
-resolve.  However, there are also cases, where there is no single cause
-and explanation, where LAMMPS can only detect symptoms of an error but
-not the exact cause, or where the explanation needs to be more detailed than
-what can be fit into a message printed by the program.  The following are
-discussions of such cases.
+Many errors and warnings that LAMMPS outputs are self-explanatory and
+thus straightforward to resolve.  However, there are also cases where
+there is no single cause or simple explanation that can be provided in a
+short message printed by LAMMPS.  Therefore, more detailed discussions
+of such scenarios are provided here; first on a more general level and
+then for specific errors.  In the latter cases, LAMMPS will output a
+short message and then provide a URL that links to a specific section on
+this page.
+
+-------
+
+.. contents:: Individual paragraphs
+
+------
+
+General troubleshooting advice
+------------------------------
+
+Below are suggestions that can help to understand the causes of problems
+with simulations leading to errors or unexpected results.
+
+.. _hint01:
+
+Create a small test system
+^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Debugging problems often requires running a simulation many times with
+small modifications, thus it can be a huge time saver to first assemble
+a small test system input that has the same issue, but will take much
+time until it triggers the error condition.  Also, it will be easier to
+see what happens.
+
+.. _hint02:
+
+Visualize your trajectory
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To better understand what is causing problems, it is often very useful
+to visualize the system close to the point of failure.  It may be
+necessary to have LAMMPS output trajectory frames rather frequently.  To
+avoid gigantic files, you can use :doc:`dump_modify delay <dump_modify>`
+to delay output until the critical section is reached, and you can use a
+smaller test system (see above).
+
+.. _hint03:
+
+Parallel versus serial
+^^^^^^^^^^^^^^^^^^^^^^
+
+Issues where something is "lost" or "missing" often exhibit that issue
+only when running in parallel.  That doesn't mean there is no problem,
+only the symptoms are not triggering an error quickly.  Correspondingly,
+errors may be triggered faster with more processors and thus smaller
+sub-domains.
+
+.. _hint04:
+
+Segmentation Fault
+^^^^^^^^^^^^^^^^^^
+
+A segmentation fault is an error reported by the **operating system**
+and not LAMMPS itself.  It happens when a process tries to access a
+memory address that is not available.  This can have **many** reasons:
+memory has not been allocated, a memory buffer is not large enough, a
+memory address is computed from an incorrect index, a memory buffer is
+used after it has been freed, some general memory corruption.  When
+investigating a segmentation fault (aka segfault), it is important to
+determine which process is causing it; it may not always be LAMMPS.  For
+example, some MPI library implementations report a segmentation fault
+from their "mpirun" or "mpiexec" command when the application has been
+terminated unexpectedly.
+
+While a segmentation fault is likely an indication of a bug in LAMMPS,
+it need not always be; it can also be the consequence of too aggressive
+simulation settings.  For time critical code paths, LAMMPS will assume
+the user has chosen the settings carefully and will not make any checks
+to avoid to avoid performance penalties.
+
+A crucial step in resolving a segmentation fault is to identify the
+exact location in the code where it happens.  Please see `Errors_debug`
+for a couple of examples showing how to do this on a Linux machine.
+With this information -- a simple way to reproduce the segmentation
+fault and the exact :doc:`LAMMPS version <Manual_version>` and platform
+you are running on -- you can contact the LAMMPS developers or post in
+the LAMMPS forum to get assistance.
+
+.. _hint05:
+
+Fast moving atoms
+^^^^^^^^^^^^^^^^^
+
+Fast moving atoms may be "lost" or "missing" when their velocity becomes
+so large that they can cross a sub-domain within one timestep.  This
+often happens when atoms are too close, but atoms may also "move" too
+fast from sub-domain to sub-domain if the box changes rapidly.
+E.g. when setting a large an initial box with :doc:`shrink-wrap boundary
+conditions <boundary>` that collapses on the first step (in this case
+the solution is often using 'm' instead of 's' as a boundary condition).
+
+To reduce the impact of "close contacts", one can remove those atoms or
+molecules with something like :doc:`delete_atoms overlap 0.1 all all
+<delete_atoms>`.  With periodic boundaries, a close contact pair of
+atoms may be on opposite sides of the simulation box.  Another option
+would be to first run a minimization (aka quench) before starting
+the MD.  Reducing the time step can also help.  Many times, one just
+needs to "ease" the system into a balanced state and can then switch to
+more aggressive settings.
+
+The speed of atoms during an MD run depends on the steepness of the
+potential function and their mass.  Since the positions and velocities
+of atoms are computed with finite timesteps, the timestep needs to be
+small enough for stable numeric integration of the trajectory.  If the
+timestep is too large during initialization (or other instances of
+extreme dynamics), using :doc:`fix nve/limit <fix_nve_limit>` or
+:doc:`fix dt/reset <fix_dt_reset>` temporarily can help to avoid too
+large updates or adapt the timestep according to the displacements.
+
+.. _hint06:
+
+Ignoring lost atoms
+^^^^^^^^^^^^^^^^^^^
+
+It is tempting to use the :doc:`thermo_modify lost ignore
+<thermo_modify>` to avoid LAMMPS aborting with an error on lost atoms.
+This setting should, however, *only* be used when atoms *should* leave
+the system.  In general, ignoring a problem does not solve it.
+
+.. _hint07:
+
+Pressure, forces, positions becoming NaN or Inf
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Some potentials can overflow or have a division by zero with close
+contacts or bad geometries (for the given force styles in use) leading
+to forces that can no longer be represented as numbers.  Those will show
+as "NaN" or "Inf".  On most machines, the program will continue, but
+there is no way to recover from it and those NaN or Inf values will
+propagate.  So-called :doc:`"soft-core" potentials <pair_fep_soft>` or
+the :doc:`"soft" repulsive-only pair style <pair_soft>` are less prone
+for this behavior (depending on the settings in use) and can be used at
+the beginning of a simulation.  Also, single precision numbers can
+overflow much faster, so for the GPU or INTEL package it may be
+beneficial to run with double precision initially before switching to
+mixed or single precision for faster execution when the system has
+relaxed.
+
+.. _hint08:
+
+Communication cutoff
+^^^^^^^^^^^^^^^^^^^^
+
+The communication cutoff determines the "overlap" between sub-domains
+and atoms in these regions are referred to in LAMMPS as "ghost atoms".
+This region has to be large enough to contain all atoms of a bond,
+angle, dihedral, or improper with just one atom in the actual
+sub-domain.  Typically, this cutoff is set to the largest cutoff from
+the :doc:`pair style(s) <pair_style>` plus the :doc:`neighbor list skin
+distance <neighbor>` and will typically be sufficient for all bonded
+interactions.  But if the pair style cutoff is small, this may not be
+enough.  LAMMPS will print a warning in this case using some heuristic
+based on the equilibrium bond length, but that still may not be
+sufficient for cases where the force constants are small and thus bonds
+may be stretched very far.  The communication cutoff can be adjusted
+with :doc:`comm_modify cutoff \<value\> <comm_modify>`, but setting this
+too large will waste CPU time and memory.
+
+.. _hint09:
+
+Neighbor list settings
+^^^^^^^^^^^^^^^^^^^^^^
+
+Every time LAMMPS rebuilds the neighbor lists, LAMMPS will also check
+for "lost" or "missing" atoms.  Thus it can help to use very
+conservative :doc:`neighbor list settings <neigh_modify>` and then
+examine the neighbor list statistics if the neighbor list rebuild can be
+safely delayed.  Rebuilding the neighbor list less frequently
+(i.e. through increasing the *delay* or *every*) setting has diminishing
+returns and increasing risks.
+
+.. _hint10:
+
+Units
+^^^^^
+
+A frequent cause for a variety of problems is due to using the wrong
+:doc:`units <units>` settings for a particular potentials, especially
+when reading them from a potential file.  Most of the (example)
+potentials bundled with LAMMPS have a "UNITS:" tag that allows LAMMPS to
+check of the units are consistent with what is intended, but potential
+files from publications or potential parameter databases may lack this
+metadata information and thus will not error out or warn when using the
+wrong setting.  Most potential files usually use "metal" units, but some
+are parameterized for other settings, most notably :doc:`ReaxFF
+potentials <pair_reaxff>` that use "real" units.
+
+Also, individual parameters for :doc:`pair_coeff <pair_coeff>` commands
+taken from publications or other MD software may need to be converted
+and sometimes in unexpected ways.  Thus some careful checking is
+recommended.
+
+.. _hint11:
+
+No error message printed
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+In some cases -- especially when running in parallel with MPI -- LAMMPS
+may stop without displaying an error.  But the fact that nothing was
+displayed does not mean there was not an error message. Instead it is
+highly likely that the message was written to a buffer and LAMMPS was
+aborted before the buffer was output.  Usually, output buffers are
+output for every line of output, but sometimes this is delayed until
+4096 or 8192 bytes of output have been accumulated.  This buffering for
+screen and logfile output can be disabled by using the :ref:`-nb
+or -nonbuf <nonbuf>` command-line flag.  This is most often needed when
+debugging crashing multi-replica calculations.
+
+.. _hint12:
+
+Errors before or after the simulation box is created
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As critical step in a LAMMPS input is when the simulation box is
+defined, either with a :doc:`create_box command <create_box>`, a
+:doc:`read_data command <read_data>`, or a :doc:`read_restart command
+<read_restart>`.  After this step, certain settings are locked in (e.g.
+units, or number of atom, bond, angle, dihedral, improper types) and
+cannot be changed after that.  Consequently, commands that change such
+settings (e.g. :doc:`units <units>`) are only allowed before the box is
+defined.  Very few commands can be used before and after, like
+:doc:`pair_style <pair_style>` (but not :doc:`pair_coeff <pair_coeff>`).
+Most LAMMPS commands must be used after the simulation box is created.
+
+Consequently, LAMMPS will stop with an error, if a command is used in
+the wrong place.  This is not always obvious.  So index or string style
+:doc:`variables <variable>` can be expanded anywhere in the input, but
+equal style (or similar) variables can only be expanded before the box
+is defined if they do not reference anything that cannot be defined
+before the box (e.g. a compute or fix reference or a thermo keyword).
+
+------
 
 .. _err0001:
 
@@ -23,19 +257,20 @@ The header section informs LAMMPS how many entries or lines are expected
 in the various sections (like Atoms, Masses, Pair Coeffs, *etc.*\ ) of
 the data file.  If there is a mismatch, LAMMPS will either keep reading
 beyond the end of a section or stop reading before the section has
-ended.  In that case the next line will not contain a recognized keyword.
+ended.  In that case the next line will not contain a recognized
+keyword.
 
-Such a mismatch can also happen when the first line of the data
-is *not* a comment as required by the format, but a line with a valid
-header keyword.  That would result in LAMMPS expecting, for instance,
-0 atoms because the "atoms" header line is the first line and thus
-treated as a comment.
+Such a mismatch can also happen when the first line of the data is *not*
+a comment as required by the format, but a line with a valid header
+keyword.  That would result in LAMMPS expecting, for instance, 0 atoms
+because the "atoms" header line is the first line and thus treated as a
+comment.
 
 Another possibility to trigger this error is to have a keyword in the
 data file that corresponds to a fix (e.g. :doc:`fix cmap <fix_cmap>`)
 but the :doc:`read_data <read_data>` command is missing the (optional)
-arguments that identify the fix and the header keyword and section
-keyword or those arguments are inconsistent with the keywords in the
+arguments that identify the fix and its header and section keywords.
+Alternatively, those arguments are inconsistent with the keywords in the
 data file.
 
 .. _err0002:
@@ -45,12 +280,705 @@ Incorrect format in ... section of data file
 
 This error happens when LAMMPS reads the contents of a section of a
 :doc:`data file <read_data>` and the number of parameters in the line
-differs from what is expected.  This most commonly happens, when the
-atom style is different from what is expected for a specific data file
-since changing the atom style usually changes the format of the line.
+differs from what is expected.  This most commonly happens when the atom
+style is different from what is expected for a specific data file since
+changing the atom style usually changes the format of the line.
 
-This error can also happen when the number of entries indicated in the
+This error can also occur when the number of entries indicated in the
 header of a data file (e.g. the number of atoms) is larger than the
 number of lines provided (e.g. in the corresponding Atoms section)
-and then LAMMPS will continue reading into the next section and that
-would have a completely different format.
+causing LAMMPS to continue reading into the next section which has a
+completely different format.
+
+.. _err0003:
+
+Illegal variable command: expected X arguments but found Y
+----------------------------------------------------------
+
+This error indicates that a variable command has the wrong number of
+arguments.  A common reason for this is that the variable expression has
+whitespace, but is not enclosed in single or double quotes.
+
+To explain, the LAMMPS input parser reads and processes lines.  The
+resulting line is broken down into "words".  Those are usually
+individual commands, labels, names, and values separated by whitespace
+(a space or tab character).  For "words" that may contain whitespace,
+they have to be enclosed in single (') or double (") quotes.  The parser
+will then remove the outermost pair of quotes and pass that string as
+"word" to the variable command.
+
+Thus missing quotes or accidental extra whitespace will trigger this
+error because the unquoted whitespace will result in the text being
+broken into more "words", i.e. the variable expression being split.
+
+.. _err0004:
+
+Out of range atoms - cannot compute ...
+---------------------------------------
+
+The PPPM (and also PPPMDisp and MSM) methods need to assemble a grid of
+electron density data derived from the (partial) charges assigned to the
+atoms.  These charges are smeared out across multiple grid points (see
+:doc:`kspace_modify order <kspace_modify>`).  When running in parallel
+with MPI, LAMMPS uses a :doc:`domain decomposition scheme
+<Developer_par_part>` where each processor manages a subset of atoms and
+thus also a grid representing the density.  The processor's grid covers
+the actual volume of the sub-domain and some extra space corresponding
+to the :doc:`neighbor list skin <neighbor>`.  These are then
+:doc:`combined and redistributed <Developer_par_long>` for parallel
+processing of the long-range component of the Coulomb interaction.
+
+The ``Out of range atoms`` error can happen when atoms move too fast,
+the neighbor list skin is too small, or the neighbor lists are not
+updated frequently enough.  The smeared charges cannot then be fully
+assigned to the density grid for all atoms.  LAMMPS checks for this
+condition and stops with an error.  Most of the time, this is an
+indication of a system with very high forces, often at the beginning of
+a simulation or when boundary conditions are changed.  The error becomes
+more likely with more MPI processes.
+
+There are multiple options to explore for avoiding the error.  The best
+choice depends strongly on the individual system, and often a
+combination of changes is required.  For example, more conservative MD
+parameter settings can be used (larger neighbor skin, shorter time step,
+more frequent neighbor list updates).  Sometimes, it helps to revisit
+the system generation and avoid close contacts when building it.
+Otherwise one can use the :doc:`delete_atoms overlap<delete_atoms>`
+command to delete those close contact atoms or run a minimization before
+the MD.  It can also help to temporarily use a cutoff-Coulomb pair style
+and no kspace style until the system has somewhat equilibrated and then
+switch to the long-range solver.
+
+.. _err0005:
+
+Bond (or angle, dihedral, improper, cmap, or shake) atoms missing
+-----------------------------------------------------------------
+
+The second atom needed to compute a particular bond (or the third or
+fourth atom for angle, dihedral, or improper) is missing on the
+indicated timestep and processor.  Typically, this is because the two
+bonded atoms have become too far apart relative to the communication
+cutoff distance for ghost atoms.  By default, the communication cutoff
+is set by the pair cutoff.  However, to accommodate larger distances
+between topologically connected atoms, it can be manually adjusted using
+:doc:`comm_modify <comm_modify>` at the cost of increased communication
+and more ghost atoms.  However, missing bond atoms may also indicate
+that there are unstable dynamics which caused the atoms to blow apart.
+In this scenario, increasing the communication distance will not solve
+the underlying issue.  Rather, see :ref:`Fast moving atoms <hint05>` and
+:ref:`Neighbor list settings <hint09>` in the general troubleshooting
+section above for ideas to fix unstable dynamics.
+
+If atoms are intended to be lost during a simulation (e.g. due to open
+boundary conditions or :doc:`fix evaporate <fix_evaporate>`) such that
+two bonded atoms may be lost at different times from each other, this
+error can be converted to a warning or turned off using the *lost/bond*
+keyword in the :doc:`thermo_modify <thermo_modify>` command.
+
+.. _err0006:
+
+Non-numeric atom coords or pressure or box dimensions - simulation unstable
+---------------------------------------------------------------------------
+
+This error usually occurs due to overly aggressive simulation settings
+or issues with the system geometry or the potential.  See
+:ref:`Pressure, forces, positions becoming NaN or Inf <hint07>` above in
+the general troubleshooting section.  This error is more likely to
+happen during equilibration, so it can help to do a minimization before
+or even add a second or third minimization after running a few
+equilibration MD steps.  It also is more likely when directly using a
+Nose-Hoover (or other) barostat, and thus it may be advisable to run
+with only a thermostat for a bit until the potential energy has
+stabilized.
+
+.. _err007:
+
+Fix used in ... not computed at compatible time
+-----------------------------------------------
+
+Many fix styles are invoked only every *nevery* timesteps, which means
+their data is only valid on those steps.  When data from a fix is used
+as input for a compute, a dump, another fix, or thermo output, it must
+read that data at timesteps when the fix in question was invoked, i.e.
+on timesteps that are multiples of its *nevery* setting.  If this is not
+the case, LAMMPS will stop with an error.  To remedy this, it may be
+required to change the output frequency or the *nevery* setting of the
+fix.
+
+.. _err0008:
+
+Lost atoms ...
+--------------
+
+A simulation stopping with an error due to lost atoms can have multiple
+causes.  By default, LAMMPS checks for whether the total number of atoms
+is consistent with the sum of atoms "owned" by MPI processors every time
+that thermodynamic output is written.  In the majority of cases, lost
+atoms are unexpected and a result of extremely high velocities causing
+instabilities in the system.  Such velocities can result from a variety
+of issues.  For ideas on how to track down issues with unexpected lost
+atoms, see :ref:`Fast moving atoms <hint05>` and :ref:`Neighbor list
+settings <hint09>` in the general troubleshooting section above.  In
+specific situations however, losing atoms is expected material behavior
+(e.g. with sputtering and surface evaporation simulations), and an
+unwanted crash can be avoided by changing the :doc:`thermo_modify lost
+<thermo_modify>` keyword from the default 'error' to 'warn' or 'ignore'
+(though heed the advice in :ref:`Ignoring lost atoms <hint06>` above!).
+
+.. _err0009:
+
+Too many neighbor bins
+----------------------
+
+The simulation box is or has become too large relative to the size of a
+neighbor bin (which in turn depends on the largest pair-wise cutoff by
+default) such that LAMMPS is unable to store the needed number of bins.
+This typically implies the simulation box has expanded too far.  That
+can occur when some atoms move rapidly apart with shrink-wrap boundaries
+or when a fix (like fix deform or a barostat) excessively grows the
+simulation box.  This can also happen if the largest pair-wise cutoff is
+small.  In this case, the error can be avoided by using the
+:doc:`neigh_modify command <neigh_modify>` to set the bin width to a
+suitably large value.
+
+.. _err0010:
+
+Unrecognized ... style ... is part of ... package which is not enabled in this LAMMPS binary
+--------------------------------------------------------------------------------------------
+
+The LAMMPS executable (binary) being used was not compiled with a
+package containing the specified style.  This indicates that the
+executable needs to be re-built after enabling the correct package in
+the relevant Makefile or CMake build directory.  See
+:doc:`Section 3. Build LAMMPS <Build>` for more details.  One can check
+if the expected package and pair style is present in the executable by
+running it with the ``-help`` (or ``-h``) flag on the command line.  One
+common oversight, especially for beginner LAMMPS users, is enabling the
+package but forgetting to run commands to rebuild (e.g., to run the
+final ``make`` or ``cmake`` command).
+
+If this error occurs with an executable that the user does not control
+(e.g., through a module on HPC clusters), the user will need to get in
+contact with the relevant person or people who can update the
+executable.
+
+.. _err011:
+
+Energy or stress was not tallied by pair style
+----------------------------------------------
+
+This warning can be printed by computes from the :ref:`TALLY package
+<PKG-TALLY>`.  Those use a callback mechanism that only work for regular
+pair-wise additive pair styles like :doc:`Lennard-Jones <pair_lj>`,
+:doc:`Morse <pair_morse>`, :doc:`Born-Meyer-Huggins <pair_born>`, and
+similar.  Such required callbacks have not been implemented for
+many-body potentials so one would have to implement them to add
+compatibility with these computes (which may be difficult to do in a
+generic fashion).  Whether this warning indicates that contributions to
+the computed properties are missing depends on the groups used.  At any
+rate, careful testing of the results is advised when this warning
+appears.
+
+.. _err0012:
+
+fmt::format_error
+-----------------
+
+LAMMPS uses the `{fmt} library <https://fmt.dev>`_ for advanced string
+formatting tasks.  This is similar to the ``printf()`` family of
+functions from the standard C library, but more flexible.  If there is a
+bug in the LAMMPS code and the format string does not match the list of
+arguments or has some other error, this error message will be shown.
+You should contact the LAMMPS developers and report the bug as a `GitHub
+Bug Report Issue <https://github.com/lammps/lammps/issues>`_ along with
+sufficient information to easily reproduce it.
+
+
+.. _err0013:
+
+Substitution for illegal variable
+---------------------------------
+
+A variable in an input script or a variable expression was not found in
+the list of valid variables.  The most common reason for this is a typo
+somewhere in the input file such that the expression uses an invalid
+variable name.  The second most common reason is omitting the curly
+braces for a direct variable with a name that is not a single letter.
+For example:
+
+.. code-block:: LAMMPS
+
+   variable cutoff index 10.0
+   pair_style lj/cut ${cutoff}  # this is correct
+   pair_style lj/cut $cutoff    # this is incorrect, LAMMPS looks for 'c' instead of 'cutoff'
+   variable c      index 5.0    # if $c is defined, LAMMPS subsitutes only '$c' and reads: 5utoff
+
+Another potential source of this error may be invalid command line
+variables (-var or -v argument) used when launching LAMMPS from an
+interactive shell or shell scripts.  An uncommon source for this error
+is using the :doc:`next command <next>` to advance through a list of
+values provided by an index style variable.  If there is no remaining
+element in the list, LAMMPS will delete the variable and any following
+expansion or reference attempt will trigger the error.
+
+Users with harder-to-track variable errors might also find reading the
+:doc:`Parsing rules for input scripts <Commands_parse>` helpful.
+
+.. _err0014:
+
+Bond atom missing in image check or box size check
+--------------------------------------------------
+
+This can be either an error or a warning depending on your
+:doc:`thermo_modify settings <thermo_modify>`.  It is flagged in a part
+of the LAMMPS code where it updates the domain decomposition and before
+it builds the neighbor lists.  It checks that both atoms of a bond are
+within the communication cutoff of a subdomain.  It is usually caused by
+atoms moving too fast (see the :ref:`paragraph on fast moving atoms
+<hint05>`), or by the :doc:`communication cutoff being too small
+<comm_modify>`, or by waiting too long between :doc:`sub-domain and
+neighbor list updates <neigh_modify>`.
+
+.. _err0015:
+
+Cannot use neighbor bins - box size \<\< cutoff
+-----------------------------------------------
+
+LAMMPS is unable to build neighbor bins since the size of the box is
+much smaller than an interaction cutoff in at least one of its
+dimensions.  Typically, this error is triggered when the simulation box
+has one very thin dimension. If a cubic neighbor bin had to fit exactly
+within the thin dimension, then an inordinate amount of bins would be
+created to fill space.  This error can be avoided using the generally
+slower :doc:`nsq neighbor style <neighbor>` or by increasing the size of
+the smallest box lengths.
+
+.. _err0016:
+
+Did not assign all atoms correctly
+----------------------------------
+
+This error happens most commonly when :doc:`reading a data file
+<read_data>` under :doc:`non-periodic boundary conditions<boundary>`.
+Only atoms with positions **inside** the simulation box will be read and
+thus any atoms outside the box will be skipped and the total atom count
+will not match, which triggers the error.  This does not happen with
+periodic boundary conditions where atoms outside the principal box will
+be "wrapped" into the principal box and their image flags set
+accordingly.
+
+Similar errors can happen with the :doc:`replicate command<replicate>`
+or the :doc:`read_restart command<read_restart>`.  In these cases the
+cause may be a problematic geometry, an insufficient communication
+cutoff, or a bug in the LAMMPS source code.  In these cases it is
+advisable to set up :ref:`small test case <hint01>` for testing and
+debugging.  This will be required in case you need to get help from a
+LAMMPS developer.
+
+.. _err0017:
+
+Domain too large for neighbor bins
+----------------------------------
+
+The domain has become extremely large so that neighbor bins cannot be
+used.  Too many neighbor bins would need to be created to fill space.
+Most likely, one or more atoms have been blown a great distance out of
+the simulation box or a fix (like fix deform or a barostat) has
+excessively grown the simulation box.
+
+.. _err0018:
+
+Step X: (h)bondchk failed
+-------------------------
+
+This error is a consequence of the heuristic memory allocations for
+buffers of the regular ReaxFF version.  In ReaxFF simulations, the lists
+of bonds and hydrogen bonds can change due to chemical reactions.  The
+default approach, however, assumes that these changes are not very
+large, so it allocates buffers for the current system setup plus a
+safety margin.  This can be adjusted with the :doc:`safezone, mincap,
+and minhbonds settings of the pair style <pair_reaxff>`, but only to
+some extent.  When equilibrating a new system, or simulating a sparse
+system in parallel, this can be difficult to control and become
+wasteful.  A simple workaround is often to break a simulation down in
+multiple chunks.  A better approach, however, is to compile and use the
+KOKKOS package version of ReaxFF (you do not need a GPU for that, but
+can also compile it in serial or OpenMP mode), which uses a more robust
+memory allocation approach.
+
+.. _err0019:
+
+Numeric index X is out of bounds
+--------------------------------
+
+This error most commonly happens when setting force field coefficients
+with either the :doc:`pair_coeff <pair_coeff>`, the :doc:`bond_coeff
+<bond_coeff>`, the :doc:`angle_coeff <angle_coeff>`, the
+:doc:`dihedral_coeff <dihedral_coeff>`, or the :doc:`improper_coeff
+<improper_coeff>` command.  These commands accept type labels, explicit
+numbers, and wildcards for ranges of numbers.  If the numeric value of
+any of these is outside the valid range (defined by the number of
+corresponding types), LAMMPS will stop with this error.  A few other
+commands and styles also allow ranges of numbers and check using the
+same method and thus print the same kind of error.
+
+The cause is almost always a typo in the input or a logic error when
+defining the values or ranges.  So one needs to carefully review the
+input.  Along with the error, LAMMPS will print the valid range as a
+hint.
+
+.. _err0020:
+
+Compute, fix, or variable vector or array is accessed out-of-range
+------------------------------------------------------------------
+
+When accessing an individual element of a global vector or array or a
+per-atom vector or array provided by a compute or fix or atom-style or
+vector-style variable or data from a specific atom, an index in square
+brackets ("[ ]") (or two indices) must be provided to determine which
+element to access and it must be in a valid range or else LAMMPS would
+access invalid data or crash with a segmentation fault.  In the two most
+common cases, where this data is accessed, :doc:`variable expressions
+<variable>` and :doc:`thermodynamic output <thermo_style>`, LAMMPS will
+check for valid indices and stop with an error otherwise.
+
+While LAMMPS is written in C++ (which uses 0 based indexing) these
+indices start at 1 (i.e. similar to Fortran).  Any index smaller than 1
+or larger than the maximum allowed value should trigger this error.
+Since this kind of error frequently happens with rather complex
+expressions, it is recommended to test these with small test systems,
+where the values can be tracked with output files for all relevant
+properties at every step.
+
+.. _err0021:
+
+Incorrect args for pair coefficients (also bond/angle/dihedral/improper coefficients)
+-------------------------------------------------------------------------------------
+
+The parameters in the :doc:`pair_coeff <pair_coeff>` command for a
+specified :doc:`pair_style <pair_style>` have a missing or erroneous
+argument.  The same applies when seeing this error for :doc:`bond_coeff
+<bond_coeff>`, :doc:`angle_coeff <angle_coeff>`, :doc:`dihedral_coeff
+<dihedral_coeff>`, or :doc:`improper_coeff <improper_coeff>` and their
+respective style commands when using the MOLECULE or EXTRA-MOLECULE
+packages.  The cases below describe some ways to approach pair
+coefficient errors, but the same strategies apply to bonded systems as
+well.
+
+Outside of normal typos, this error can have several sources.  In all
+cases, the first step is to compare the command arguments to the
+expected format found in the corresponding :doc:`pair_style
+<pair_style>` page.  This can reveal cases where, for example, a pair
+style was changed, but the pair coefficients were not updated.  This can
+happen especially with pair style variants such as :doc:`pair_style eam
+<pair_eam>` vs. :doc:`pair_style eam/alloy <pair_style>` that look very
+similar but accept different parameters (the latter 'eam/alloy' variant
+takes element type names while 'eam' does not).
+
+Another common source of coefficient errors is when using multiple pair
+styles with commands such as :doc:`pair_style hybrid <pair_hybrid>`.
+Using hybrid pair styles requires adding an extra "label" argument in
+the coefficient commands that designates which pair style the command
+line refers to.  Moreover, if the same pair style is used multiple
+times, this label must be followed by an additional numeric argument.
+Also, different pair styles may require different arguments.
+
+This error message might also require a close look at other LAMMPS input
+files that are read in by the input script, such as data files or
+restart files.
+
+.. _err0022:
+
+Energy was not tallied on needed timestep (also virial, per-atom energy, per-atom virial)
+-----------------------------------------------------------------------------------------
+
+This error is generated when LAMMPS attempts to access an out-of-date or
+non-existent energy, pressure, or virial.  For efficiency reasons,
+LAMMPS does *not* calculate these quantities when the forces are
+calculated on every timestep or iteration.  Global quantities are only
+calculated when they are needed for :doc:`thermo <thermo_style>` output
+(at the beginning, end, and at regular intervals specified by the
+:doc:`thermo <thermo>` command).  Similarly, per-atom quantities are
+only calculated if they are needed to write per-atom energy or virial to
+a dump file.  This system works fine for simple input scripts.  However,
+the many user-specified `variable`, `fix`, and `compute` commands that
+LAMMPS provides make it difficult to anticipate when a quantity will be
+requested.  In some use cases, LAMMPS will figure out that a quantity is
+needed and arrange for it to be calculated on that timestep e.g. if it
+is requested by :doc:`fix ave/time <fix_ave_time>` or similar commands.
+If that fails, it can be detected by a mismatch between the current
+timestep and when a quantity was last calculated, in which case an error
+message of this type is generated.
+
+The most common cause of this type of error is requesting a quantity
+before the start of the simulation.
+
+.. code-block:: LAMMPS
+
+   # run 0 post no               # this will fix the error
+   variable e equal pe           # requesting energy compute
+   print "Potential energy = $e" # this will generate the error
+   run 1000                      # start of simulation
+
+This situation can be avoided by adding in a "run 0" command, as
+explained in more detail in the "Variable Accuracy" section of the
+:doc:`variable <variable>` doc page.
+
+Another cause is requesting a quantity on a timestep that is not a
+thermo or dump output timestep.  This can often be remedied by
+increasing the frequency of thermo or dump output.
+
+.. _err0023:
+
+Molecule auto special bond generation overflow
+----------------------------------------------
+
+In order to correctly apply the :doc:`special_bonds <special_bonds>`
+settings (also known as "exclusions"), LAMMPS needs to maintain for each
+atom a list of atoms that are connected to this atom, either directly
+with a bond or indirectly through bonding with an intermediate atom(s).
+The purpose is to either remove or tag those pairs of atoms in the
+neighbor list.  This information is stored with individual atoms and
+thus the maximum number of such "special" neighbors is set when the
+simulation box is created.  When reading (relative) geometry and
+topology of a 'molecule' from a :doc:`molecule file <molecule>`, LAMMPS
+will build the list of such "special" neighbors for the molecule atom
+(if not given in the molecule file explicitly).  The error is triggered
+when the resulting list is too long for the space reserved when creating
+the simulation box.  The solution is to increase the corresponding
+setting.  Overestimating this value will only consume more memory, and
+is thus a safe choice.
+
+.. _err0024:
+
+Molecule topology/atom exceeds system topology/atom
+---------------------------------------------------
+
+LAMMPS uses :doc:`domain decomposition <Developer_par_part>` to
+distribute data (i.e. atoms) across the MPI processes in parallel runs.
+This includes topology data about bonds, angles, dihedrals, impropers
+and :doc:`"special" neighbors <special_bonds>`.  This information is
+stored with either one or all atoms involved in such a topology entry
+(which of the two option applies depends on the :doc:`newton <newton>`
+setting for bonds).  When reading a data file, LAMMPS analyzes the
+requirements for this file and then the values are "locked in" and
+cannot be extended.
+
+So loading a molecule file that requires more of the topology per atom
+storage or adding a data file with such needs will lead to an error.  To
+avoid the error, one or more of the `extra/XXX/per/atom` keywords are
+required to extend the corresponding storage.  It is no problem to
+choose those numbers generously and have more storage reserved than
+actually needed, but having these numbers set too small will lead to an
+error.
+
+.. _err0025:
+
+Molecule topology type exceeds system topology type
+---------------------------------------------------
+
+The total number of atom, bond, angle, dihedral, and improper types is
+"locked in" when LAMMPS creates the simulation box.  This can happen
+through either the :doc:`create_box <create_box>`, the :doc:`read_data
+<read_data>`, or the :doc:`read_restart <read_restart>` command.  After
+this it is not possible to refer to an additional type.  So loading a
+molecule file that uses additional types or adding a data file that
+would require additional types will lead to an error.  To avoid the
+error, one or more of the `extra/XXX/types` keywords are required to
+extend the maximum number of the individual types.
+
+.. _err0026:
+
+Molecule attributes do not match system attributes
+--------------------------------------------------
+
+Choosing an :doc:`atom_style <atom_style>` in LAMMPS determines which
+per-atom properties are available.  In a :doc:`molecule file
+<molecule>`, however, it is possible to add sections (for example Masses
+or Charges) that are not supported by the atom style.  Masses for
+example, are usually not a per-atom property, but defined through the
+atom type.  Thus it would not be required to have a Masses section and
+the included data would be ignored.  LAMMPS prints this warning to
+inform about this case.
+
+.. _err0027:
+
+Inconsistent image flags
+------------------------
+
+This warning happens when the distance between the *unwrapped* x-, y-,
+or z-components of the coordinates of a bond is larger than half the box
+with periodic boundaries or larger than the box with non-periodic
+boundaries.  It means that the positions and image flags have become
+inconsistent.  LAMMPS will still compute bonded interactions based on
+the closest periodic images of the atoms and thus in most cases the
+results will be correct.  However they can cause problems when such
+atoms are used with the fix rigid or replicate commands.  Thus, it is
+good practice to update the system so that the message does not appear.
+It will help with future manipulations of the system.
+
+There is one case where this warning *must* appear: when you have a
+chain of connected bonds that pass through the entire box and connect
+back to the first atom in the chain through periodic boundaries,
+i.e. some kind of "infinite polymer".  In that case, the bond image
+flags *must* be inconsistent for the one bond that reaches back to the
+beginning of the chain.
+
+
+.. _err0028:
+
+No fixes with time integration, atoms won't move
+------------------------------------------------
+
+This warning will be issued if LAMMPS encounters a :doc:`run <run>`
+command that does not have a preceding :doc:`fix <fix>` command that
+updates atom/object positions and velocities per step.  In other words,
+there are no fixes detected that perform velocity-Verlet time
+integration, such as :doc:`fix nve <fix_nve>`.  Note that this alert
+does not mean that there are no active fixes.  LAMMPS has a very wide
+variety of fixes, many of which do not move objects but also operate
+through steps, such as printing outputs (e.g. :doc:`fix print
+<fix_print>`), performing calculations (e.g. :doc:`fix ave/time
+<fix_ave_time>`), or changing other system parameters (e.g. :doc:`fix
+dt/reset <fix_dt_reset>`).  It is up to the user to determine whether
+the lack of a time-integrating fix is intentional or not.
+
+
+.. _err0029:
+
+System is not charge neutral, net charge = ...
+----------------------------------------------
+
+the sum of charges in the system is not zero.  When a system is not
+charge-neutral, methods that evolve/manipulate per-atom charges,
+evaluate Coulomb interactions, evaluate Coulomb forces, or
+evaluate/manipulate other properties relying on per-atom charges may
+raise this warning.  A non-zero net charge most commonly arises after
+setting per-atom charges :doc:`set <set>` such that the sum is non-zero
+or by reading in a system through :doc:`read_data <read_data>` where the
+per-atom charges do not sum to zero.  However, a loss of charge
+neutrality may occur in other less common ways, like when charge
+equilibration methods (e.g., :doc:`fix qeq <fix_qeq>`) fail.
+
+A similar warning/error may be raised when using certain charge
+equilibration methods: :doc:`fix qeq <fix_qeq>`, :doc:`fix qeq/comb
+<fix_qeq_comb>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`, and :doc:`fix
+qtpie/reaxff <fix_qtpie_reaxff>`.  In such cases, this warning/error
+will be raised for the fix :doc:`group <group>` when the group has a
+non-zero net charge.
+
+When the system is expected to be charge-neutral, this warning often
+arises due to an error in the lammps input (e.g., an incorrect :doc:`set
+<set>` command, error in the data file read by :doc:`read_data
+<read_data>`, incorrectly grouping atoms with charge, etc.).  If the
+system is NOT expected to be charge-neutral, the user should make sure
+that the method(s) used are appropriate for systems with a non-zero net
+charge.  Some commonly used fixes for charge equilibration :doc:`fix qeq
+<fix_qeq>`, pair styles that include charge interactions
+:doc:`pair_style coul/XXX <pair_coul>`, and kspace methods
+:doc:`kspace_style <kspace_style>` can, in theory, support systems with
+non-zero net charge.  However, non-zero net charge can lead to spurious
+artifacts.  The severity of these artifacts depends on the magnitude of
+total charge, system size, and methods used.  Before running simulations
+or calculations for systems with non-zero net charge, users should test
+for artifacts and convergence of properties.
+
+.. _err0030:
+
+Variable evaluation before simulation box is defined
+----------------------------------------------------
+
+This error happens, when trying to expand or use an equal- or atom-style
+variable (or an equivalent style), where the expression contains a
+reference to something (e.g. a compute reference, a property of an atom,
+or a thermo keyword) that is not allowed to be used before the
+simulation box is defined.  See the paragraph on :ref:`errors before or
+after the simulation box is created <hint12>` for additional
+information.
+
+.. _err0031:
+
+Invalid thermo keyword 'X' in variable formula
+----------------------------------------------
+
+This error message is often misleading.  It is caused when evaluating a
+:doc:`variable command <variable>` expression and LAMMPS comes across a
+string that it does not recognize.  LAMMPS first checks if a string is a
+reference to a compute, fix, custom property, or another variable by
+looking at the first 2-3 characters (and if it is, it checks whether the
+referenced item exists).  Next LAMMPS checks if the string matches one
+of the available functions or constants.  If that fails, LAMMPS will
+assume that this string is a :doc:`thermo keyword <thermo_style>` and
+let the code for printing thermodynamic output return the corresponding
+value.  However, if this fails too, since the string is not a thermo
+keyword, LAMMPS stops with the 'Invalid thermo keyword' error.  But it
+is also possible, that there is just a typo in the name of a valid
+variable function.  Thus it is recommended to check the failing variable
+expression very carefully.
+
+.. _err0032:
+
+One or more atoms are time integrated more than once
+----------------------------------------------------
+
+This is probably an error since you typically do not want to advance the
+positions or velocities of an atom more than once per timestep.  This
+typically happens when there are multiple fix commands that advance atom
+positions with overlapping groups.  Also, for some fix styles it is not
+immediately obvious that they include time integration.  Please check
+the documentation carefully.
+
+.. _err0033:
+
+XXX command before simulation box is defined
+--------------------------------------------
+
+This error occurs when trying to execute a LAMMPS command that requires
+information about the system dimensions, or the number atom, bond,
+angle, dihedral, or improper types, or the number of atoms or similar
+data that is only available *after* the simulation box has been created.
+See the paragraph on :ref:`errors before or after the simulation box is
+created <hint12>` for additional information.
+
+.. _err0034:
+
+XXX command after simulation box is defined
+--------------------------------------------
+
+This error occurs when trying to execute a LAMMPS command that changes a
+global setting *after* it is locked in when the simulation box is
+created (for instance defining the :doc:`atom style <atom_style>`,
+:doc:`dimension <dimension>`, :doc:`newton <newton>`, or :doc:`units
+<units>` setting).  These settings may only be changed *before* the
+simulation box has been created.  See the paragraph on :ref:`errors
+before or after the simulation box is created <hint12>` for additional
+information.
+
+.. _err0035:
+
+Error messages ending in 'Please contact the LAMMPS developers'
+---------------------------------------------------------------
+
+Such error messages indicate that something unexpected has happened and
+that it will require a good understanding of the details of the design
+of LAMMPS to resolve this.  This can be due to some bug in contributed
+code, and oversight when updating functionality, a feature that is
+scheduled to be removed or reaching a combination of flags and settings
+that should not be possible or similar.
+
+Even if you find a way to work around this error or warning, you should
+contact the LAMMPS developers and prepare a minimal set of inputs that
+can be used to reproduce this error or warning.  By providing the input,
+the LAMMPS developers can then assess whether additional action is
+needed and who else to contact about this, if needed.
+
+There are multiple ways to get into contact and report your issue. In
+order of preference there are:
+
+- Submit a bug report `issue in the LAMMPS GitHub
+  <https://github.com/lammps/lammps/issues>` repository
+- Post a message in the "LAMMPS Development" forum in the
+  `MatSci Community Discourse <https://matsci.org/c/lammps/lammps-development/42>`_
+- Send an email to ``developers@lammps.org``
+- Send an email to an :doc:`individual LAMMPS developer <Intro_authors>`
+  that you know and trust

doc/src/Errors_warnings.rst

@@ -1,11 +1,15 @@
 Warning messages
 ================
 
-This is an alphabetic list of the WARNING messages LAMMPS prints out
-and the reason why.  If the explanation here is not sufficient, the
-documentation for the offending command may help.  Warning messages
-also list the source file and line number where the warning was
-generated.  For example, a message like this:
+This is an alphabetic list of some of the WARNING messages LAMMPS prints
+out and the reason why.  If the explanation here is not sufficient, the
+documentation for the offending command may help.  This is a historic
+list and no longer updated.  Instead the LAMMPS developers are trying
+to provide more details right with the error message or link to a
+paragraph with :doc:`detailed explanations <Errors_details>`.
+
+Warning messages also list the source file and line number where the
+warning was generated.  For example, a message like this:
 
 .. parsed-literal::
 
@@ -14,7 +18,7 @@ generated.  For example, a message like this:
 means that line #187 in the file src/domain.cpp generated the error.
 Looking in the source code may help you figure out what went wrong.
 
-Doc page with :doc:`ERROR messages <Errors_messages>`
+Please also see the page with :doc:`Error messages <Errors_messages>`
 
 ----------
 
@@ -28,16 +32,10 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    cutoff is set too short or the angle has blown apart and an atom is
    too far away.
 
-*Angle style in data file differs from currently defined angle style*
-   Self-explanatory.
-
 *Angles are defined but no angle style is set*
    The topology contains angles, but there are no angle forces computed
    since there was no angle_style command.
 
-*Atom style in data file differs from currently defined atom style*
-   Self-explanatory.
-
 *Bond atom missing in box size check*
    The second atom needed to compute a particular bond is missing on this
    processor.  Typically this is because the pairwise cutoff is set too
@@ -53,9 +51,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    processor.  Typically this is because the pairwise cutoff is set too
    short or the bond has blown apart and an atom is too far away.
 
-*Bond style in data file differs from currently defined bond style*
-   Self-explanatory.
-
 *Bonds are defined but no bond style is set*
    The topology contains bonds, but there are no bond forces computed
    since there was no bond_style command.
@@ -68,9 +63,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    length, multiplying by the number of bonds in the interaction (e.g. 3
    for a dihedral) and adding a small amount of stretch.
 
-*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
-   Self-explanatory.
-
 *Calling write_dump before a full system init.*
    The write_dump command is used before the system has been fully
    initialized as part of a 'run' or 'minimize' command. Not all dump
@@ -86,18 +78,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    This means the temperature associated with the rigid bodies may be
    incorrect on this timestep.
 
-*Cannot include log terms without 1/r terms; setting flagHI to 1*
-   Self-explanatory.
-
-*Cannot include log terms without 1/r terms; setting flagHI to 1.*
-   Self-explanatory.
-
-*Charges are set, but coulombic solver is not used*
-   Self-explanatory.
-
-*Charges did not converge at step %ld: %lg*
-   Self-explanatory.
-
 *Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost*
    The communication cutoff defaults to the maximum of what is inferred from
    pair and bond styles (will be zero, if none are defined) and what is specified
@@ -123,9 +103,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    is not changed automatically and the warning may be ignored depending
    on the specific system being simulated.
 
-*Communication cutoff is too small for SNAP micro load balancing, increased to %lf*
-   Self-explanatory.
-
 *Compute cna/atom cutoff may be too large to find ghost atom neighbors*
    The neighbor cutoff used may not encompass enough ghost atoms
    to perform this operation correctly.
@@ -158,9 +135,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    Conformation of the 4 listed dihedral atoms is extreme; you may want
    to check your simulation geometry.
 
-*Dihedral style in data file differs from currently defined dihedral style*
-   Self-explanatory.
-
 *Dihedrals are defined but no dihedral style is set*
    The topology contains dihedrals, but there are no dihedral forces computed
    since there was no dihedral_style command.
@@ -177,9 +151,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Estimated error in splitting of dispersion coeffs is %g*
    Error is greater than 0.0001 percent.
 
-*Ewald/disp Newton solver failed, using old method to estimate g_ewald*
-   Self-explanatory. Choosing a different cutoff value may help.
-
 *FENE bond too long*
    A FENE bond has stretched dangerously far.  It's interaction strength
    will be truncated to attempt to prevent the bond from blowing up.
@@ -192,9 +163,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    A FENE bond has stretched dangerously far.  It's interaction strength
    will be truncated to attempt to prevent the bond from blowing up.
 
-*Fix halt condition for fix-id %s met on step %ld with value %g*
-   Self explanatory.
-
 *Fix SRD walls overlap but fix srd overlap not set*
    You likely want to set this in your input script.
 
@@ -238,21 +206,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Fix property/atom mol or charge w/out ghost communication*
    A model typically needs these properties defined for ghost atoms.
 
-*Fix qeq CG convergence failed (%g) after %d iterations at %ld step*
-   Self-explanatory.
-
 *Fix qeq has non-zero lower Taper radius cutoff*
    Absolute value must be <= 0.01.
 
 *Fix qeq has very low Taper radius cutoff*
    Value should typically be >= 5.0.
 
-*Fix qeq/dynamic tolerance may be too small for damped dynamics*
-   Self-explanatory.
-
-*Fix qeq/fire tolerance may be too small for damped fires*
-   Self-explanatory.
-
 *Fix rattle should come after all other integration fixes*
    This fix is designed to work after all other integration fixes change
    atom positions.  Thus it should be the last integration fix specified.
@@ -285,9 +244,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    The user-specified force accuracy cannot be achieved unless the table
    feature is disabled by using 'pair_modify table 0'.
 
-*Geometric mixing assumed for 1/r\^6 coefficients*
-   Self-explanatory.
-
 *Group for fix_modify temp != fix group*
    The fix_modify command is specifying a temperature computation that
    computes a temperature on a different group of atoms than the fix
@@ -310,46 +266,14 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    Conformation of the 4 listed improper atoms is extreme; you may want
    to check your simulation geometry.
 
-*Improper style in data file differs from currently defined improper style*
-   Self-explanatory.
-
 *Impropers are defined but no improper style is set*
    The topology contains impropers, but there are no improper forces computed
    since there was no improper_style command.
 
-*Inconsistent image flags*
-   The image flags for a pair on bonded atoms appear to be inconsistent.
-   Inconsistent means that when the coordinates of the two atoms are
-   unwrapped using the image flags, the two atoms are far apart.
-   Specifically they are further apart than half a periodic box length.
-   Or they are more than a box length apart in a non-periodic dimension.
-   This is usually due to the initial data file not having correct image
-   flags for the two atoms in a bond that straddles a periodic boundary.
-   They should be different by 1 in that case.  This is a warning because
-   inconsistent image flags will not cause problems for dynamics or most
-   LAMMPS simulations.  However they can cause problems when such atoms
-   are used with the fix rigid or replicate commands.  Note that if you
-   have an infinite periodic crystal with bonds then it is impossible to
-   have fully consistent image flags, since some bonds will cross
-   periodic boundaries and connect two atoms with the same image
-   flag.
-
 *Increasing communication cutoff for GPU style*
    The pair style has increased the communication cutoff to be consistent with
    the communication cutoff requirements for this pair style when run on the GPU.
 
-*KIM Model does not provide 'energy'; Potential energy will be zero*
-   Self-explanatory.
-
-*KIM Model does not provide 'forces'; Forces will be zero*
-   Self-explanatory.
-
-*KIM Model does not provide 'particleEnergy'; energy per atom will be zero*
-   Self-explanatory.
-
-*KIM Model does not provide 'particleVirial'; virial per atom will be zero*
-   Self-explanatory.
-
 *Kspace_modify slab param < 2.0 may cause unphysical behavior*
    The kspace_modify slab parameter should be larger to ensure periodic
    grids padded with empty space do not overlap.
@@ -401,20 +325,10 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    box, or moved further than one processor's subdomain away before
    reneighboring.
 
-*MSM mesh too small, increasing to 2 points in each direction*
-   Self-explanatory.
-
 *Mismatch between velocity and compute groups*
    The temperature computation used by the velocity command will not be
    on the same group of atoms that velocities are being set for.
 
-*Mixing forced for lj coefficients*
-   Self-explanatory.
-
-*Molecule attributes do not match system attributes*
-   An attribute is specified (e.g. diameter, charge) that is
-   not defined for the specified atom style.
-
 *Molecule has bond topology but no special bond settings*
    This means the bonded atoms will not be excluded in pairwise
    interactions.
@@ -449,9 +363,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *More than one compute damage/atom*
    It is not efficient to use compute ke/atom more than once.
 
-*More than one compute dilatation/atom*
-   Self-explanatory.
-
 *More than one compute erotate/sphere/atom*
    It is not efficient to use compute erorate/sphere/atom more than once.
 
@@ -464,24 +375,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *More than one compute orientorder/atom*
    It is not efficient to use compute orientorder/atom more than once.
 
-*More than one compute plasticity/atom*
-   Self-explanatory.
-
-*More than one compute sna/atom*
-   Self-explanatory.
-
-*More than one compute sna/grid*
-   Self-explanatory.
-
-*More than one compute sna/grid/local*
-   Self-explanatory.
-
-*More than one compute snad/atom*
-   Self-explanatory.
-
-*More than one compute snav/atom*
-   Self-explanatory.
-
 *More than one fix poems*
    It is not efficient to use fix poems more than once.
 
@@ -557,21 +450,12 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Pair COMB charge %.10f with force %.10f hit min barrier*
    Something is possibly wrong with your model.
 
-*Pair brownian needs newton pair on for momentum conservation*
-   Self-explanatory.
-
-*Pair dpd needs newton pair on for momentum conservation*
-   Self-explanatory.
-
 *Pair dsmc: num_of_collisions > number_of_A*
    Collision model in DSMC is breaking down.
 
 *Pair dsmc: num_of_collisions > number_of_B*
    Collision model in DSMC is breaking down.
 
-*Pair style in data file differs from currently defined pair style*
-   Self-explanatory.
-
 *Pair style restartinfo set but has no restart support*
    This pair style has a bug, where it does not support reading and
    writing information to a restart file, but does not set the member
@@ -681,9 +565,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    cluster specified by the fix shake command is numerically suspect.  LAMMPS
    will set it to 0.0 and continue.
 
-*Shell command '%s' failed with error '%s'*
-   Self-explanatory.
-
 *Shell command returned with non-zero status*
    This may indicate the shell command did not operate as expected.
 
@@ -694,15 +575,9 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    This will lead to invalid constraint forces in the SHAKE/RATTLE
    computation.
 
-*Simulations might be very slow because of large number of structure factors*
-   Self-explanatory.
-
 *Slab correction not needed for MSM*
    Slab correction is intended to be used with Ewald or PPPM and is not needed by MSM.
 
-*Specifying an 'subset' value of '0' is equivalent to no 'subset' keyword*
-   Self-explanatory.
-
 *System is not charge neutral, net charge = %g*
    The total charge on all atoms on the system is not 0.0.
    For some KSpace solvers this is only a warning.
@@ -734,9 +609,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    assumed to also be for all atoms.  Thus the pressure printed by thermo
    could be inaccurate.
 
-*The fix ave/spatial command has been replaced by the more flexible fix ave/chunk and compute chunk/atom commands -- fix ave/spatial will be removed in the summer of 2015*
-   Self-explanatory.
-
 *The minimizer does not re-orient dipoles when using fix efield*
    This means that only the atom coordinates will be minimized,
    not the orientation of the dipoles.
@@ -745,9 +617,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    More than the maximum # of neighbors was found multiple times.  This
    was unexpected.
 
-*Too many inner timesteps in fix ttm*
-   Self-explanatory.
-
 *Too many neighbors in CNA for %d atoms*
    More than the maximum # of neighbors was found multiple times.  This
    was unexpected.
@@ -775,24 +644,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    The deformation will heat the SRD particles so this can
    be dangerous.
 
-*Using kspace solver on system with no charge*
-   Self-explanatory.
-
-*Using largest cut-off for lj/long/dipole/long long long*
-   Self-explanatory.
-
-*Using largest cutoff for buck/long/coul/long*
-   Self-explanatory.
-
-*Using largest cutoff for lj/long/coul/long*
-   Self-explanatory.
-
-*Using largest cutoff for pair_style lj/long/tip4p/long*
-   Self-explanatory.
-
-*Using package gpu without any pair style defined*
-   Self-explanatory.
-
 *Using pair potential shift with pair_modify compute no*
    The shift effects will thus not be computed.
 

doc/src/Examples.rst

@@ -54,7 +54,7 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | body        | body particles, 2d system                                        |
 +-------------+------------------------------------------------------------------+
-| bpm         | BPM simulations of pouring elastic grains and plate impact       |
+| bpm         | simulations of solid elastic/plastic deformation and fracture    |
 +-------------+------------------------------------------------------------------+
 | cmap        | CMAP 5-body contributions to CHARMM force field                  |
 +-------------+------------------------------------------------------------------+
@@ -146,6 +146,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | streitz     | use of Streitz/Mintmire potential with charge equilibration      |
 +-------------+------------------------------------------------------------------+
+| stress_vcm  | removing binned rigid body motion from binned stress profile     |
++-------------+------------------------------------------------------------------+
 | tad         | temperature-accelerated dynamics of vacancy diffusion in bulk Si |
 +-------------+------------------------------------------------------------------+
 | threebody   | regression test input for a variety of manybody potentials       |

doc/src/Fortran.rst

@@ -16,7 +16,7 @@ compiled alongside the code using it from the source code in
 ``fortran/lammps.f90`` *and* with the same compiler used to build the
 rest of the Fortran code that interfaces to LAMMPS.  When linking, you
 also need to :doc:`link to the LAMMPS library <Build_link>`.  A typical
-command line for a simple program using the Fortran interface would be:
+command for a simple program using the Fortran interface would be:
 
 .. code-block:: bash
 
@@ -91,12 +91,12 @@ function and triggered with the optional logical argument set to
      CALL lmp%close(.TRUE.)
    END PROGRAM testlib
 
-It is also possible to pass command line flags from Fortran to C/C++ and
+It is also possible to pass command-line flags from Fortran to C/C++ and
 thus make the resulting executable behave similarly to the standalone
 executable (it will ignore the `-in/-i` flag, though).  This allows
-using the command line to configure accelerator and suffix settings,
+using the command-line to configure accelerator and suffix settings,
 configure screen and logfile output, or to set index style variables
-from the command line and more.  Here is a correspondingly adapted
+from the command-line and more.  Here is a correspondingly adapted
 version of the previous example:
 
 .. code-block:: fortran
@@ -108,7 +108,7 @@ version of the previous example:
      CHARACTER(LEN=128), ALLOCATABLE :: command_args(:)
      INTEGER :: i, argc
 
-     ! copy command line flags to `command_args()`
+     ! copy command-line flags to `command_args()`
      argc = COMMAND_ARGUMENT_COUNT()
      ALLOCATE(command_args(0:argc))
      DO i=0, argc
@@ -321,6 +321,14 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    :ftype set_string_variable: subroutine
    :f set_internal_variable: :f:subr:`set_internal_variable`
    :ftype set_internal_variable: subroutine
+   :f eval: :f:func:`eval`
+   :ftype eval: function
+   :f clearstep_compute: :f:subr:`clearstep_compute`
+   :ftype clearstep_compute: subroutine
+   :f addstep_compute: :f:subr:`addstep_compute`
+   :ftype addstep_compute: subroutine
+   :f addstep_compute_all: :f:subr:`addstep_compute_all`
+   :ftype addstep_compute_all: subroutine
    :f gather_atoms: :f:subr:`gather_atoms`
    :ftype gather_atoms: subroutine
    :f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@@ -448,7 +456,7 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
    compiled with MPI support, it will also initialize MPI, if it has
    not already been initialized before.
 
-   The *args* argument with the list of command line parameters is
+   The *args* argument with the list of command-line parameters is
    optional and so it the *comm* argument with the MPI communicator.
    If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
    more details please see the documentation of :cpp:func:`lammps_open`.
@@ -954,6 +962,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
       :f:func:`extract_atom` between runs.
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional arrays returned from :f:func:`extract_atom` will be
       **transposed** from equivalent arrays in C, and they will be indexed
@@ -1066,6 +1075,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    you based on data from the :cpp:class:`Compute` class.
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional arrays returned from :f:func:`extract_compute` will be
       **transposed** from equivalent arrays in C, and they will be indexed
@@ -1324,6 +1334,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    :rtype data: polymorphic
 
    .. admonition:: Array index order
+      :class: tip
 
       Two-dimensional global, per-atom, or local array data from
       :f:func:`extract_fix` will be **transposed** from equivalent arrays in
@@ -1448,11 +1459,62 @@ Procedures Bound to the :f:type:`lammps` Derived Type
    an internal-style variable, an error is generated.
 
    :p character(len=*) name: name of the variable
-   :p read(c_double) val:  new value to assign to the variable
+   :p real(c_double) val:  new value to assign to the variable
    :to: :cpp:func:`lammps_set_internal_variable`
 
 --------
 
+.. f:function:: eval(expr)
+
+   This function is a wrapper around :cpp:func:`lammps_eval` that takes a
+   LAMMPS equal style variable string, evaluates it and returns the resulting
+   scalar value as a floating-point number.
+
+   .. versionadded:: 4Feb2025
+
+   :p character(len=\*) expr: string to be evaluated
+   :to: :cpp:func:`lammps_eval`
+   :r value [real(c_double)]: result of the evaluated string
+
+--------
+
+.. f:subroutine:: clearstep_compute()
+
+   Clear whether a compute has been invoked
+
+   .. versionadded:: 4Feb2025
+
+   :to: :cpp:func:`lammps_clearstep_compute`
+
+--------
+
+.. f:subroutine:: addstep_compute(nextstep)
+
+   Add timestep to list of future compute invocations
+   if the compute has been invoked on the current timestep
+
+   .. versionadded:: 4Feb2025
+
+   overloaded for 32-bit and 64-bit integer arguments
+
+   :p integer(kind=8 or kind=4) nextstep: next timestep
+   :to: :cpp:func:`lammps_addstep_compute`
+
+--------
+
+.. f:subroutine:: addstep_compute_all(nextstep)
+
+   Add timestep to list of future compute invocations
+
+   .. versionadded:: 4Feb2025
+
+   overloaded for 32-bit and 64-bit integer arguments
+
+   :p integer(kind=8 or kind=4) nextstep: next timestep
+   :to: :cpp:func:`lammps_addstep_compute_all`
+
+--------
+
 .. f:subroutine:: gather_atoms(name, count, data)
 
    This function calls :cpp:func:`lammps_gather_atoms` to gather the named
@@ -2711,8 +2773,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
         END SUBROUTINE external_callback
       END INTERFACE
 
-   where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and
-   ``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if
+   where ``c_bigint`` is ``c_int64_t`` and ``c_tagint`` is ``c_int64_t`` if
    ``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise.
 
    The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited

doc/src/Howto.rst

@@ -40,6 +40,7 @@ Settings howto
    Howto_walls
    Howto_nemd
    Howto_dispersion
+   Howto_bulk2slab
 
 Analysis howto
 ==============
@@ -103,6 +104,7 @@ Tutorials howto
    Howto_github
    Howto_lammps_gui
    Howto_moltemplate
+   Howto_python
    Howto_pylammps
    Howto_wsl
 

doc/src/Howto_barostat.rst

@@ -10,20 +10,21 @@ and/or pressure (P) is specified by the user, and the thermostat or
 barostat attempts to equilibrate the system to the requested T and/or
 P.
 
-Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Two
+Barostatting in LAMMPS is performed by :doc:`fixes <fix>`.  Three
 barostatting methods are currently available: Nose-Hoover (npt and
-nph) and Berendsen:
+nph), Berendsen, and various linear controllers in deform/pressure:
 
 * :doc:`fix npt <fix_nh>`
 * :doc:`fix npt/sphere <fix_npt_sphere>`
 * :doc:`fix npt/asphere <fix_npt_asphere>`
 * :doc:`fix nph <fix_nh>`
 * :doc:`fix press/berendsen <fix_press_berendsen>`
+* :doc:`fix deform/pressure <fix_deform_pressure>`
 
 The :doc:`fix npt <fix_nh>` commands include a Nose-Hoover thermostat
 and barostat.  :doc:`Fix nph <fix_nh>` is just a Nose/Hoover barostat;
-it does no thermostatting.  Both :doc:`fix nph <fix_nh>` and :doc:`fix press/berendsen <fix_press_berendsen>` can be used in conjunction
-with any of the thermostatting fixes.
+it does no thermostatting.  The fixes :doc:`nph <fix_nh>`, :doc:`press/berendsen <fix_press_berendsen>`, and :doc:`deform/pressure <fix_deform_pressure>`
+can be used in conjunction with any of the thermostatting fixes.
 
 As with the :doc:`thermostats <Howto_thermostat>`, :doc:`fix npt <fix_nh>`
 and :doc:`fix nph <fix_nh>` only use translational motion of the
@@ -44,9 +45,9 @@ a temperature or pressure compute to a barostatting fix.
 .. note::
 
    As with the thermostats, the Nose/Hoover methods (:doc:`fix npt <fix_nh>` and :doc:`fix nph <fix_nh>`) perform time integration.
-   :doc:`Fix press/berendsen <fix_press_berendsen>` does NOT, so it should
-   be used with one of the constant NVE fixes or with one of the NVT
-   fixes.
+   :doc:`Fix press/berendsen <fix_press_berendsen>` and :doc:`fix deform/pressure <fix_deform_pressure>`
+   do NOT, so they should be used with one of the constant NVE fixes or with
+   one of the NVT fixes.
 
 Thermodynamic output, which can be setup via the
 :doc:`thermo_style <thermo_style>` command, often includes pressure

doc/src/Howto_bpm.rst

@@ -42,12 +42,14 @@ such as those created by pouring grains using :doc:`fix pour
 
 ----------
 
-Currently, there are two types of bonds included in the BPM package. The
+Currently, there are three types of bonds included in the BPM package. The
 first bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies
 pairwise, central body forces. Point particles must have :doc:`bond atom
 style <atom_style>` and may be thought of as nodes in a spring
 network. An optional multibody term can be used to adjust the network's
-Poisson's ratio. Alternatively, the second bond style, :doc:`bond bpm/rotational
+Poisson's ratio. The :doc:`bpm/spring/plastic <bond_bpm_spring_plastic>`
+bond style is similar except it adds a plastic yield strain.
+Alternatively, the third bond style, :doc:`bond bpm/rotational
 <bond_bpm_rotational>`, resolves tangential forces and torques arising
 with the shearing, bending, and twisting of the bond due to rotation or
 displacement of particles.  Particles are similar to those used in the

doc/src/Howto_bulk2slab.rst

@@ -0,0 +1,160 @@
+===========================
+Convert bulk system to slab
+===========================
+
+A regularly encountered simulation problem is how to convert a bulk
+system that has been run for a while to equilibrate into a slab system
+with some vacuum space and free surfaces.  The challenge here is that
+one cannot just change the box dimensions with the :doc:`change_box
+command <change_box>` or edit the box boundaries in a data file because
+some atoms will have non-zero image flags from diffusing around.
+
+Changing the box dimensions results in an undesired displacement of
+those atoms, since the image flags indicate how many times the box
+length in x-, y-, or z-direction needs to be added or subtracted to get
+the "unwrapped" coordinates.  By changing the box dimension this
+distance is changed and thus those atoms move unphysically relative to
+their neighbors with zero image flags.  Setting image flags forcibly to
+zero creates problems because that could break apart molecules by having
+one atom of a bond on the top of the system and the other at the bottom.
+
+.. _bulk2slab:
+.. figure:: JPG/rhodo-both.jpg
+   :figwidth: 80%
+   :figclass: align-center
+
+   Snapshots of the bulk Rhodopsin in lipid layer and water system (right)
+   and the generated slab geometry (left)
+
+.. admonition:: Disclaimer
+   :class: note
+
+   The following workflow will work for many bulk systems, but not all.
+   Some systems cannot be converted (e.g. polymers with bonds to the
+   same molecule across periodic boundaries, sometimes called "infinite
+   polymers").  The amount of vacuum that needs to be added depends on
+   the length of the molecules where the system is split (the example
+   here splits where there is water with short molecules).  In some
+   cases, the system may need to be re-centered in the box first using
+   the :doc:`displace_atoms command <displace_atoms>`.  Also, the time
+   spent on strong thermalization and equilibration will depend on the
+   specific system and its thermodynamic conditions.
+
+Below is a suggested workflow using the :doc:`Rhodopsin benchmark input
+<Speed_bench>` for demonstration.  The figure shows the state *before*
+the procedure on the left (with unwrapped atoms that have diffused out
+of the box) and *after* on the right (with the vacuum added above and
+below).  The procedure is implemented by modifying a copy of the
+``in.rhodo`` input file.  The first lines up to and including the
+:doc:`read_data command <read_data>` remain unchanged.  Then we insert
+the following lines to add vacuum to the z direction above and below the
+system:
+
+.. code-block:: LAMMPS
+
+   variable       delta index 10.0
+   reset_atoms    image all
+   write_dump     all custom rhodo-unwrap.lammpstrj id xu yu zu
+   change_box     all z final $(zlo-2.0*v_delta) $(zhi+2.0*v_delta) &
+                      boundary p p f
+   read_dump      rhodo-unwrap.lammpstrj 0 x y z box no replace yes
+   kspace_modify  slab 3.0
+
+Specifically, the :doc:`variable delta <variable>` (set to 10.0)
+represents a distance that determines the amount of vacuum added: we add
+twice its value in each direction to the z-dimension; thus in total
+:math:`40 \AA` get added.  The :doc:`reset_atoms image all
+<reset_atoms>` command shall reset any image flags to become either 0 or
+:math:`\pm 1` and thus have the minimum distance from the center of the
+simulation box, but the correct relative distance for bonded atoms.
+
+The :doc:`write_dump command <write_dump>` then writes out the resulting
+*unwrapped* coordinates of the system.  After expanding the box,
+coordinates that were outside the box should now be inside and the
+unwrapped coordinates will become "wrapped", while atoms outside the
+periodic boundaries will be wrapped back into the box and their image
+flags in those directions restored.
+
+The :doc:`change_box command <change_box>` adds the desired
+distance to the low and high box boundary in z-direction and then changes
+the :doc:`boundary to "p p f" <boundary>` which will force the image
+flags in z-direction to zero and create an undesired displacement for
+the atoms with non-zero image flags.
+
+With the :doc:`read_dump command <read_dump>` we read back and replace
+partially incorrect coordinates with the previously saved, unwrapped
+coordinates.  It is important to ignore the box dimensions stored in the
+dump file.  We want to preserve the expanded box.  Finally, we turn on
+the slab correction for the PPPM long-range solver with the
+:doc:`kspace_modify command <kspace_modify>` as required when using a
+long range Coulomb solver for non-periodic z-dimension.
+
+Next we replace the :doc:`fix npt command <fix_nh>` with:
+
+.. code-block:: LAMMPS
+
+   fix            2 nvt temp 300.0 300.0 10.0
+
+We now have an open system and thus the adjustment of the cell in
+z-direction is no longer required.  Since splitting the bulk water
+region where the vacuum is inserted, creates surface atoms with high
+potential energy, we reduce the thermostat time constant from 100.0 to
+10.0 to remove excess kinetic energy resulting from that change faster.
+
+Also the high potential energy of the surface atoms can cause that some
+of them are ejected from the slab.  In order to suppress that, we add
+soft harmonic walls to push back any atoms that want to leave the slab.
+To determine the position of the wall, we first need to to determine the
+extent of the atoms in z-direction and then place the harmonic walls
+based on that information:
+
+.. code-block:: LAMMPS
+
+   compute         zmin all reduce min z
+   compute         zmax all reduce max z
+   thermo_style    custom zlo c_zmin zhi c_zmax
+   run             0 post no
+   fix             3 all wall/harmonic zhi $(c_zmax+v_delta) 10.0 0.0 ${delta} &
+                                       zlo $(c_zmin-v_delta) 10.0 0.0 ${delta}
+
+The two :doc:`compute reduce <compute_reduce>` command determine the
+minimum and maximum z-coordinate across all atoms.  In order to trigger
+the execution of the compute commands we need to "consume" them.  This
+is done with the :doc:`thermo_style custom <thermo_style>` command
+followed by the :doc:`run 0 <run>` command.  This avoids and error
+accessing the min/max values determined by the compute commands to
+compute the location of the wall in lower and upper direction.  This
+uses the previously defined *delta* variable to determine the distance
+of the wall from the extent of the system and the cutoff for the wall
+interaction.  This way only atoms that move beyond the min/max values in
+z-direction will experience a restoring force, nudging them back to the
+slab.  The force constant of :math:`10.0 \frac{\mathrm{kcal/mol}}{\AA}`
+was determined empirically.
+
+Adding these "restoring" soft walls assist in making the free surfaces
+above and below the slab flat, instead of having rugged or ondulated
+surfaces.  The impact of the walls can be changed by adjusting the force
+constant, cutoff, and position of the wall.
+
+Finally, we replace the :doc:`run 100 <run>` of the original input with:
+
+.. code-block:: LAMMPS
+
+   run             1000 post no
+
+   unfix           3
+   fix             2 all nvt temp 300.0 300.0 100.0
+   run             1000 post no
+
+   write_data      data.rhodo-slab
+
+This runs the system converted to a slab first for 1000 MD steps using
+the walls and stronger Nose-Hoover thermostat.  Then the walls are
+removed with :doc:`unfix 3 <unfix>` and the thermostat time constant
+reset to 100.0 and the system run for another 1000 steps.  Finally the
+resulting slab geometry is written to a new data file
+``data.rhodo-slab`` with a :doc:`write_data command <write_data>`.  The
+number of MD steps required to reach a proper equilibrium state is very
+likely larger.  The number of 1000 steps (corresponding to 2
+picoseconds) was chosen for demonstration purposes, so that the
+procedure can be easily and quickly tested.

doc/src/Howto_cmake.rst

@@ -56,7 +56,7 @@ using a shell like Bash or Zsh.
    Visual Studio IDE with the bundled CMake or from the Windows command prompt using
    a separately installed CMake package, both using the native Microsoft Visual C++
    compilers and (optionally) the Microsoft MPI SDK.  This tutorial, however, only
-   covers unix-like command line interfaces.
+   covers unix-like command-line interfaces.
 
 We also assume that you have downloaded and unpacked a recent LAMMPS source code package
 or used Git to create a clone of the LAMMPS sources on your compilation machine.
@@ -277,7 +277,7 @@ Setting options
 ---------------
 
 Options that enable, disable or modify settings are modified by setting
-the value of CMake variables. This is done on the command line with the
+the value of CMake variables. This is done on the command-line with the
 *-D* flag in the format ``-D VARIABLE=value``, e.g. ``-D
 CMAKE_BUILD_TYPE=Release`` or ``-D BUILD_MPI=on``.  There is one quirk:
 when used before the CMake directory, there may be a space between the
@@ -376,7 +376,7 @@ Using presets
 -------------
 
 Since LAMMPS has a lot of optional features and packages, specifying
-them all on the command line can be tedious. Or when selecting a
+them all on the command-line can be tedious. Or when selecting a
 different compiler toolchain, multiple options have to be changed
 consistently and that is rather error prone. Or when enabling certain
 packages, they require consistent settings to be operated in a
@@ -384,7 +384,7 @@ particular mode.  For this purpose, we are providing a selection of
 "preset files" for CMake in the folder ``cmake/presets``.  They
 represent a way to pre-load or override the CMake configuration cache by
 setting or changing CMake variables.  Preset files are loaded using the
-*-C* command line flag. You can combine loading multiple preset files or
+*-C* command-line flag. You can combine loading multiple preset files or
 change some variables later with additional *-D* flags.  A few examples:
 
 .. code-block:: bash

doc/src/Howto_github.rst

@@ -163,7 +163,7 @@ After everything is done, add the files to the branch and commit them:
    *git rm*, *git mv* for adding, removing, renaming individual files,
    respectively, and then *git commit* to finalize the commit.
    Carefully check all pending changes with *git status* before
-   committing them.  If you find doing this on the command line too
+   committing them.  If you find doing this on the command-line too
    tedious, consider using a GUI, for example the one included in git
    distributions written in Tk, i.e. use *git gui* (on some Linux
    distributions it may be required to install an additional package to
@@ -487,10 +487,10 @@ updates are back-ported from the *develop* branch to the *maintenance*
 branch and occasionally merged to *stable* as an update release.
 
 Furthermore, the naming of the release tags now follow the pattern
-"patch_<Day><Month><Year>" to simplify comparisons between releases.
-For stable releases additional "stable_<Day><Month><Year>" tags are
+"patch\_<Day><Month><Year>" to simplify comparisons between releases.
+For stable releases additional "stable\_<Day><Month><Year>" tags are
 applied and update releases are tagged with
-"stable_<Day><Month><Year>_update<Number>", Finally, all releases and
+"stable\_<Day><Month><Year>\_update<Number>", Finally, all releases and
 submissions are subject to automatic testing and code checks to make
 sure they compile with a variety of compilers and popular operating
 systems.  Some unit and regression testing is applied as well.

doc/src/Howto_lammps_gui.rst

@@ -20,8 +20,11 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
    (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
    Sur or later), and Windows (version 10 or later) :ref:`are available
    <lammps_gui_install>` for download.  Non-MPI LAMMPS executables (as
-   ``lmp``) for running LAMMPS from the command line and :doc:`some
+   ``lmp``) for running LAMMPS from the command-line and :doc:`some
    LAMMPS tools <Tools>` compiled executables are also included.
+   Also, the pre-compiled LAMMPS-GUI packages include the WHAM executables
+   from http://membrane.urmc.rochester.edu/content/wham/ for use with
+   LAMMPS tutorials.
 
    The source code for LAMMPS-GUI is included in the LAMMPS source code
    distribution and can be found in the ``tools/lammps-gui`` folder.  It
@@ -29,16 +32,16 @@ to the online LAMMPS documentation for known LAMMPS commands and styles.
    <Build_cmake>`.
 
 LAMMPS-GUI tries to provide an experience similar to what people
-traditionally would have running LAMMPS using a command line window and
+traditionally would have running LAMMPS using a command-line window and
 the console LAMMPS executable but just rolled into a single executable:
 
 - writing & editing LAMMPS input files with a text editor
-- run LAMMPS on those input file with selected command line flags
+- run LAMMPS on those input file with selected command-line flags
 - extract data from the created files and visualize it with and
   external software
 
 That procedure is quite effective for people proficient in using the
-command line, as that allows them to use tools for the individual steps
+command-line, as that allows them to use tools for the individual steps
 that they are most comfortable with.  In fact, it is often *required* to
 adopt this workflow when running LAMMPS simulations on high-performance
 computing facilities.
@@ -61,13 +64,18 @@ simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
 since you only need to learn how to use a single program for most tasks
 and thus time can be saved and people can focus on learning LAMMPS.
 The tutorials at https://lammpstutorials.github.io/ are specifically
-updated for use with LAMMPS-GUI.
+updated for use with LAMMPS-GUI and can their tutorial materials can
+be downloaded and loaded directly from the GUI.
 
 Another design goal is to keep the barrier low when replacing part of
 the functionality of LAMMPS-GUI with external tools.  That said, LAMMPS-GUI
 has some unique functionality that is not found elsewhere:
 
 - auto-adapting to features available in the integrated LAMMPS library
+- auto-completion for LAMMPS commands and options
+- context-sensitive online help
+- start and stop of simulations via mouse or keyboard
+- monitoring of simulation progress
 - interactive visualization using the :doc:`dump image <dump_image>`
   command with the option to copy-paste the resulting settings
 - automatic slide show generation from dump image out at runtime
@@ -100,10 +108,11 @@ MacOS 11 and later
 ^^^^^^^^^^^^^^^^^^
 
 After downloading the ``LAMMPS-macOS-multiarch-GUI-<version>.dmg``
-installer package, you need to double-click it and then, in the window
-that opens, drag the app bundle as indicated into the "Applications"
-folder.  The follow the instructions in the "README.txt" file to
-get access to the other included executables.
+application bundle disk image, you need to double-click it and then, in
+the window that opens, drag the app bundle as indicated into the
+"Applications" folder.  Afterwards, the disk image can be unmounted.
+Then follow the instructions in the "README.txt" file to get access to
+the other included command-line executables.
 
 Linux on x86\_64
 ^^^^^^^^^^^^^^^^
@@ -117,15 +126,25 @@ into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
 
 The second variant uses `flatpak <https://www.flatpak.org>`_ and
 requires the flatpak management and runtime software to be installed.
-After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
+After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``
 flatpak bundle, you can install it with ``flatpak install --user
-LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``.  After installation,
+LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``.  After installation,
 LAMMPS-GUI should be integrated into your desktop environment under
 "Applications > Science" but also can be launched from the console with
 ``flatpak run org.lammps.lammps-gui``.  The flatpak bundle also includes
 the console LAMMPS executable ``lmp`` which can be launched to run
-simulations with, for example: ``flatpak run --command=lmp
-org.lammps.lammps-gui -in in.melt``.
+simulations with, for example with:
+
+.. code-block:: sh
+
+   flatpak run --command=lmp org.lammps.lammps-gui -in in.melt
+
+Other bundled command-line executables are run the same way and can be
+listed with:
+
+.. code-block:: sh
+
+   ls $(flatpak info --show-location org.lammps.lammps-gui )/files/bin
 
 
 Compiling from Source
@@ -165,9 +184,9 @@ window is stored when exiting and restored when starting again.
 Opening Files
 ^^^^^^^^^^^^^
 
-The LAMMPS-GUI application can be launched without command line arguments
+The LAMMPS-GUI application can be launched without command-line arguments
 and then starts with an empty buffer in the *Editor* window.  If arguments
-are given LAMMPS will use first command line argument as the file name for
+are given LAMMPS will use first command-line argument as the file name for
 the *Editor* buffer and reads its contents into the buffer, if the file
 exists.  All further arguments are ignored.  Files can also be opened via
 the *File* menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
@@ -261,14 +280,21 @@ Output Window
 
 By default, when starting a run, an *Output* window opens that displays
 the screen output of the running LAMMPS calculation, as shown below.
-This text would normally be seen in the command line window.
+This text would normally be seen in the command-line window.
 
 .. image:: JPG/lammps-gui-log.png
    :align: center
    :scale: 50%
 
 LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
-updates the *Output* window regularly during a run.
+updates the *Output* window regularly during a run.  If there are any
+warnings or errors in the LAMMPS output, they are highlighted by using
+bold text colored in red.  There is a small panel at the bottom center
+of the *Output* window showing how many warnings and errors were
+detected and how many lines the entire output has.  By clicking on the
+button on the right with the warning symbol or by using the keyboard
+shortcut `Ctrl-N` (`Command-N` on macOS), you can jump to the next
+line with a warning or error.
 
 By default, the *Output* window is replaced each time a run is started.
 The runs are counted and the run number for the current run is displayed
@@ -398,7 +424,7 @@ below.
 Like for the *Output* and *Charts* windows, its content is continuously
 updated during a run.  It will show "(none)" if there are no variables
 defined.  Note that it is also possible to *set* :doc:`index style
-variables <variable>`, that would normally be set via command line
+variables <variable>`, that would normally be set via command-line
 flags, via the "Set Variables..." dialog from the *Run* menu.
 LAMMPS-GUI automatically defines the variable "gui_run" to the current
 value of the run counter.  That way it is possible to automatically
@@ -775,11 +801,11 @@ General Settings:
 
 - *Echo input to log:* when checked, all input commands, including
   variable expansions, are echoed to the *Output* window. This is
-  equivalent to using `-echo screen` at the command line.  There is no
+  equivalent to using `-echo screen` at the command-line.  There is no
   log *file* produced by default, since LAMMPS-GUI uses `-log none`.
 - *Include citation details:* when checked full citation info will be
   included to the log window.  This is equivalent to using `-cite
-  screen` on the command line.
+  screen` on the command-line.
 - *Show log window by default:* when checked, the screen output of a
   LAMMPS run will be collected in a log window during the run
 - *Show chart window by default:* when checked, the thermodynamic
@@ -828,7 +854,7 @@ Accelerators:
 
 This tab enables selection of an accelerator package for LAMMPS to use
 and is equivalent to using the `-suffix` and `-package` flags on the
-command line.  Only settings supported by the LAMMPS library and local
+command-line.  Only settings supported by the LAMMPS library and local
 hardware are available.  The `Number of threads` field allows setting
 the maximum number of threads for the accelerator packages that use
 threads.

doc/src/Howto_moltemplate.rst

@@ -2,14 +2,18 @@ Moltemplate Tutorial
 ====================
 
 In this tutorial, we are going to use the tool :ref:`Moltemplate
-<moltemplate>` to set up a classical molecular dynamic simulation using
-the :ref:`OPLS-AA force field <OPLSAA96>`. The first
-task is to describe an organic compound and create a complete input deck
-for LAMMPS. The second task is to map the OPLS-AA force field to a
-molecular sample created with an external tool, e.g. PACKMOL, and
-exported as a PDB file.  The files used in this tutorial can be found
-in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
-source code distribution.
+<Moltemplate1>` from https://moltemplate.org/ to set up a classical
+molecular dynamic simulation using the :ref:`OPLS-AA force field
+<oplsaa2024>`. The first task is to describe an organic compound and
+create a complete input deck for LAMMPS.  The second task is to use
+moltemplate to build a polymer.  The third task is to map the OPLS-AA
+force field to a molecular sample created with an external tool,
+e.g. PACKMOL, and exported as a PDB file.  The files used in this
+tutorial can be found in the ``tools/moltemplate/tutorial-files`` folder
+of the LAMMPS source code distribution.
+
+Many more examples can be found here: https://moltemplate.org/examples.html
+
 
 Simulating an organic solvent
 """""""""""""""""""""""""""""
@@ -17,14 +21,13 @@ Simulating an organic solvent
 This example aims to create a cubic box of the organic solvent
 formamide.
 
-The first step is to create a molecular topology in the
-LAMMPS-template (LT) file format representing a single molecule, which
-will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
+The first step is to create a molecular topology in the LAMMPS-template
+(LT) file format representing a single molecule, which will be
+stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
 This command states that the object ``_FAM`` is based on an existing
 object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
 definitions, partial charges, masses and bond-angle rules for many organic
 and biological compounds.
-
 The atomic structure is the starting point to populate the command
 ``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
 LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
@@ -36,21 +39,23 @@ to the ``molID``, except that the same variable is used for the whole
 molecule. The atom types are assigned using ``@``-type variables. The
 assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
 the OPLS-AA atom types defined in the "In Charges" section of the file
-``oplsaa.lt``, looking for a reasonable match with the description of the atom.
+``oplsaa2024.lt``, looking for a reasonable match with the description of the atom.
 The resulting file (``formamide.lt``) follows:
 
 .. code-block:: bash
 
+   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt  # defines OPLSAA
+
    _FAM inherits OPLSAA {
 
      # atomID    molID  atomType  charge  coordX  coordY  coordZ
      write('Data Atoms') {
-       $atom:C00 $mol   @atom:177  0.00    0.100   0.490   0.0
-       $atom:O01 $mol   @atom:178  0.00    1.091  -0.250   0.0
-       $atom:N02 $mol   @atom:179  0.00   -1.121  -0.181   0.0
-       $atom:H03 $mol   @atom:182  0.00   -2.013   0.272   0.0
-       $atom:H04 $mol   @atom:182  0.00   -1.056  -1.190   0.0
-       $atom:H05 $mol   @atom:221  0.00    0.144   1.570   0.0
+       $atom:C00  $mol  @atom:235  0.00    0.100   0.490   0.0
+       $atom:O01  $mol  @atom:236  0.00    1.091  -0.250   0.0
+       $atom:N02  $mol  @atom:237  0.00   -1.121  -0.181   0.0
+       $atom:H03  $mol  @atom:240  0.00   -2.013   0.272   0.0
+       $atom:H04  $mol  @atom:240  0.00   -1.056  -1.190   0.0
+       $atom:H05  $mol  @atom:279  0.00    0.144   1.570   0.0
      }
 
      # A list of the bonds in the molecule:
@@ -64,16 +69,17 @@ The resulting file (``formamide.lt``) follows:
      }
    }
 
-You don't have to specify the charge in this example because they will
-be assigned according to the atom type. Analogously, only a
-"Data Bond List" section is needed as the atom type will determine the
-bond type. The other bonded interactions (e.g. angles,
-dihedrals, and impropers) will be automatically generated by
+You don't have to specify the charge in this example because the OPLSAA
+force-field assigns charge according to the atom type.  (This is not true
+when using other force fields.)  A "Data Bond List" section is needed as
+the atom type will determine the bond type. The other bonded interactions
+(e.g. angles, dihedrals, and impropers) will be automatically generated by
 Moltemplate.
 
-If the simulation is non-neutral, or Moltemplate complains that you have
-missing bond, angle, or dihedral types, this means at least one of your
-atom types is incorrect.
+If the simulation is not charge-neutral, or Moltemplate complains that
+you have missing bond, angle, or dihedral types, this probably means that
+at least one of your atom types is incorrect (or that perhaps there is no
+suitable atom type currently defined in the ``oplsaa2024.lt`` file).
 
 The second step is to create a master file with instructions to build a
 starting structure and the LAMMPS commands to run an NPT simulation. The
@@ -81,11 +87,9 @@ master file (``solv_01.lt``) follows:
 
 .. code-block:: bash
 
-   # Import the force field.
-   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
-   import formamide.lt # after oplsaa.lt, as it depends on it.
+   import formamide.lt  # Defines "_FAM" and OPLSAA
 
-   # Create the input sample.
+   # Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6
    solv = new _FAM [5].move( 4.6, 0, 0)
                    [5].move( 0, 4.6, 0)
                    [5].move( 0, 0, 4.6)
@@ -98,8 +102,11 @@ master file (``solv_01.lt``) follows:
     -11.5 11.5 zlo zhi
    }
 
-   # Create an input deck for LAMMPS.
-   write_once("In Init"){
+   # Note: The lines below in the "In Run" section are often omitted.
+
+   write_once("In Run"){
+    # Create an input deck for LAMMPS.
+    # Run an NPT simulation.
     # Input variables.
     variable run    string solv_01   # output name
     variable ts     equal  1         # timestep
@@ -109,12 +116,6 @@ master file (``solv_01.lt``) follows:
     variable equi   equal  5000      # Equilibration steps
     variable prod   equal  30000     # Production steps
 
-    # PBC (set them before the creation of the box).
-    boundary p p p
-   }
-
-   # Run an NPT simulation.
-   write_once("In Run"){
     # Derived variables.
     variable tcouple equal \$\{ts\}*100
     variable pcouple equal \$\{ts\}*1000
@@ -143,7 +144,7 @@ master file (``solv_01.lt``) follows:
     unfix NPT
    }
 
-The first two commands insert the content of files ``oplsaa.lt`` and
+The first two commands insert the content of files ``oplsaa2024.lt`` and
 ``formamide.lt`` into the master file. At this point, we can use the
 command ``solv = new _FAM [N]`` to create N copies of a molecule of type
 ``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
@@ -153,21 +154,37 @@ the sample was created from scratch, we also specify the simulation box
 size in the "Data Boundary" section.
 
 The LAMMPS setting for the force field are specified in the file
-``oplsaa.lt`` and are written automatically in the input deck. We also
+``oplsaa2024.lt`` and are written automatically in the input deck. We also
 specify the boundary conditions and a set of variables in
-the "In Init" section. The remaining commands to run an NPT simulation
+the "In Init" section.
+
+The remaining commands to run an NPT simulation
 are written in the "In Run" section. Note that in this script, LAMMPS
 variables are protected with the escape character ``\`` to distinguish
 them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
 variable that is written in the input deck as ``${run}``.
 
+(Note: Moltemplate can be slow to run, so you need to change you run
+settings frequently, I recommended moving those commands (from "In Run")
+out of your .lt files and into a separate file.  Moltemplate creates a
+file named ``run.in.EXAMPLE`` for this purpose.  You can put your run
+settings and fixes that file and then invoke LAMMPS using
+``mpirun -np 4 lmp -in run.in.EXAMPLE`` instead.)
+
+
 Compile the master file with:
 
 .. code-block:: bash
 
-   moltemplate.sh -overlay-all solv_01.lt
+   moltemplate.sh solv_01.lt
+   cleanup_moltemplate.sh   # <-- optional: see below
 
-And execute the simulation with the following:
+(Note: The optional "cleanup_moltemplate.sh" command deletes
+unused atom types, which sometimes makes LAMMPS run faster.
+But it does not work with many-body pair styles or dreiding-style h-bonds.
+Fortunately most force fields, including OPLSAA, don't use those features.)
+
+Then execute the simulation with the following:
 
 .. code-block:: bash
 
@@ -180,15 +197,116 @@ And execute the simulation with the following:
    Snapshot of the sample at the beginning and end of the simulation.
    Rendered with Ovito.
 
+
+Building a simple polymer
+"""""""""""""""""""""""""
+Moltemplate is particularly useful for building polymers (and other molecules
+with sub-units).  As an simple example, consider butane:
+
+.. figure:: JPG/butane.jpg
+
+The ``butane.lt`` file below defines Butane as a polymer containing
+4 monomers (of type ``CH3``, ``CH2``, ``CH2``, ``CH3``).
+
+.. code-block:: bash
+
+   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt  # defines OPLSAA
+
+   CH3 inherits OPLSAA {
+
+     # atomID    molID   atomType  charge   coordX   coordY    coordZ
+     write("Data Atoms") {
+       $atom:c  $mol:... @atom:54   0.0   0.000000  0.4431163  0.000000
+       $atom:h1 $mol:... @atom:60   0.0   0.000000  1.0741603  0.892431
+       $atom:h2 $mol:... @atom:60   0.0   0.000000  1.0741603 -0.892431
+       $atom:h3 $mol:... @atom:60   0.0  -0.892431 -0.1879277  0.000000
+     }
+     # (Using "$mol:..." indicates this object ("CH3") is part of a larger
+     #  molecule. Moltemplate will share the molecule-ID with that molecule.)
+
+     # A list of the bonds within the "CH3" molecular sub-unit:
+     # BondID   AtomID1   AtomID2
+     write('Data Bond List') {
+       $bond:ch1 $atom:c $atom:h1
+       $bond:ch2 $atom:c $atom:h2
+       $bond:ch3 $atom:c $atom:h3
+     }
+   }
+
+   CH2 inherits OPLSAA {
+
+     # atomID    molID   atomType  charge   coordX   coordY    coordZ
+     write("Data Atoms") {
+       $atom:c  $mol:... @atom:57   0.0   0.000000  0.4431163  0.000000
+       $atom:h1 $mol:... @atom:60   0.0   0.000000  1.0741603  0.892431
+       $atom:h2 $mol:... @atom:60   0.0   0.000000  1.0741603 -0.892431
+     }
+
+     # A list of the bonds within the "CH2" molecular sub-unit:
+     # BondID   AtomID1   AtomID2
+     write('Data Bond List') {
+       $bond:ch1 $atom:c $atom:h1
+       $bond:ch2 $atom:c $atom:h2
+     }
+   }
+
+   Butane inherits OPLSAA {
+
+     create_var {$mol}  # optional:force all monomers to share the same molecule-ID
+
+     # - Create 4 monomers
+     # - Move them along the X axis using ".move()",
+     # - Rotate them 180 degrees with respect to the previous monomer
+     monomer1 = new CH3
+     monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0)
+     monomer3 = new CH2.move(2.5066446,0,0)
+     monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0)
+
+     # A list of the bonds connecting different monomers together:
+     write('Data Bond List') {
+       $bond:b1  $atom:monomer1/c $atom:monomer2/c
+       $bond:b2  $atom:monomer2/c $atom:monomer3/c
+       $bond:b3  $atom:monomer3/c $atom:monomer4/c
+     }
+   }
+
+Again, you don't have to specify the charge in this example because OPLSAA
+assigns charges according to the atom type.
+
+This ``Butane`` object is a molecule which can be used anywhere other molecules
+can be used.  (You can arrange ``Butane`` molecules on a lattice, as we did previously.
+You can also modify individual butane molecules by adding or deleting atoms or bonds.
+You can add bonds between specific butane molecules or use ``Butane`` as a
+sub-unit to define even larger molecules.  See the moltemplate manual for details.)
+
+
+
+
+
+
+How to build a complex polymer
+""""""""""""""""""""""""""""""""""""""""""
+A similar procedure can be used to create more complicated polymers,
+such as the NIPAM polymer example shown below.  For details, see:
+
+https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/NIPAM_polymer+water+ions
+
+
+
+
 Mapping an existing structure
 """""""""""""""""""""""""""""
 
 Another helpful way to use Moltemplate is mapping an existing molecular
-sample to a force field. This is useful when a complex sample is
-assembled from different simulations or created with specialized
-software (e.g. PACKMOL). As in the previous example, all molecular
-species in the sample must be defined using single-molecule Moltemplate
-objects.  For this example, we use a short polymer in a box containing
+sample to a force field. This is useful when a complex sample is assembled
+from different simulations or created with specialized software (e.g. PACKMOL).
+(Note: The previous link shows how to build this entire system from scratch
+using only moltemplate.  However here we will assume instead that we obtained
+a PDB file for this system using PACKMOL.)
+
+As in the previous examples, all molecular species in the sample
+are defined using single-molecule Moltemplate objects.
+For this example, we use a short polymer in a box containing
 water molecules and ions in the PDB file ``model.pdb``.
 
 It is essential to understand that the order of atoms in the PDB file
@@ -246,25 +364,25 @@ The resulting master LT file defining short annealing at a fixed volume
 .. code-block:: bash
 
    # Use the OPLS-AA force field for all species.
-   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
+   import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
    import PolyNIPAM.lt
 
    # Define the SPC water and ions as in the OPLS-AA
    Ca inherits OPLSAA {
      write("Data Atoms"){
-       $atom:a1  $mol:. @atom:354 0.0  0.00000 0.00000 0.000000
+       $atom:a1  $mol:. @atom:412 0.0  0.00000 0.00000 0.000000
      }
    }
    Cl inherits OPLSAA {
      write("Data Atoms"){
-       $atom:a1  $mol:. @atom:344 0.0  0.00000 0.00000 0.000000
+       $atom:a1  $mol:. @atom:401 0.0  0.00000 0.00000 0.000000
      }
    }
    SPC inherits OPLSAA {
      write("Data Atoms"){
-       $atom:O  $mol:. @atom:76 0.  0.0000000 0.00000 0.000000
-       $atom:H1 $mol:. @atom:77 0.  0.8164904 0.00000 0.5773590
-       $atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
+       $atom:O  $mol:. @atom:9991 0.  0.0000000 0.00000 0.0000000
+       $atom:H1 $mol:. @atom:9990 0.  0.8164904 0.00000 0.5773590
+       $atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
      }
      write("Data Bond List") {
        $bond:OH1 $atom:O $atom:H1
@@ -285,8 +403,15 @@ The resulting master LT file defining short annealing at a fixed volume
      0 26 zlo zhi
    }
 
-   # Define the input variables.
    write_once("In Init"){
+     boundary p p p  # "p p p" is the default. This line is optional.
+     neighbor 3 bin  # (This line is also optional in this example.)
+   }
+
+   # Note: The lines below in the "In Run" section are often omitted.
+
+   # Run an NVT simulation.
+   write_once("In Run"){
      # Input variables.
      variable run    string sample01  # output name
      variable ts     equal  2         # timestep
@@ -294,13 +419,6 @@ The resulting master LT file defining short annealing at a fixed volume
      variable p      equal  1.        # equilibrium pressure
      variable equi   equal  30000     # equilibration steps
 
-     # PBC (set them before the creation of the box).
-     boundary p p p
-     neighbor        3 bin
-   }
-
-   # Run an NVT simulation.
-   write_once("In Run"){
      # Set the output.
      thermo          1000
      thermo_style    custom step etotal evdwl ecoul elong ebond eangle &
@@ -314,8 +432,8 @@ The resulting master LT file defining short annealing at a fixed volume
      write_data \$\{run\}.min
 
      # Set the constrains.
-     group watergroup type @atom:76 @atom:77
-     fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
+     group watergroup type @atom:9991 @atom:9990
+     fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH
 
      # Short annealing.
      timestep        \$\{ts\}
@@ -327,7 +445,7 @@ The resulting master LT file defining short annealing at a fixed volume
 
 
 In this example, the water model is SPC and it is defined in the
-``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``.  For
+``oplsaa2024.lt`` file with atom types ``@atom:9991`` and ``@atom:9990``.  For
 water we also use the ``group`` and ``fix shake`` commands with
 Moltemplate ``@``-type variables, to ensure consistency with the
 numerical values assigned during compilation. To identify the bond and
@@ -336,19 +454,20 @@ are:
 
 .. code-block:: bash
 
-   replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
-   replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
+   replace{ @atom:9991 @atom:9991_bspcO_aspcO_dspcO_ispcO }
+   replace{ @atom:9990 @atom:9990_bspcH_aspcH_dspcH_ispcH }
 
 From which we can identify the following "Data Bonds By Type":
-``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
-"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
-@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
+``@bond:spcO_spcH @atom:*_bspcO*_a*_d*_i* @atom:*_bspcH*_a*_d*_i*``
+and "Data Angles By Type":
+``@angle:spcH_spcO_spcH @atom:*_b*_aspcH*_d*_i* @atom:*_b*_aspcO*_d*_i* @atom:*_b*_aspcH*_d*_i*``
 
 Compile the master file with:
 
 .. code-block:: bash
 
-   moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
+   moltemplate.sh -pdb model.pdb sample01.lt
+   cleanup_moltemplate.sh
 
 And execute the simulation with the following:
 
@@ -363,8 +482,13 @@ And execute the simulation with the following:
    Sample visualized with Ovito loading the trajectory into the DATA
    file written after minimization.
 
+
 ------------
 
-.. _OPLSAA96:
+.. _oplsaa2024:
 
-**(OPLS-AA)**  Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
+**(OPLS-AA)**  Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024).
+
+.. _Moltemplate1:
+
+**(Moltemplate)**  Jewett et al., J. Mol. Biol., 433(11), 166841 (2021)

doc/src/Howto_peri.rst

@@ -197,7 +197,7 @@ The LPS model has a force scalar state
 .. math::
 
    \underline{t} = \frac{3K\theta}{m}\underline{\omega}\,\underline{x} +
-   \alpha \underline{\omega}\,\underline{e}^{\rm d}, \qquad\qquad\textrm{(3)}
+   \alpha \underline{\omega}\,\underline{e}^\mathrm{d}, \qquad\qquad\textrm{(3)}
 
 with :math:`K` the bulk modulus and :math:`\alpha` related to the shear
 modulus :math:`G` as
@@ -242,14 +242,14 @@ scalar state are defined, respectively, as
 
 .. math::
 
-   \underline{e}^{\rm i}=\frac{\theta \underline{x}}{3}, \qquad
-   \underline{e}^{\rm d} = \underline{e}- \underline{e}^{\rm i},
+   \underline{e}^\mathrm{i}=\frac{\theta \underline{x}}{3}, \qquad
+   \underline{e}^\mathrm{d} = \underline{e}- \underline{e}^\mathrm{i},
 
 
 where the arguments of the state functions and the vectors on which they
 operate are omitted for simplicity. We note that the LPS model is linear
 in the dilatation :math:`\theta`, and in the deviatoric part of the
-extension :math:`\underline{e}^{\rm d}`.
+extension :math:`\underline{e}^\mathrm{d}`.
 
 .. note::
 
@@ -738,8 +738,8 @@ command.
 
 This can be done, for example, by using the built-in visualizer of the
 :doc:`dump image or dump movie <dump_image>` command to create snapshot
-images or a movie. Below are example command lines for using dump image
-with the :ref:`example listed below <periexample>` and a set of images
+images or a movie. Below are example command for using dump image with
+the :ref:`example listed below <periexample>` and a set of images
 created for steps 300, 600, and 2000 this way.
 
 .. code-block:: LAMMPS

doc/src/Howto_pylammps.rst

@@ -1,564 +1,6 @@
 PyLammps Tutorial
 =================
 
-.. contents::
-
-Overview
---------
-
-:py:class:`PyLammps <lammps.PyLammps>` is a Python wrapper class for
-LAMMPS which can be created on its own or use an existing
-:py:class:`lammps Python <lammps.lammps>` object.  It creates a simpler,
-more "pythonic" interface to common LAMMPS functionality, in contrast to
-the :py:class:`lammps <lammps.lammps>` wrapper for the LAMMPS :ref:`C
-language library interface API <lammps_c_api>` which is written using
-`Python ctypes <ctypes_>`_.  The :py:class:`lammps <lammps.lammps>`
-wrapper is discussed on the :doc:`Python_head` doc page.
-
-Unlike the flat `ctypes <ctypes_>`_ interface, PyLammps exposes a
-discoverable API.  It no longer requires knowledge of the underlying C++
-code implementation.  Finally, the :py:class:`IPyLammps
-<lammps.IPyLammps>` wrapper builds on top of :py:class:`PyLammps
-<lammps.PyLammps>` and adds some additional features for `IPython
-integration <ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for
-embedded visualization output from :doc:`dump style image <dump_image>`.
-
-.. _ctypes: https://docs.python.org/3/library/ctypes.html
-.. _ipython: https://ipython.org/
-.. _jupyter: https://jupyter.org/
-
-Comparison of lammps and PyLammps interfaces
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-lammps.lammps
-"""""""""""""
-
-* uses `ctypes <ctypes_>`_
-* direct memory access to native C++ data with optional support for NumPy arrays
-* provides functions to send and receive data to LAMMPS
-* interface modeled after the LAMMPS :ref:`C language library interface API <lammps_c_api>`
-* requires knowledge of how LAMMPS internally works (C pointers, etc)
-* full support for running Python with MPI using `mpi4py <https://mpi4py.readthedocs.io>`_
-* no overhead from creating a more Python-like interface
-
-lammps.PyLammps
-"""""""""""""""
-
-* higher-level abstraction built on *top* of the original :py:class:`ctypes based interface <lammps.lammps>`
-* manipulation of Python objects
-* communication with LAMMPS is hidden from API user
-* shorter, more concise Python
-* better IPython integration, designed for quick prototyping
-* designed for serial execution
-* additional overhead from capturing and parsing the LAMMPS screen output
-
-Quick Start
------------
-
-System-wide Installation
-^^^^^^^^^^^^^^^^^^^^^^^^
-
-Step 1: Building LAMMPS as a shared library
-"""""""""""""""""""""""""""""""""""""""""""
-
-To use LAMMPS inside of Python it has to be compiled as shared
-library. This library is then loaded by the Python interface. In this
-example we enable the MOLECULE package and compile LAMMPS with PNG, JPEG
-and FFMPEG output support enabled.
-
-Step 1a: For the CMake based build system, the steps are:
-
-.. code-block:: bash
-
-   mkdir $LAMMPS_DIR/build-shared
-   cd  $LAMMPS_DIR/build-shared
-
-   # MPI, PNG, Jpeg, FFMPEG are auto-detected
-   cmake ../cmake -DPKG_MOLECULE=yes -DBUILD_LIB=yes -DBUILD_SHARED_LIBS=yes
-   make
-
-Step 1b: For the legacy, make based build system, the steps are:
-
-.. code-block:: bash
-
-   cd $LAMMPS_DIR/src
-
-   # add packages if necessary
-   make yes-MOLECULE
-
-   # compile shared library using Makefile
-   make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
-
-Step 2: Installing the LAMMPS Python package
-""""""""""""""""""""""""""""""""""""""""""""
-
-PyLammps is part of the lammps Python package. To install it simply install
-that package into your current Python installation with:
-
-.. code-block:: bash
-
-   make install-python
-
-.. note::
-
-   Recompiling the shared library requires re-installing the Python package
-
-Installation inside of a virtualenv
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-You can use virtualenv to create a custom Python environment specifically tuned
-for your workflow.
-
-Benefits of using a virtualenv
-""""""""""""""""""""""""""""""
-
-* isolation of your system Python installation from your development installation
-* installation can happen in your user directory without root access (useful for HPC clusters)
-* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
-* you can even install specific old versions of a package if necessary
-
-**Prerequisite (e.g. on Ubuntu)**
-
-.. code-block:: bash
-
-   apt-get install python-virtualenv
-
-Creating a virtualenv with lammps installed
-"""""""""""""""""""""""""""""""""""""""""""
-
-.. code-block:: bash
-
-   # create virtualenv named 'testing'
-   virtualenv $HOME/python/testing
-
-   # activate 'testing' environment
-   source $HOME/python/testing/bin/activate
-
-Now configure and compile the LAMMPS shared library as outlined above.
-When using CMake and the shared library has already been build, you
-need to re-run CMake to update the location of the python executable
-to the location in the virtual environment with:
-
-.. code-block:: bash
-
-   cmake . -DPython_EXECUTABLE=$(which python)
-
-   # install LAMMPS package in virtualenv
-   (testing) make install-python
-
-   # install other useful packages
-   (testing) pip install matplotlib jupyter mpi4py
-
-   ...
-
-   # return to original shell
-   (testing) deactivate
-
-Creating a new instance of PyLammps
------------------------------------
-
-To create a PyLammps object you need to first import the class from the lammps
-module. By using the default constructor, a new *lammps* instance is created.
-
-.. code-block:: python
-
-   from lammps import PyLammps
-   L = PyLammps()
-
-You can also initialize PyLammps on top of this existing *lammps* object:
-
-.. code-block:: python
-
-   from lammps import lammps, PyLammps
-   lmp = lammps()
-   L = PyLammps(ptr=lmp)
-
-Commands
---------
-
-Sending a LAMMPS command with the existing library interfaces is done using
-the command method of the lammps object instance.
-
-For instance, let's take the following LAMMPS command:
-
-.. code-block:: LAMMPS
-
-   region box block 0 10 0 5 -0.5 0.5
-
-In the original interface this command can be executed with the following
-Python code if *L* was a lammps instance:
-
-.. code-block:: python
-
-   L.command("region box block 0 10 0 5 -0.5 0.5")
-
-With the PyLammps interface, any command can be split up into arbitrary parts
-separated by white-space, passed as individual arguments to a region method.
-
-.. code-block:: python
-
-   L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
-
-Note that each parameter is set as Python literal floating-point number. In the
-PyLammps interface, each command takes an arbitrary parameter list and transparently
-merges it to a single command string, separating individual parameters by white-space.
-
-The benefit of this approach is avoiding redundant command calls and easier
-parameterization. In the original interface parameterization needed to be done
-manually by creating formatted strings.
-
-.. code-block:: python
-
-   L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
-
-In contrast, methods of PyLammps accept parameters directly and will convert
-them automatically to a final command string.
-
-.. code-block:: python
-
-   L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
-
-System state
-------------
-
-In addition to dispatching commands directly through the PyLammps object, it
-also provides several properties which allow you to query the system state.
-
-L.system
-   Is a dictionary describing the system such as the bounding box or number of atoms
-
-L.system.xlo, L.system.xhi
-   bounding box limits along x-axis
-
-L.system.ylo, L.system.yhi
-   bounding box limits along y-axis
-
-L.system.zlo, L.system.zhi
-   bounding box limits along z-axis
-
-L.communication
-   configuration of communication subsystem, such as the number of threads or processors
-
-L.communication.nthreads
-   number of threads used by each LAMMPS process
-
-L.communication.nprocs
-   number of MPI processes used by LAMMPS
-
-L.fixes
-   List of fixes in the current system
-
-L.computes
-   List of active computes in the current system
-
-L.dump
-   List of active dumps in the current system
-
-L.groups
-   List of groups present in the current system
-
-Working with LAMMPS variables
------------------------------
-
-LAMMPS variables can be both defined and accessed via the PyLammps interface.
-
-To define a variable you can use the :doc:`variable <variable>` command:
-
-.. code-block:: python
-
-   L.variable("a index 2")
-
-A dictionary of all variables is returned by L.variables
-
-you can access an individual variable by retrieving a variable object from the
-L.variables dictionary by name
-
-.. code-block:: python
-
-   a = L.variables['a']
-
-The variable value can then be easily read and written by accessing the value
-property of this object.
-
-.. code-block:: python
-
-   print(a.value)
-   a.value = 4
-
-Retrieving the value of an arbitrary LAMMPS expressions
--------------------------------------------------------
-
-LAMMPS expressions can be immediately evaluated by using the eval method. The
-passed string parameter can be any expression containing global thermo values,
-variables, compute or fix data.
-
-.. code-block:: python
-
-   result = L.eval("ke") # kinetic energy
-   result = L.eval("pe") # potential energy
-
-   result = L.eval("v_t/2.0")
-
-Accessing atom data
--------------------
-
-All atoms in the current simulation can be accessed by using the L.atoms list.
-Each element of this list is an object which exposes its properties (id, type,
-position, velocity, force, etc.).
-
-.. code-block:: python
-
-   # access first atom
-   L.atoms[0].id
-   L.atoms[0].type
-
-   # access second atom
-   L.atoms[1].position
-   L.atoms[1].velocity
-   L.atoms[1].force
-
-Some properties can also be used to set:
-
-.. code-block:: python
-
-   # set position in 2D simulation
-   L.atoms[0].position = (1.0, 0.0)
-
-   # set position in 3D simulation
-   L.atoms[0].position = (1.0, 0.0, 1.)
-
-Evaluating thermo data
-----------------------
-
-Each simulation run usually produces thermo output based on system state,
-computes, fixes or variables. The trajectories of these values can be queried
-after a run via the L.runs list. This list contains a growing list of run data.
-The first element is the output of the first run, the second element that of
-the second run.
-
-.. code-block:: python
-
-   L.run(1000)
-   L.runs[0] # data of first 1000 time steps
-
-   L.run(1000)
-   L.runs[1] # data of second 1000 time steps
-
-Each run contains a dictionary of all trajectories. Each trajectory is
-accessible through its thermo name:
-
-.. code-block:: python
-
-   L.runs[0].thermo.Step # list of time steps in first run
-   L.runs[0].thermo.Ke   # list of kinetic energy values in first run
-
-Together with matplotlib plotting data out of LAMMPS becomes simple:
-
-.. code-block:: python
-
-   import matplotlib.plot as plt
-   steps = L.runs[0].thermo.Step
-   ke    = L.runs[0].thermo.Ke
-   plt.plot(steps, ke)
-
-Error handling with PyLammps
-----------------------------
-
-Using C++ exceptions in LAMMPS for errors allows capturing them on the
-C++ side and rethrowing them on the Python side.  This way you can handle
-LAMMPS errors through the Python exception handling mechanism.
-
-.. warning::
-
-   Capturing a LAMMPS exception in Python can still mean that the
-   current LAMMPS process is in an illegal state and must be
-   terminated. It is advised to save your data and terminate the Python
-   instance as quickly as possible.
-
-Using PyLammps in IPython notebooks and Jupyter
------------------------------------------------
-
-If the LAMMPS Python package is installed for the same Python interpreter as
-IPython, you can use PyLammps directly inside of an IPython notebook inside of
-Jupyter. Jupyter is a powerful integrated development environment (IDE) for
-many dynamic languages like Python, Julia and others, which operates inside of
-any web browser. Besides auto-completion and syntax highlighting it allows you
-to create formatted documents using Markup, mathematical formulas, graphics and
-animations intermixed with executable Python code. It is a great format for
-tutorials and showcasing your latest research.
-
-To launch an instance of Jupyter simply run the following command inside your
-Python environment (this assumes you followed the Quick Start instructions):
-
-.. code-block:: bash
-
-   jupyter notebook
-
-IPyLammps Examples
-------------------
-
-Examples of IPython notebooks can be found in the python/examples/pylammps
-subdirectory. To open these notebooks launch *jupyter notebook* inside this
-directory and navigate to one of them. If you compiled and installed
-a LAMMPS shared library with exceptions, PNG, JPEG and FFMPEG support
-you should be able to rerun all of these notebooks.
-
-Validating a dihedral potential
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-This example showcases how an IPython Notebook can be used to compare a simple
-LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
-Four atoms are placed in the simulation and the dihedral potential is applied on
-them using a datafile. Then one of the atoms is rotated along the central axis by
-setting its position from Python, which changes the dihedral angle.
-
-.. code-block:: python
-
-   phi = [d \* math.pi / 180 for d in range(360)]
-
-   pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
-
-   pe = []
-   for p in pos:
-       L.atoms[3].position = p
-       L.run(0)
-       pe.append(L.eval("pe"))
-
-By evaluating the potential energy for each position we can verify that
-trajectory with the analytical formula.  To compare both solutions, we plot
-both trajectories over each other using matplotlib, which embeds the generated
-plot inside the IPython notebook.
-
-.. image:: JPG/pylammps_dihedral.jpg
-   :align: center
-
-Running a Monte Carlo relaxation
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-This second example shows how to use PyLammps to create a 2D Monte Carlo Relaxation
-simulation, computing and plotting energy terms and even embedding video output.
-
-Initially, a 2D system is created in a state with minimal energy.
-
-.. image:: JPG/pylammps_mc_minimum.jpg
-   :align: center
-
-It is then disordered by moving each atom by a random delta.
-
-.. code-block:: python
-
-   random.seed(27848)
-   deltaperturb = 0.2
-
-   for i in range(L.system.natoms):
-       x, y = L.atoms[i].position
-       dx = deltaperturb \* random.uniform(-1, 1)
-       dy = deltaperturb \* random.uniform(-1, 1)
-       L.atoms[i].position  = (x+dx, y+dy)
-
-   L.run(0)
-
-.. image:: JPG/pylammps_mc_disordered.jpg
-   :align: center
-
-Finally, the Monte Carlo algorithm is implemented in Python. It continuously
-moves random atoms by a random delta and only accepts certain moves.
-
-.. code-block:: python
-
-   estart = L.eval("pe")
-   elast = estart
-
-   naccept = 0
-   energies = [estart]
-
-   niterations = 3000
-   deltamove = 0.1
-   kT = 0.05
-
-   natoms = L.system.natoms
-
-   for i in range(niterations):
-       iatom = random.randrange(0, natoms)
-       current_atom = L.atoms[iatom]
-
-       x0, y0 = current_atom.position
-
-       dx = deltamove \* random.uniform(-1, 1)
-       dy = deltamove \* random.uniform(-1, 1)
-
-       current_atom.position = (x0+dx, y0+dy)
-
-       L.run(1, "pre no post no")
-
-       e = L.eval("pe")
-       energies.append(e)
-
-       if e <= elast:
-           naccept += 1
-           elast = e
-       elif random.random() <= math.exp(natoms\*(elast-e)/kT):
-           naccept += 1
-           elast = e
-       else:
-           current_atom.position = (x0, y0)
-
-The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
-
-.. image:: JPG/pylammps_mc_energies_plot.jpg
-   :align: center
-
-The IPython notebook also shows how to use dump commands and embed video files
-inside of the IPython notebook.
-
-Using PyLammps and mpi4py (Experimental)
-----------------------------------------
-
-PyLammps can be run in parallel using `mpi4py
-<https://mpi4py.readthedocs.io>`_. This python package can be installed
-using
-
-.. code-block:: bash
-
-   pip install mpi4py
-
-.. warning::
-
-   Usually, any :py:class:`PyLammps <lammps.PyLammps>` command must be
-   executed by *all* MPI processes. However, evaluations and querying
-   the system state is only available on MPI rank 0.  Using these
-   functions from other MPI ranks will raise an exception.
-
-The following is a short example which reads in an existing LAMMPS input
-file and executes it in parallel.  You can find in.melt in the
-examples/melt folder.  Please take note that the
-:py:meth:`PyLammps.eval() <lammps.PyLammps.eval>` is called only from
-MPI rank 0.
-
-.. code-block:: python
-
-   from mpi4py import MPI
-   from lammps import PyLammps
-
-   L = PyLammps()
-   L.file("in.melt")
-
-   if MPI.COMM_WORLD.rank == 0:
-       print("Potential energy: ", L.eval("pe"))
-
-   MPI.Finalize()
-
-To run this script (melt.py) in parallel using 4 MPI processes we invoke the
-following mpirun command:
-
-.. code-block:: bash
-
-   mpirun -np 4 python melt.py
-
-Feedback and Contributing
--------------------------
-
-If you find this Python interface useful, please feel free to provide feedback
-and ideas on how to improve it to Richard Berger (richard.berger@outlook.com). We also
-want to encourage people to write tutorial style IPython notebooks showcasing LAMMPS usage
-and maybe their latest research results.
+The PyLammps interface is deprecated and will be removed in a future release of
+LAMMPS. As such, the PyLammps version of this tutorial has been removed and is
+replaced by the :doc:`Python_head`.

doc/src/Howto_python.rst

@@ -0,0 +1,464 @@
+LAMMPS Python Tutorial
+======================
+
+.. contents::
+
+-----
+
+Overview
+--------
+
+The :py:class:`lammps <lammps.lammps>` Python module is a wrapper class for the
+LAMMPS :ref:`C language library interface API <lammps_c_api>` which is written using
+`Python ctypes <ctypes_>`_.  The design choice of this wrapper class is to
+follow the C language API closely with only small changes related to Python
+specific requirements and to better accommodate object oriented programming.
+
+In addition to this flat `ctypes <ctypes_>`_ interface, the
+:py:class:`lammps <lammps.lammps>` wrapper class exposes a discoverable
+API that doesn't require as much knowledge of the underlying C language
+library interface or LAMMPS C++ code implementation.
+
+Finally, the API exposes some additional features for `IPython integration
+<ipython_>`_ into `Jupyter notebooks <jupyter_>`_, e.g. for embedded
+visualization output from :doc:`dump style image <dump_image>`.
+
+.. _ctypes: https://docs.python.org/3/library/ctypes.html
+.. _ipython: https://ipython.org/
+.. _jupyter: https://jupyter.org/
+
+-----
+
+Quick Start
+-----------
+
+System-wide or User Installation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Step 1: Building LAMMPS as a shared library
+"""""""""""""""""""""""""""""""""""""""""""
+
+To use LAMMPS inside of Python it has to be compiled as shared library.
+This library is then loaded by the Python interface.  In this example we
+enable the :ref:`MOLECULE package <PKG-MOLECULE>` and compile LAMMPS
+with :ref:`PNG, JPEG and FFMPEG output support <graphics>` enabled.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         mkdir $LAMMPS_DIR/build-shared
+         cd  $LAMMPS_DIR/build-shared
+
+         # MPI, PNG, Jpeg, FFMPEG are auto-detected
+         cmake ../cmake -DPKG_MOLECULE=yes -DPKG_PYTHON=on -DBUILD_SHARED_LIBS=yes
+         make
+
+   .. tab:: Traditional make
+
+      .. code-block:: bash
+
+         cd $LAMMPS_DIR/src
+
+         # add LAMMPS packages if necessary
+         make yes-MOLECULE
+         make yes-PYTHON
+
+         # compile shared library using Makefile
+         make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
+
+Step 2: Installing the LAMMPS Python module
+"""""""""""""""""""""""""""""""""""""""""""
+
+Next install the LAMMPS Python module into your current Python installation with:
+
+.. code-block:: bash
+
+   make install-python
+
+This will create a so-called `"wheel"
+<https://packaging.python.org/en/latest/discussions/package-formats/#what-is-a-wheel>`_
+and then install the LAMMPS Python module from that "wheel" into either
+into a system folder (provided the command is executed with root
+privileges) or into your personal Python module folder.
+
+.. note::
+
+   Recompiling the shared library requires re-installing the Python
+   package.
+
+.. _externally_managed:
+
+.. admonition:: Handling an "externally-managed-environment" Error
+   :class: Hint
+
+   Some Python installations made through Linux distributions
+   (e.g. Ubuntu 24.04LTS or later) will prevent installing the LAMMPS
+   Python module into a system folder or a corresponding folder of the
+   individual user as attempted by ``make install-python`` with an error
+   stating that an *externally managed* python installation must be only
+   managed by the same package package management tool.  This is an
+   optional setting, so not all Linux distributions follow it currently
+   (Spring 2025).  The reasoning and explanations for this error can be
+   found in the `Python Packaging User Guide
+   <https://packaging.python.org/en/latest/specifications/externally-managed-environments/>`_
+
+   These guidelines suggest to create a virtual environment and install
+   the LAMMPS Python module there (see below).  This is generally a good
+   idea and the LAMMPS developers recommend this, too.  If, however, you
+   want to proceed and install the LAMMPS Python module regardless, you
+   can install the "wheel" file (see above) manually with the ``pip``
+   command by adding the ``--break-system-packages`` flag.
+
+Installation inside of a virtual environment
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+You can use virtual environments to create a custom Python environment
+specifically tuned for your workflow.
+
+Benefits of using a virtualenv
+""""""""""""""""""""""""""""""
+
+* isolation of your system Python installation from your development installation
+* installation can happen in your user directory without root access (useful for HPC clusters)
+* installing packages through pip allows you to get newer versions of packages than e.g., through apt-get or yum package managers (and without root access)
+* you can even install specific old versions of a package if necessary
+
+**Prerequisite (e.g. on Ubuntu)**
+
+.. code-block:: bash
+
+   apt-get install python-venv
+
+Creating a virtualenv with lammps installed
+"""""""""""""""""""""""""""""""""""""""""""
+
+.. code-block:: bash
+
+   # create virtual envrionment named 'testing'
+   python3 -m venv $HOME/python/testing
+
+   # activate 'testing' environment
+   source $HOME/python/testing/bin/activate
+
+Now configure and compile the LAMMPS shared library as outlined above.
+When using CMake and the shared library has already been build, you
+need to re-run CMake to update the location of the python executable
+to the location in the virtual environment with:
+
+.. code-block:: bash
+
+   cmake . -DPython_EXECUTABLE=$(which python)
+
+   # install LAMMPS package in virtualenv
+   (testing) make install-python
+
+   # install other useful packages
+   (testing) pip install matplotlib jupyter mpi4py pandas
+
+   ...
+
+   # return to original shell
+   (testing) deactivate
+
+-------
+
+Creating a new lammps instance
+------------------------------
+
+To create a lammps object you need to first import the class from the lammps
+module. By using the default constructor, a new :py:class:`lammps
+<lammps.lammps>` instance is created.
+
+.. code-block:: python
+
+   from lammps import lammps
+   L = lammps()
+
+See the :doc:`LAMMPS Python documentation <Python_create>` for how to customize
+the instance creation with optional arguments.
+
+-----
+
+Commands
+--------
+
+Sending a LAMMPS command with the library interface is done using
+the ``command`` method of the lammps object.
+
+For instance, let's take the following LAMMPS command:
+
+.. code-block:: LAMMPS
+
+   region box block 0 10 0 5 -0.5 0.5
+
+This command can be executed with the following Python code if ``L`` is a ``lammps``
+instance:
+
+.. code-block:: python
+
+   L.command("region box block 0 10 0 5 -0.5 0.5")
+
+For convenience, the ``lammps`` class also provides a command wrapper ``cmd``
+that turns any LAMMPS command into a regular function call:
+
+.. code-block:: python
+
+   L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
+
+Note that each parameter is set as Python number literal. With
+the wrapper each command takes an arbitrary parameter list and transparently
+merges it to a single command string, separating individual parameters by
+white-space.
+
+The benefit of this approach is avoiding redundant command calls and easier
+parameterization. With the ``command`` function each call needs to be assembled
+manually using formatted strings.
+
+.. code-block:: python
+
+   L.command(f"region box block {xlo} {xhi} {ylo} {yhi} {zlo} {zhi}")
+
+The wrapper accepts parameters directly and will convert
+them automatically to a final command string.
+
+.. code-block:: python
+
+   L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
+
+.. note::
+
+   When running in IPython you can use Tab-completion after ``L.cmd.`` to see
+   all available LAMMPS commands.
+
+-----
+
+Accessing atom data
+-------------------
+
+All per-atom properties that are part of the :doc:`atom style
+<atom_style>` in the current simulation can be accessed using the
+:py:meth:`extract_atoms() <lammps.lammps.extract_atoms()>` method.  This
+can be retrieved as ctypes objects or as NumPy arrays through the
+lammps.numpy module.  Those represent the *local* atoms of the
+individual sub-domain for the current MPI process and may contain
+information for the local ghost atoms or not depending on the property.
+Both can be accessed as lists, but for the ctypes list object the size
+is not known and hast to be retrieved first to avoid out-of-bounds
+accesses.
+
+.. code-block:: python
+
+   nlocal = L.extract_setting("nlocal")
+   nall = L.extract_setting("nall")
+   print("Number of local atoms ", nlocal, "  Number of local and ghost atoms ", nall);
+
+   # access via ctypes directly
+   atom_id = L.extract_atom("id")
+   print("Atom IDs", atom_id[0:nlocal])
+
+   # access through numpy wrapper
+   atom_type = L.numpy.extract_atom("type")
+   print("Atom types", atom_type)
+
+   x = L.numpy.extract_atom("x")
+   v = L.numpy.extract_atom("v")
+   print("positions array shape", x.shape)
+   print("velocity array shape", v.shape)
+   # turn on communicating velocities to ghost atoms
+   L.cmd.comm_modify("vel", "yes")
+   v = L.numpy.extract_atom('v')
+   print("velocity array shape", v.shape)
+
+Some properties can also be set from Python since internally the
+data of the C++ code is accessed directly:
+
+.. code-block:: python
+
+   # set position in 2D simulation
+   x[0] = (1.0, 0.0)
+
+   # set position in 3D simulation
+   x[0] = (1.0, 0.0, 1.)
+
+------
+
+Retrieving the values of thermodynamic data and variables
+---------------------------------------------------------
+
+To access thermodynamic data from the last completed timestep,
+you can use the :py:meth:`get_thermo() <lammps.lammps.get_thermo>`
+method, and to extract the value of (compatible) variables, you
+can use the :py:meth:`extract_variable() <lammps.lammps.extract_variable>`
+method.
+
+.. code-block:: python
+
+   result = L.get_thermo("ke") # kinetic energy
+   result = L.get_thermo("pe") # potential energy
+
+   result = L.extract_variable("t") / 2.0
+
+Error handling
+--------------
+
+We are using C++ exceptions in LAMMPS for errors and the C language
+library interface captures and records them.  This allows checking
+whether errors have happened in Python during a call into LAMMPS and
+then re-throw the error as a Python exception.  This way you can handle
+LAMMPS errors in the conventional way through the Python exception
+handling mechanism.
+
+.. warning::
+
+   Capturing a LAMMPS exception in Python can still mean that the
+   current LAMMPS process is in an illegal state and must be
+   terminated.  It is advised to save your data and terminate the Python
+   instance as quickly as possible.
+
+Using LAMMPS in IPython notebooks and Jupyter
+---------------------------------------------
+
+If the LAMMPS Python package is installed for the same Python
+interpreter as IPython, you can use LAMMPS directly inside of an IPython
+notebook inside of Jupyter. Jupyter is a powerful integrated development
+environment (IDE) for many dynamic languages like Python, Julia and
+others, which operates inside of any web browser.  Besides
+auto-completion and syntax highlighting it allows you to create
+formatted documents using Markup, mathematical formulas, graphics and
+animations intermixed with executable Python code.  It is a great format
+for tutorials and showcasing your latest research.
+
+To launch an instance of Jupyter simply run the following command inside your
+Python environment (this assumes you followed the Quick Start instructions):
+
+.. code-block:: bash
+
+   jupyter notebook
+
+Interactive Python Examples
+---------------------------
+
+Examples of IPython notebooks can be found in the ``python/examples/ipython``
+subdirectory. To open these notebooks launch ``jupyter notebook`` inside this
+directory and navigate to one of them. If you compiled and installed
+a LAMMPS shared library with PNG, JPEG and FFMPEG support
+you should be able to rerun all of these notebooks.
+
+Validating a dihedral potential
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This example showcases how an IPython Notebook can be used to compare a simple
+LAMMPS simulation of a harmonic dihedral potential to its analytical solution.
+Four atoms are placed in the simulation and the dihedral potential is applied on
+them using a datafile. Then one of the atoms is rotated along the central axis by
+setting its position from Python, which changes the dihedral angle.
+
+.. code-block:: python
+
+   phi = [d \* math.pi / 180 for d in range(360)]
+
+   pos = [(1.0, math.cos(p), math.sin(p)) for p in phi]
+
+   x = L.numpy.extract_atom("x")
+
+   pe = []
+   for p in pos:
+       x[3] = p
+       L.cmd.run(0, "post", "no")
+       pe.append(L.get_thermo("pe"))
+
+By evaluating the potential energy for each position we can verify that
+trajectory with the analytical formula.  To compare both solutions, we plot
+both trajectories over each other using matplotlib, which embeds the generated
+plot inside the IPython notebook.
+
+.. image:: JPG/pylammps_dihedral.jpg
+   :align: center
+
+Running a Monte Carlo relaxation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+This second example shows how to use the `lammps` Python interface to create a
+2D Monte Carlo Relaxation simulation, computing and plotting energy terms and
+even embedding video output.
+
+Initially, a 2D system is created in a state with minimal energy.
+
+.. image:: JPG/pylammps_mc_minimum.jpg
+   :align: center
+
+It is then disordered by moving each atom by a random delta.
+
+.. code-block:: python
+
+   random.seed(27848)
+   deltaperturb = 0.2
+   x = L.numpy.extract_atom("x")
+   natoms = x.shape[0]
+
+   for i in range(natoms):
+       dx = deltaperturb \* random.uniform(-1, 1)
+       dy = deltaperturb \* random.uniform(-1, 1)
+       x[i][0] += dx
+       x[i][1] += dy
+
+   L.cmd.run(0, "post", "no")
+
+.. image:: JPG/pylammps_mc_disordered.jpg
+   :align: center
+
+Finally, the Monte Carlo algorithm is implemented in Python. It continuously
+moves random atoms by a random delta and only accepts certain moves.
+
+.. code-block:: python
+
+   estart = L.get_thermo("pe")
+   elast = estart
+
+   naccept = 0
+   energies = [estart]
+
+   niterations = 3000
+   deltamove = 0.1
+   kT = 0.05
+
+   for i in range(niterations):
+       x = L.numpy.extract_atom("x")
+       natoms = x.shape[0]
+       iatom = random.randrange(0, natoms)
+       current_atom = x[iatom]
+
+       x0 = current_atom[0]
+       y0 = current_atom[1]
+
+       dx = deltamove \* random.uniform(-1, 1)
+       dy = deltamove \* random.uniform(-1, 1)
+
+       current_atom[0] = x0 + dx
+       current_atom[1] = y0 + dy
+
+       L.cmd.run(1, "pre no post no")
+
+       e = L.get_thermo("pe")
+       energies.append(e)
+
+       if e <= elast:
+           naccept += 1
+           elast = e
+       elif random.random() <= math.exp(natoms\*(elast-e)/kT):
+           naccept += 1
+           elast = e
+       else:
+           current_atom[0] = x0
+           current_atom[1] = y0
+
+The energies of each iteration are collected in a Python list and finally plotted using matplotlib.
+
+.. image:: JPG/pylammps_mc_energies_plot.jpg
+   :align: center
+
+The IPython notebook also shows how to use dump commands and embed video files
+inside of the IPython notebook.

doc/src/Howto_rheo.rst

@@ -15,8 +15,9 @@ details of the system, or develop new capabilities. For instance, the numerics
 associated with calculating gradients, reproducing kernels, etc. are separated
 into distinct classes to simplify the development of new integration schemes
 which can call these calculations. Additional numerical details can be found in
-:ref:`(Clemmer) <howto_rheo_clemmer>`. Example movies illustrating some of these
-capabilities are found at https://www.lammps.org/movies.html#rheopackage.
+:ref:`(Palermo) <howto_rheo_palermo>` and :ref:`(Clemmer) <howto_rheo_clemmer>`.
+Example movies illustrating some of these capabilities are found at
+https://www.lammps.org/movies.html#rheopackage.
 
 Note, if you simply want to run a traditional SPH simulation, the :ref:`SPH package
 <PKG-SPH>` package is likely better suited for your application. It has fewer advanced
@@ -70,7 +71,7 @@ particles to solid (e.g. with the :doc:`set <set>` command), (b) create bpm
 bonds between the particles (see the :doc:`bpm howto <Howto_bpm>` page for
 more details), and (c) use :doc:`pair rheo/solid <pair_rheo_solid>` to
 apply repulsive contact forces between distinct solid bodies. Akin to pair rheo,
-pair rheo/solid considers a particles fluid/solid phase to determine whether to
+pair rheo/solid considers a particle's fluid/solid phase to determine whether to
 apply forces. However, unlike pair rheo, pair rheo/solid does obey special bond
 settings such that contact forces do not have to be calculated between two bonded
 solid particles in the same elastic body.
@@ -79,10 +80,10 @@ In systems with thermal evolution, fix rheo/thermal can optionally set a
 melting/solidification temperature allowing particles to dynamically swap their
 state between fluid and solid when the temperature exceeds or drops below the
 critical temperature, respectively. Using the *react* option, one can specify a maximum
-bond length and a bond type. Then, when solidifying, particles will search their
+bond length and a bond type. Then, when solidifying, particles search their
 local neighbors and automatically create bonds with any neighboring solid particles
-in range. For BPM bond styles, bonds will then use the immediate position of the two
-particles to calculate a reference state. When melting, particles will delete any
+in range. For BPM bond styles, bonds then use the immediate position of the two
+particles to calculate a reference state. When melting, particles delete any
 bonds of the specified type when reverting to a fluid state. Special bonds are updated
 as bonds are created/broken.
 
@@ -107,6 +108,10 @@ criteria for creating/deleting a bond or altering force calculations).
 
 ----------
 
+.. _howto_rheo_palermo:
+
+**(Palermo)** Palermo, Wolf, Clemmer, O'Connor, Phys. Fluids, 36, 113337 (2024).
+
 .. _howto_rheo_clemmer:
 
 **(Clemmer)** Clemmer, Pierce, O'Connor, Nevins, Jones, Lechman, Tencer, Appl. Math. Model., 130, 310-326 (2024).

doc/src/Howto_triclinic.rst

@@ -249,23 +249,23 @@ as follows:
 
 .. math::
 
-  a   = & {\rm lx} \\
-  b^2 = &  {\rm ly}^2 +  {\rm xy}^2 \\
-  c^2 = &  {\rm lz}^2 +  {\rm xz}^2 +  {\rm yz}^2 \\
-  \cos{\alpha} = & \frac{{\rm xy}*{\rm xz} + {\rm ly}*{\rm yz}}{b*c} \\
-  \cos{\beta}  = & \frac{\rm xz}{c} \\
-  \cos{\gamma} = & \frac{\rm xy}{b} \\
+  a   = & \mathrm{lx} \\
+  b^2 = &  \mathrm{ly}^2 + \mathrm{xy}^2 \\
+  c^2 = &  \mathrm{lz}^2 + \mathrm{xz}^2 + \mathrm{yz}^2 \\
+  \cos{\alpha} = & \frac{\mathrm{xy}*\mathrm{xz} + \mathrm{ly}*\mathrm{yz}}{b*c} \\
+  \cos{\beta}  = & \frac{\mathrm{xz}}{c} \\
+  \cos{\gamma} = & \frac{\mathrm{xy}}{b} \\
 
 The inverse relationship can be written as follows:
 
 .. math::
 
-  {\rm lx}   = & a \\
-  {\rm xy}   = & b \cos{\gamma}  \\
-  {\rm xz}   = & c \cos{\beta}\\
-  {\rm ly}^2 = & b^2 - {\rm xy}^2 \\
-  {\rm yz}   = & \frac{b*c \cos{\alpha} - {\rm xy}*{\rm xz}}{\rm ly} \\
-  {\rm lz}^2 = & c^2 - {\rm xz}^2 - {\rm yz}^2 \\
+  \mathrm{lx}   = & a \\
+  \mathrm{xy}   = & b \cos{\gamma}  \\
+  \mathrm{xz}   = & c \cos{\beta}\\
+  \mathrm{ly}^2 = & b^2 - \mathrm{xy}^2 \\
+  \mathrm{yz}   = & \frac{b*c \cos{\alpha} - \mathrm{xy}*\mathrm{xz}}{\mathrm{ly}} \\
+  \mathrm{lz}^2 = & c^2 - \mathrm{xz}^2 - \mathrm{yz}^2 \\
 
 The values of *a*, *b*, *c*, :math:`\alpha` , :math:`\beta`, and
 :math:`\gamma` can be printed out or accessed by computes using the

doc/src/Howto_wsl.rst

@@ -260,7 +260,7 @@ Switch into the :code:`examples/melt` folder:
 
    cd ../examples/melt
 
-To run this example in serial, use the following command line:
+To run this example in serial, use the following command:
 
 .. code-block::
 

doc/src/Install_git.rst

@@ -52,6 +52,7 @@ your machine and "release" is one of the 3 branches listed above.
 between them at any time using "git checkout <branch name>".)
 
 .. admonition:: Saving time and disk space when using ``git clone``
+   :class: note
 
    The complete git history of the LAMMPS project is quite large because
    it contains the entire commit history of the project since fall 2006,
@@ -60,7 +61,7 @@ between them at any time using "git checkout <branch name>".)
    files (mostly by accident).  If you do not need access to the entire
    commit history (most people don't), you can speed up the "cloning"
    process and reduce local disk space requirements by using the
-   ``--depth`` git command line flag.  That will create a "shallow clone"
+   ``--depth`` git command-line flag.  That will create a "shallow clone"
    of the repository, which contains only a subset of the git history.
    Using a depth of 1000 is usually sufficient to include the head
    commits of the *develop*, the *release*, and the *maintenance*

doc/src/Install_mac.rst

@@ -5,8 +5,7 @@ LAMMPS can be downloaded, built, and configured for macOS with `Homebrew
 <homebrew_>`_.  (Alternatively, see the installation instructions for
 :doc:`downloading an executable via Conda <Install_conda>`.)  The
 following LAMMPS packages are unavailable at this time because of
-additional requirements not yet met: GPU, KOKKOS, MSCG, POEMS,
-VORONOI.
+additional requirements not yet met: GPU, KOKKOS.
 
 After installing Homebrew, you can install LAMMPS on your system with
 the following commands:

doc/src/Intro_authors.rst

@@ -8,6 +8,8 @@ send an email to all of them at this address: "developers at
 lammps.org".  General questions about LAMMPS should be posted in the
 `LAMMPS forum on MatSci <https://matsci.org/lammps/>`_.
 
+.. We need to keep this file in sync with https://www.lammps.org/authors.html
+
 .. raw:: latex
 
    \small
@@ -27,7 +29,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
    * - `Steve Plimpton <sjp_>`_
      - SNL (retired)
      - sjplimp at gmail.com
-     - MD kernels, parallel algorithms & scalability, code structure and design
+     - original author, MD kernels, parallel algorithms & scalability, code structure and design
    * - `Aidan Thompson <at_>`_
      - SNL
      - athomps at sandia.gov

doc/src/Intro_overview.rst

@@ -20,13 +20,21 @@ acceleration.
 .. _lws: https://www.lammps.org
 .. _omp: https://www.openmp.org
 
-LAMMPS is written in C++ and requires a compiler that is at least
-compatible with the C++-11 standard.  Earlier versions were written in
-F77, F90, and C++-98.  See the `History page
+LAMMPS is written in C++ and currently requires a compiler that is at
+least compatible with the C++-11 standard.  Earlier versions were
+written in F77, F90, and C++-98.  See the `History page
 <https://www.lammps.org/history.html>`_ of the website for details.  All
 versions can be downloaded as source code from the `LAMMPS website
 <lws_>`_.
 
+Through a :ref:`C language API <lammps_c_api>` LAMMPS functionality can
+be accessed and managed from other programming languages rather than
+running the LAMMPS executable.  Ready to use modules for :ref:`Python
+<lammps_python_api>` and :ref:`Fortran <lammps_fortran_api>` exist, and
+an example :ref:`SWIG interface file <swig>` as well as example C files
+for dynamically loading LAMMPS as a shared library into other
+executables are provided.
+
 LAMMPS is designed to be easy to modify or extend with new capabilities,
 such as new force fields, atom types, boundary conditions, or
 diagnostics.  See the :doc:`Modify` section of for more details.

doc/src/Intro_portability.rst

@@ -13,10 +13,14 @@ Programming language standards
 
 Most of the C++ code currently requires a compiler compatible with the
 C++11 standard, the KOKKOS package currently requires C++17.  Most of
-the Python code is written to be compatible with Python 3.5 or later or
-Python 2.7.  Some Python scripts *require* Python 3 and a few others
-still need to be ported from Python 2 to Python 3.
+the Python code is written to be compatible with Python 3.6 or later.
 
+.. deprecated:: 2Apr2025
+
+Python 2.x is no longer supported and trying to use it, e.g. for the
+LAMMPS Python module should result in an error.  If you come across
+some part of the LAMMPS distribution that is not (yet) compatible with
+Python 3, please notify the LAMMPS developers.
 
 Build systems
 ^^^^^^^^^^^^^
@@ -24,8 +28,8 @@ Build systems
 LAMMPS can be compiled from source code using a (traditional) build
 system based on shell scripts, a few shell utilities (grep, sed, cat,
 tr) and the GNU make program. This requires running within a Bourne
-shell (``/bin/sh``).  Alternatively, a build system with different back ends
-can be created using CMake.  CMake must be at least version 3.16.
+shell (``/bin/sh``).  Alternatively, a build system with different back
+ends can be created using CMake.  CMake must be at least version 3.16.
 
 Operating systems
 ^^^^^^^^^^^^^^^^^

doc/src/Library.rst

@@ -131,16 +131,15 @@ run LAMMPS in serial mode.
 
 .. _lammps_python_api:
 
-LAMMPS Python APIs
-==================
+LAMMPS Python API
+=================
 
 The LAMMPS Python module enables calling the LAMMPS C library API from
 Python by dynamically loading functions in the LAMMPS shared library through
 the `Python ctypes module <https://docs.python.org/3/library/ctypes.html>`_.
 Because of the dynamic loading, it is **required** that LAMMPS is compiled
 in :ref:`"shared" mode <exe>`.  The Python interface is object-oriented, but
-otherwise tries to be very similar to the C library API.  Three different
-Python classes to run LAMMPS are available and they build on each other.
+otherwise tries to be very similar to the C library API.
 More information on this is in the :doc:`Python_head`
 section of the manual.  Use of the LAMMPS Python module is described in
 :doc:`Python_module`.

doc/src/Library_add.rst

@@ -19,9 +19,9 @@ there are now a few requirements for including new changes or extensions.
     be added.
   - New features should also be implemented and documented not just
     for the C interface, but also the Python and Fortran interfaces.
-  - All additions should work and be compatible with ``-DLAMMPS_BIGBIG``,
-    ``-DLAMMPS_SMALLBIG``, ``-DLAMMPS_SMALLSMALL`` as well as when
-    compiling with and without MPI support.
+  - All additions should work and be compatible with
+    ``-DLAMMPS_BIGBIG``, ``-DLAMMPS_SMALLBIG`` as well as when compiling
+    with and without MPI support.
   - The ``library.h`` file should be kept compatible to C code at
     a level similar to C89. Its interfaces may not reference any
     custom data types (e.g. ``bigint``, ``tagint``, and so on) that

doc/src/Library_execute.rst

@@ -7,6 +7,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_command`
 - :cpp:func:`lammps_commands_list`
 - :cpp:func:`lammps_commands_string`
+- :cpp:func:`lammps_expand`
 
 --------------------
 
@@ -79,3 +80,8 @@ Below is a short example using some of these functions.
 .. doxygenfunction:: lammps_commands_string
    :project: progguide
 
+-----------------------
+
+.. doxygenfunction:: lammps_expand
+   :project: progguide
+

doc/src/Library_objects.rst

@@ -1,5 +1,5 @@
-Compute, fixes, variables
-=========================
+Computes, fixes, variables
+==========================
 
 This section documents accessing or modifying data stored by computes,
 fixes, or variables in LAMMPS using the following functions:
@@ -12,6 +12,10 @@ fixes, or variables in LAMMPS using the following functions:
 - :cpp:func:`lammps_set_string_variable`
 - :cpp:func:`lammps_set_internal_variable`
 - :cpp:func:`lammps_variable_info`
+- :cpp:func:`lammps_eval`
+- :cpp:func:`lammps_clearstep_compute`
+- :cpp:func:`lammps_addstep_compute_all`
+- :cpp:func:`lammps_addstep_compute`
 
 -----------------------
 
@@ -55,6 +59,26 @@ fixes, or variables in LAMMPS using the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_eval
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_clearstep_compute
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_addstep_compute_all
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_addstep_compute
+   :project: progguide
+
+-----------------------
+
 .. doxygenenum:: _LMP_DATATYPE_CONST
 
 .. doxygenenum:: _LMP_STYLE_CONST

doc/src/Library_utility.rst

@@ -20,6 +20,7 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_force_timeout`
 - :cpp:func:`lammps_has_error`
 - :cpp:func:`lammps_get_last_error_message`
+- :cpp:func:`lammps_set_show_error`
 - :cpp:func:`lammps_python_api_version`
 
 The :cpp:func:`lammps_free` function is a clean-up function to free
@@ -110,6 +111,11 @@ where such memory buffers were allocated that require the use of
 
 -----------------------
 
+.. doxygenfunction:: lammps_set_show_error
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_python_api_version
    :project: progguide
 

doc/src/Manual_version.rst

@@ -2,9 +2,15 @@ What does a LAMMPS version mean
 -------------------------------
 
 The LAMMPS "version" is the date when it was released, such as 1 May
-2014.  LAMMPS is updated continuously, and we aim to keep it working
-correctly and reliably at all times.  Also, several variants of static
-code analysis are run regularly to maintain or improve the overall code
+2014.  LAMMPS is updated continuously, and with the help of extensive
+automated testing (mostly applied *before* changes are included) we aim
+to keep it working correctly and reliably at all times, but there also
+are regular *feature releases* with new and expanded functionality, and
+there are designated *stable releases* that receive updates with bug
+fixes back-ported from the development branch.
+
+In addition to automated testing, several variants of static code
+analysis are run regularly to maintain or improve the overall code
 quality, consistency, and compliance with programming standards, best
 practices and style conventions.  You can follow its development in a
 public `git repository on GitHub <https://github.com/lammps/lammps>`_.
@@ -19,17 +25,18 @@ Identifying the Version
 
 The version date is printed to the screen and log file every time you
 run LAMMPS.  There also is an indication, if a LAMMPS binary was
-compiled from version with modifications **after** a release.
-It is also visible in the file src/version.h and in the LAMMPS directory
-name created when you unpack a downloaded tarball.  And it is on the
-first page of the :doc:`manual <Manual>`.
+compiled from version with modifications **after** a release, either
+from the development version or the maintenance version of the last
+stable release. It is also visible in the file src/version.h and in the
+LAMMPS directory name created when you unpack a downloaded tarball.  And
+it is on the first page of the :doc:`manual <Manual>`.
 
 * If you browse the HTML pages of the online version of the LAMMPS
   manual, they will by default describe the most current feature release
   version of LAMMPS.  In the navigation bar on the bottom left, there is
   the option to view instead the documentation for the most recent
   *stable* version or the documentation corresponding to the state of
-  the development branch.
+  the development branch *develop*.
 * If you browse the HTML pages included in your downloaded tarball, they
   describe the version you have, which may be older than the online
   version.
@@ -48,8 +55,9 @@ Development
 Modifications of the LAMMPS source code (like bug fixes, code
 refactoring, updates to existing features, or addition of new features)
 are organized into pull requests.  Pull requests will be merged into the
-*develop* branch of the git repository after they pass automated testing
-and code review by the LAMMPS developers.
+*develop* branch of the LAMMPS git repository on GitHub after they pass
+automated testing and code review by :doc:`core LAMMPS developers
+<Intro_authors>`.
 
 Feature Releases
 """"""""""""""""
@@ -62,8 +70,7 @@ repository is updated with every such *feature release* and a tag in the
 format ``patch_1May2014`` is added.  A summary of the most important
 changes of these releases for the current year are posted on `this
 website page <https://www.lammps.org/bug.html>`_.  More detailed release
-notes are `available on GitHub
-<https://github.com/lammps/lammps/releases/>`_.
+notes are `available on GitHub <https://github.com/lammps/lammps/releases/>`_.
 
 Stable Releases
 """""""""""""""
@@ -71,18 +78,18 @@ Stable Releases
 About once a year, we release a *stable release* version of LAMMPS.
 This is done after a "stabilization period" where we apply only bug
 fixes and small, non-intrusive changes to the *develop* branch but no
-new features.  At the same time, the code is subjected to more detailed
-and thorough manual testing than the default automated testing.
-After such a *stable release*, both the *release* and the *stable*
-branches are updated and two tags are applied, a ``patch_1May2014`` format
-and a ``stable_1May2014`` format tag.
+new features to the core code.  At the same time, the code is subjected
+to more detailed and thorough manual testing than the default automated
+testing.  After such a *stable release*, both the *release* and the
+*stable* branches are updated and two tags are applied, a
+``patch_1May2014`` format and a ``stable_1May2014`` format tag.
 
 Stable Release Updates
 """"""""""""""""""""""
 
-Between *stable releases*, we collect bug fixes and updates back-ported
-from the *develop* branch in a branch called *maintenance*.  From the
-*maintenance* branch we make occasional *stable update releases* and
-update the *stable* branch accordingly.  The first update to the
-``stable_1May2014`` release would be tagged as
+Between *stable releases*, we collect bug fixes and updates that are
+back-ported from the *develop* branch in a branch called *maintenance*.
+From the *maintenance* branch we make occasional *stable update
+releases* and update the *stable* branch accordingly.  The first update
+to the ``stable_1May2014`` release would be tagged as
 ``stable_1May2014_update1``.  These updates contain no new features.

doc/src/Modify_compute.rst

@@ -45,6 +45,8 @@ class.  See compute.h for details.
 +-----------------------+------------------------------------------------------------------+
 | pair_tally_callback   | callback function for *tally*\ -style computes (optional).       |
 +-----------------------+------------------------------------------------------------------+
+| modify_param          | called when a compute_modify request is executed (optional)      |
++-----------------------+------------------------------------------------------------------+
 | memory_usage          | tally memory usage (optional)                                    |
 +-----------------------+------------------------------------------------------------------+
 

doc/src/Modify_requirements.rst

@@ -189,10 +189,8 @@ of the contribution.  As of January 2023, all previously included
 Fortran code for the LAMMPS executable has been replaced by equivalent
 C++ code.
 
-Python code must be compatible with Python 3.5 and later.  Large parts
-of LAMMPS (including the :ref:`PYTHON package <PKG-PYTHON>`) are also
-compatible with Python 2.7.  Compatibility with Python 2.7 is desirable,
-but compatibility with Python 3.5 is **required**.
+Python code currently must be compatible with Python 3.6.  If a later
+version or Python is required, it needs to be documented.
 
 Compatibility with older programming language standards is very
 important to maintain portability and availability of LAMMPS on many
@@ -208,20 +206,21 @@ Build system (strict)
 
 LAMMPS currently supports two build systems: one that is based on
 :doc:`traditional Makefiles <Build_make>` and one that is based on
-:doc:`CMake <Build_cmake>`.  Therefore, your contribution must be
-compatible with and support both build systems.
+:doc:`CMake <Build_cmake>`.  As of fall 2024, it is no longer required
+to support the traditional make build system.  New packages may choose
+to only support building with CMake.  Additions to existing packages
+must follow the requirements set by that package.
 
 For a single pair of header and implementation files that are an
 independent feature, it is usually only required to add them to
 ``src/.gitignore``.
 
 For traditional make, if your contributed files or package depend on
-other LAMMPS style files or packages also being installed
-(e.g. because your file is a derived class from the other LAMMPS
-class), then an ``Install.sh`` file is also needed to check for those
-dependencies and modifications to ``src/Depend.sh`` to trigger the checks.
-See other README and Install.sh files in other directories as
-examples.
+other LAMMPS style files or packages also being installed (e.g. because
+your file is a derived class from the other LAMMPS class), then an
+``Install.sh`` file is also needed to check for those dependencies and
+modifications to ``src/Depend.sh`` to trigger the checks.  See other
+README and Install.sh files in other directories as examples.
 
 Similarly, for CMake support, changes may need to be made to
 ``cmake/CMakeLists.txt``, some of the files in ``cmake/presets``, and

doc/src/Modify_style.rst

@@ -46,7 +46,7 @@ Include files (varied)
   but instead should be initialized either in the initializer list of
   the constructor or explicitly assigned in the body of the constructor.
   If the member variable is relevant to the functionality of a class
-  (for example when it stores a value from a command line argument), the
+  (for example when it stores a value from a command-line argument), the
   member variable declaration is followed by a brief comment explaining
   its purpose and what its values can be.  Class members that are
   pointers should always be initialized to ``nullptr`` in the

doc/src/Packages_details.rst

@@ -994,6 +994,7 @@ Additional pair styles that are less commonly used.
 
 * ``src/EXTRA-PAIR``: filenames -> commands
 * :doc:`pair_style <pair_style>`
+* ``examples/PACKAGES/dispersion``
 
 ----------
 
@@ -2171,8 +2172,8 @@ the :doc:`Build extras <Build_extras>` page.
 * ``src/OPENMP/README``
 * :doc:`Accelerator packages <Speed_packages>`
 * :doc:`OPENMP package <Speed_omp>`
-* :doc:`Command line option -suffix/-sf omp <Run_options>`
-* :doc:`Command line option -package/-pk omp <Run_options>`
+* :doc:`Command-line option -suffix/-sf omp <Run_options>`
+* :doc:`Command-line option -package/-pk omp <Run_options>`
 * :doc:`package omp <package>`
 * Search the :doc:`commands <Commands_all>` pages (:doc:`fix <Commands_fix>`, :doc:`compute <Commands_compute>`,
   :doc:`pair <Commands_pair>`, :doc:`bond, angle, dihedral, improper <Commands_bond>`,
@@ -2427,7 +2428,7 @@ ways to use LAMMPS and Python together.
 
    Building with the PYTHON package assumes you have a Python development
    environment (headers and libraries) available on your system, which needs
-   to be either Python version 2.7 or Python 3.5 and later.
+   to be Python version 3.6 or later.
 
 **Install:**
 
@@ -2789,14 +2790,15 @@ implements smoothed particle hydrodynamics (SPH) for liquids.  See the
 related :ref:`MACHDYN package <PKG-MACHDYN>` package for smooth Mach dynamics
 (SMD) for solids.
 
-This package contains ideal gas, Lennard-Jones equation of states,
-Tait, and full support for complete (i.e. internal-energy dependent)
-equations of state.  It allows for plain or Monaghans XSPH integration
-of the equations of motion.  It has options for density continuity or
-density summation to propagate the density field.  It has
-:doc:`set <set>` command options to set the internal energy and density
-of particles from the input script and allows the same quantities to
-be output with thermodynamic output or to dump files via the :doc:`compute property/atom <compute_property_atom>` command.
+This package contains ideal gas, Lennard-Jones equation of states, Tait,
+and full support for complete (i.e. internal-energy dependent) equations
+of state.  It allows for plain or Monaghans XSPH integration of the
+equations of motion.  It has options for density continuity or density
+summation to propagate the density field.  It has :doc:`set <set>`
+command options to set the internal energy and density of particles from
+the input script and allows the same quantities to be output with
+thermodynamic output or to dump files via the :doc:`compute
+property/atom <compute_property_atom>` command.
 
 **Author:** Georg Ganzenmuller (Fraunhofer-Institute for High-Speed
 Dynamics, Ernst Mach Institute, Germany).
@@ -2809,6 +2811,17 @@ Dynamics, Ernst Mach Institute, Germany).
 * ``examples/PACKAGES/sph``
 * https://www.lammps.org/movies.html#sph
 
+.. note::
+
+   Please note that the SPH PDF guide file has not been updated for
+   many years and thus does not reflect the current *syntax* of the
+   SPH package commands. For that please refer to the LAMMPS manual.
+
+.. note::
+
+   Please also note, that the :ref:`RHEO package <PKG-RHEO>` offers
+   similar functionality in a more modern and flexible implementation.
+
 ----------
 
 .. _PKG-SPIN:

doc/src/Python_atoms.rst

@@ -2,14 +2,8 @@ Per-atom properties
 ===================
 
 Similar to what is described in :doc:`Library_atoms`, the instances of
-:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`, or
-:py:class:`IPyLammps <lammps.IPyLammps>` can be used to extract atom quantities
-and modify some of them. The main difference between the interfaces is how the information
-is exposed.
-
-While the :py:class:`lammps <lammps.lammps>` is just a thin layer that wraps C API calls,
-:py:class:`PyLammps <lammps.PyLammps>` and :py:class:`IPyLammps <lammps.IPyLammps>` expose
-information as objects and properties.
+:py:class:`lammps <lammps.lammps>` can be used to extract atom quantities
+and modify some of them.
 
 In some cases the data returned is a direct reference to the original data
 inside LAMMPS cast to ``ctypes`` pointers. Where possible, the wrappers will
@@ -25,57 +19,41 @@ against invalid accesses.
    accordingly. These arrays can change sizes and order at every neighbor list
    rebuild and atom sort event as atoms are migrating between subdomains.
 
-.. tabs::
+.. code-block:: python
 
-   .. tab:: lammps API
+   from lammps import lammps
 
-      .. code-block:: python
+   lmp = lammps()
+   lmp.file("in.sysinit")
 
-         from lammps import lammps
 
-         lmp = lammps()
-         lmp.file("in.sysinit")
+   # Read/Write access via ctypes
+   nlocal = lmp.extract_global("nlocal")
+   x = lmp.extract_atom("x")
 
-         nlocal = lmp.extract_global("nlocal")
-         x = lmp.extract_atom("x")
+   for i in range(nlocal):
+      print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
 
-         for i in range(nlocal):
-            print("(x,y,z) = (", x[i][0], x[i][1], x[i][2], ")")
+   # Read/Write access via NumPy arrays
+   atom_id = L.numpy.extract_atom("id")
+   atom_type = L.numpy.extract_atom("type")
+   x = L.numpy.extract_atom("x")
+   v = L.numpy.extract_atom("v")
+   f = L.numpy.extract_atom("f")
 
-         lmp.close()
+   # set position in 2D simulation
+   x[0] = (1.0, 0.0)
 
-      **Methods**:
+   # set position in 3D simulation
+   x[0] = (1.0, 0.0, 1.)
 
-      * :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
+   lmp.close()
 
-      **Numpy Methods**:
 
-      * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
+**Methods**:
 
-   .. tab:: PyLammps/IPyLammps API
+* :py:meth:`extract_atom() <lammps.lammps.extract_atom()>`: extract a per-atom quantity
 
-      All atoms in the current simulation can be accessed by using the :py:attr:`PyLammps.atoms <lammps.PyLammps.atoms>` property.
-      Each element of this list is a :py:class:`Atom <lammps.Atom>` or :py:class:`Atom2D <lammps.Atom2D>` object. The attributes of
-      these objects provide access to their data (id, type, position, velocity, force, etc.):
-
-      .. code-block:: python
-
-         # access first atom
-         L.atoms[0].id
-         L.atoms[0].type
-
-         # access second atom
-         L.atoms[1].position
-         L.atoms[1].velocity
-         L.atoms[1].force
-
-      Some attributes can be changed:
-
-      .. code-block:: python
-
-         # set position in 2D simulation
-         L.atoms[0].position = (1.0, 0.0)
-
-         # set position in 3D simulation
-         L.atoms[0].position = (1.0, 0.0, 1.0)
+**Numpy Methods**:
 
+* :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array

doc/src/Python_create.rst

@@ -6,11 +6,10 @@ Creating or deleting a LAMMPS object
 ====================================
 
 With the Python interface the creation of a :cpp:class:`LAMMPS
-<LAMMPS_NS::LAMMPS>` instance is included in the constructors for the
-:py:class:`lammps <lammps.lammps>`, :py:class:`PyLammps <lammps.PyLammps>`,
-and :py:class:`IPyLammps <lammps.IPyLammps>` classes.
-Internally it will call either :cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C
-library API to create the class instance.
+<LAMMPS_NS::LAMMPS>` instance is included in the constructor for the
+:py:class:`lammps <lammps.lammps>` class. Internally it will call either
+:cpp:func:`lammps_open` or :cpp:func:`lammps_open_no_mpi` from the C library
+API to create the class instance.
 
 All arguments are optional.  The *name* argument allows loading a
 LAMMPS shared library that is named ``liblammps_machine.so`` instead of
@@ -26,108 +25,25 @@ to run the Python module like the library interface on a subset of the
 MPI ranks after splitting the communicator.
 
 
-Here are simple examples using all three Python interfaces:
+Here is a simple example using the LAMMPS Python interface:
 
-.. tabs::
+.. code-block:: python
 
-   .. tab:: lammps API
+   from lammps import lammps
 
-      .. code-block:: python
+   # NOTE: argv[0] is set by the lammps class constructor
+   args = ["-log", "none"]
 
-         from lammps import lammps
+   # create LAMMPS instance
+   lmp = lammps(cmdargs=args)
 
-         # NOTE: argv[0] is set by the lammps class constructor
-         args = ["-log", "none"]
+   # get and print numerical version code
+   print("LAMMPS Version: ", lmp.version())
 
-         # create LAMMPS instance
-         lmp = lammps(cmdargs=args)
+   # explicitly close and delete LAMMPS instance (optional)
+   lmp.close()
 
-         # get and print numerical version code
-         print("LAMMPS Version: ", lmp.version())
-
-         # explicitly close and delete LAMMPS instance (optional)
-         lmp.close()
-
-   .. tab:: PyLammps API
-
-      The :py:class:`PyLammps <lammps.PyLammps>` class is a wrapper around the
-      :py:class:`lammps <lammps.lammps>` class and all of its lower level functions.
-      By default, it will create a new instance of :py:class:`lammps <lammps.lammps>` passing
-      along all arguments to the constructor of :py:class:`lammps <lammps.lammps>`.
-
-      .. code-block:: python
-
-         from lammps import PyLammps
-
-         # NOTE: argv[0] is set by the lammps class constructor
-         args = ["-log", "none"]
-
-         # create LAMMPS instance
-         L = PyLammps(cmdargs=args)
-
-         # get and print numerical version code
-         print("LAMMPS Version: ", L.version())
-
-         # explicitly close and delete LAMMPS instance (optional)
-         L.close()
-
-      :py:class:`PyLammps <lammps.PyLammps>` objects can also be created on top of an existing
-      :py:class:`lammps <lammps.lammps>` object:
-
-      .. code-block:: python
-
-         from lammps import lammps, PyLammps
-         ...
-         # create LAMMPS instance
-         lmp = lammps(cmdargs=args)
-
-         # create PyLammps instance using previously created LAMMPS instance
-         L = PyLammps(ptr=lmp)
-
-      This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
-      instance is a specific way, but want to take advantage of the
-      :py:class:`PyLammps <lammps.PyLammps>` interface.
-
-   .. tab:: IPyLammps API
-
-      The :py:class:`IPyLammps <lammps.IPyLammps>` class is an extension of the
-      :py:class:`PyLammps <lammps.PyLammps>` class. It has the same construction behavior. By
-      default, it will create a new instance of :py:class:`lammps` passing
-      along all arguments to the constructor of :py:class:`lammps`.
-
-      .. code-block:: python
-
-         from lammps import IPyLammps
-
-         # NOTE: argv[0] is set by the lammps class constructor
-         args = ["-log", "none"]
-
-         # create LAMMPS instance
-         L = IPyLammps(cmdargs=args)
-
-         # get and print numerical version code
-         print("LAMMPS Version: ", L.version())
-
-         # explicitly close and delete LAMMPS instance (optional)
-         L.close()
-
-      You can also initialize IPyLammps on top of an existing :py:class:`lammps` or :py:class:`PyLammps` object:
-
-      .. code-block:: python
-
-         from lammps import lammps, IPyLammps
-         ...
-         # create LAMMPS instance
-         lmp = lammps(cmdargs=args)
-
-         # create PyLammps instance using previously created LAMMPS instance
-         L = PyLammps(ptr=lmp)
-
-      This is useful if you have to create the :py:class:`lammps <lammps.lammps>`
-      instance is a specific way, but want to take advantage of the
-      :py:class:`IPyLammps <lammps.IPyLammps>` interface.
-
-In all of the above cases, same as with the :ref:`C library API <lammps_c_api>`, this will use the
+Same as with the :ref:`C library API <lammps_c_api>`, this will use the
 ``MPI_COMM_WORLD`` communicator for the MPI library that LAMMPS was
 compiled with.
 

doc/src/Python_execute.rst

@@ -1,127 +1,123 @@
 Executing commands
 ==================
 
-Once an instance of the :py:class:`lammps <lammps.lammps>`,
-:py:class:`PyLammps <lammps.PyLammps>`, or
-:py:class:`IPyLammps <lammps.IPyLammps>` class is created, there are
+Once an instance of the :py:class:`lammps <lammps.lammps>` class is created, there are
 multiple ways to "feed" it commands. In a way that is not very different from
 running a LAMMPS input script, except that Python has many more facilities
 for structured programming than the LAMMPS input script syntax. Furthermore
 it is possible to "compute" what the next LAMMPS command should be.
 
-.. tabs::
+Same as in the equivalent :doc:`C library functions <Library_execute>`,
+commands can be read from a file, a single string, a list of strings and a
+block of commands in a single multi-line string. They are processed under the
+same boundary conditions as the C library counterparts.  The example below
+demonstrates the use of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
+:py:func:`lammps.commands_list()`, and :py:func:`lammps.commands_string()`:
 
-   .. tab:: lammps API
+.. code-block:: python
 
-      Same as in the equivalent
-      :doc:`C library functions <Library_execute>`, commands can be read from a file, a
-      single string, a list of strings and a block of commands in a single
-      multi-line string. They are processed under the same boundary conditions
-      as the C library counterparts.  The example below demonstrates the use
-      of :py:func:`lammps.file()`, :py:func:`lammps.command()`,
-      :py:func:`lammps.commands_list()`, and :py:func:`lammps.commands_string()`:
+   from lammps import lammps
+   lmp = lammps()
 
-      .. code-block:: python
+   # read commands from file 'in.melt'
+   lmp.file('in.melt')
 
-         from lammps import lammps
-         lmp = lammps()
+   # issue a single command
+   lmp.command('variable zpos index 1.0')
 
-         # read commands from file 'in.melt'
-         lmp.file('in.melt')
+   # create 10 groups with 10 atoms each
+   cmds = [f"group g{i} id {10*i+1}:{10*(i+1)}" for i in range(10)]
+   lmp.commands_list(cmds)
 
-         # issue a single command
-         lmp.command('variable zpos index 1.0')
+   # run commands from a multi-line string
+   block = """
+   clear
+   region  box block 0 2 0 2 0 2
+   create_box 1 box
+   create_atoms 1 single 1.0 1.0 ${zpos}
+   """
+   lmp.commands_string(block)
 
-         # create 10 groups with 10 atoms each
-         cmds = ["group g{} id {}:{}".format(i,10*i+1,10*(i+1)) for i in range(10)]
-         lmp.commands_list(cmds)
+For convenience, the :py:class:`lammps <lammps.lammps>` class also provides a
+command wrapper ``cmd`` that turns any LAMMPS command into a regular function
+call.
 
-         # run commands from a multi-line string
-         block = """
-         clear
-         region  box block 0 2 0 2 0 2
-         create_box 1 box
-         create_atoms 1 single 1.0 1.0 ${zpos}
-         """
-         lmp.commands_string(block)
+For instance, the following LAMMPS command
 
-   .. tab:: PyLammps/IPyLammps API
+.. code-block:: LAMMPS
 
-      Unlike the lammps API, the PyLammps/IPyLammps APIs allow running LAMMPS
-      commands by calling equivalent member functions of :py:class:`PyLammps <lammps.PyLammps>`
-      and :py:class:`IPyLammps <lammps.IPyLammps>` instances.
+   region box block 0 10 0 5 -0.5 0.5
 
-      For instance, the following LAMMPS command
+would normally be executed with the following Python code:
 
-      .. code-block:: LAMMPS
+.. code-block:: python
 
-         region box block 0 10 0 5 -0.5 0.5
+   from lammps import lammps
 
-      can be executed using with the lammps API with the following Python code if ``lmp`` is an
-      instance of :py:class:`lammps <lammps.lammps>`:
+   lmp = lammps()
+   lmp.command("region box block 0 10 0 5 -0.5 0.5")
 
-      .. code-block:: python
+With the ``cmd`` wrapper, any LAMMPS command can be split up into arbitrary parts.
+These parts are then passed to a member function with the name of the :doc:`command <Commands_all>`.
+For the :doc:`region <region>` command that means the :code:`region()` method can be called.
+The arguments of the command can be passed as one string, or
+individually.
 
-         from lammps import lammps
+.. code-block:: python
 
-         lmp = lammps()
-         lmp.command("region box block 0 10 0 5 -0.5 0.5")
+   from lammps import lammps
 
-      With the PyLammps interface, any LAMMPS command can be split up into arbitrary parts.
-      These parts are then passed to a member function with the name of the :doc:`command <Commands_all>`.
-      For the :doc:`region <region>` command that means the :code:`region()` method can be called.
-      The arguments of the command can be passed as one string, or
-      individually.
+   L = lammps()
 
-      .. code-block:: python
+   # pass command parameters as one string
+   L.cmd.region("box block 0 10 0 5 -0.5 0.5")
 
-         from lammps import PyLammps
+   # OR pass them individually
+   L.cmd.region("box block", 0, 10, 0, 5, -0.5, 0.5)
 
-         L = PyLammps()
+In the latter example, all parameters except the first are Python floating-point literals. The
+member function takes the entire parameter list and transparently merges it to a single command
+string.
 
-         # pass command parameters as one string
-         L.region("box block 0 10 0 5 -0.5 0.5")
+The benefit of this approach is avoiding redundant command calls and easier
+parameterization. With `command`, `commands_list`, and `commands_string` the
+parameterization needed to be done manually by creating formatted command
+strings.
 
-         # OR pass them individually
-         L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
+.. code-block:: python
 
-      In the latter example, all parameters except the first are Python floating-point literals. The
-      member function takes the entire parameter list and transparently merges it to a single command
-      string.
+   lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
 
-      The benefit of this approach is avoiding redundant command calls and easier
-      parameterization. In the lammps API parameterization needed to be done
-      manually by creating formatted command strings.
+In contrast, methods of the `cmd` wrapper accept parameters directly and will convert
+them automatically to a final command string.
 
-      .. code-block:: python
+.. code-block:: python
 
-         lmp.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
+   L.cmd.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
 
-      In contrast, methods of PyLammps accept parameters directly and will convert
-      them automatically to a final command string.
+.. note::
 
-      .. code-block:: python
+   When running in IPython you can use Tab-completion after ``L.cmd.`` to see
+   all available LAMMPS commands.
 
-         L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
+Using these facilities, the previous example shown above can be rewritten as follows:
 
-      Using these facilities, the example shown for the lammps API can be rewritten as follows:
+.. code-block:: python
 
-      .. code-block:: python
+   from lammps import lammps
+   L = lammps()
 
-         from lammps import PyLammps
-         L = PyLammps()
+   # read commands from file 'in.melt'
+   L.file('in.melt')
 
-         # read commands from file 'in.melt'
-         L.file('in.melt')
+   # issue a single command
+   L.cmd.variable('zpos', 'index', 1.0)
 
-         # issue a single command
-         L.variable('zpos', 'index', 1.0)
+   # create 10 groups with 10 atoms each
+   for i in range(10):
+      L.cmd.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
 
-         # create 10 groups with 10 atoms each
-         for i in range(10):
-            L.group(f"g{i}", "id", f"{10*i+1}:{10*(i+1)}")
-
-         L.clear()
-         L.region("box block", 0, 2, 0, 2, 0, 2)
-         L.create_box(1, "box")
-         L.create_atoms(1, "single", 1.0, 1.0, "${zpos}")
+   L.cmd.clear()
+   L.cmd.region("box block", 0, 2, 0, 2, 0, 2)
+   L.cmd.create_box(1, "box")
+   L.cmd.create_atoms(1, "single", 1.0, 1.0, "${zpos}")

doc/src/Python_head.rst

@@ -15,6 +15,7 @@ together.
    Python_call
    Python_formats
    Python_examples
+   Python_jupyter
    Python_error
    Python_trouble
 

doc/src/Python_install.rst

@@ -7,6 +7,10 @@ LAMMPS shared library through the Python `ctypes <ctypes_>`_
 module.  Because of the dynamic loading, it is required that LAMMPS is
 compiled in :ref:`"shared" mode <exe>`.
 
+.. versionchanged:: 2Apr2025
+
+LAMMPS currently only supports Python version 3.6 or later.
+
 Two components are necessary for Python to be able to invoke LAMMPS code:
 
 * The LAMMPS Python Package (``lammps``) from the ``python`` folder
@@ -106,13 +110,16 @@ folder that the dynamic loader searches or inside of the installed
 
       .. code-block:: bash
 
-         python install.py -p <python package> -l <shared library> -v <version.h file> [-n]
+         python install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
 
       * The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
       * the ``-l`` flag points to the LAMMPS shared library file to be installed,
       * the ``-v`` flag points to the LAMMPS version header file to extract the version date,
-      * and the optional ``-n`` instructs the script to only build a wheel file
-        but not attempt to install it.
+      * the optional ``-n`` instructs the script to only build a wheel file but not attempt
+        to install it,
+      * and the optional ``-f`` argument instructs the script to force installation even if
+        pip would otherwise refuse installation with an
+        :ref:`error about externally managed environments <externally_managed>`.
 
    .. tab:: Virtual environment
 
@@ -136,11 +143,6 @@ folder that the dynamic loader searches or inside of the installed
          # create virtual environment in folder $HOME/myenv
          python3 -m venv $HOME/myenv
 
-      For Python versions prior 3.3 you can use `virtualenv
-      <https://packaging.python.org/en/latest/key_projects/#virtualenv>`_
-      command instead of "python3 -m venv".  This step has to be done
-      only once.
-
       To activate the virtual environment type:
 
       .. code-block:: bash
@@ -199,6 +201,10 @@ folder that the dynamic loader searches or inside of the installed
 
          The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
 
+In case you run into an "externally-managed-environment" error when
+trying to install the LAMMPS Python module, please refer to
+:ref:`corresponding paragraph <externally_managed>` in the Python HOWTO
+page to learn about options for handling this error.
 
 To verify if LAMMPS can be successfully started from Python, start the
 Python interpreter, load the ``lammps`` Python module and create a
@@ -245,14 +251,14 @@ make MPI calls directly from Python in your script, if you desire.
 We have tested this with `MPI for Python <https://mpi4py.readthedocs.io/>`_
 (aka mpi4py) and you will find installation instruction for it below.
 
-Installation of mpi4py (version 3.0.3 as of Sep 2020) can be done as
+Installation of mpi4py (version 4.0.1 as of Feb 2025) can be done as
 follows:
 
 - Via ``pip`` into a local user folder with:
 
   .. code-block:: bash
 
-     pip install --user mpi4py
+     python3 -m pip install --user mpi4py
 
 - Via ``dnf`` into a system folder for RedHat/Fedora systems:
 
@@ -261,20 +267,20 @@ follows:
      # for use with OpenMPI
      sudo dnf install python3-mpi4py-openmpi
      # for use with MPICH
-     sudo dnf install python3-mpi4py-openmpi
+     sudo dnf install python3-mpi4py-mpich
 
 - Via ``pip`` into a virtual environment (see above):
 
   .. code-block:: console
 
      $ source $HOME/myenv/activate
-     (myenv)$ pip install mpi4py
+     (myenv)$ python -m pip install mpi4py
 
 - Via ``pip`` into a system folder (not recommended):
 
   .. code-block:: bash
 
-     sudo pip install mpi4py
+     sudo python3 -m pip install mpi4py
 
 For more detailed installation instructions and additional options,
 please see the `mpi4py installation <https://mpi4py.readthedocs.io/en/stable/install.html>`_ page.