Test

I did NOT author this commit, I am only pushing it because for some reason, Github does not permit Aidan to do so

Co-authored-by: Aidan Thompson <athomps@sandia.gov>

.github/CODEOWNERS

@@ -101,7 +101,8 @@ src/group.*               @sjplimp
 src/improper.*            @sjplimp
 src/info.*                @akohlmey
 src/kspace.*              @sjplimp
-src/lmptyp.h              @sjplimp
+src/lmptype.h             @sjplimp
+src/label_map.*           @jrgissing @akohlmey
 src/library.*             @sjplimp @akohlmey
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp

.github/release_steps.md

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

.github/workflows/check-cpp23.yml

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

.github/workflows/check-vla.yml

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

.github/workflows/compile-msvc.yml

@@ -1,5 +1,5 @@
-# GitHub action to build LAMMPS on Windows with Visual C++
-name: "Native Windows Compilation and Unit Tests"
+# GitHub action to test LAMMPS on Windows with Visual C++
+name: "Windows Unit Tests"
 
 on:
   push:
@@ -11,11 +11,17 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: Windows Compilation Test
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: windows-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
@@ -23,36 +29,41 @@ jobs:
       with:
         fetch-depth: 2
 
+    - name: Enable MSVC++
+      uses: lammps/setup-msvc-dev@v3
+      with:
+        arch: x64
+
+    - name: Install Ccache
+      run: |
+        choco install ccache ninja -y
+
+    - name: Set up ccache
+      uses: actions/cache@v4
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: win-unit-ccache-${{ github.sha }}
+        restore-keys: win-unit-ccache-
+
     - name: Select Python version
       uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 
     - name: Building LAMMPS via CMake
-      shell: bash
       run: |
+        ccache -z
         python3 -m pip install numpy
         python3 -m pip install pyyaml
-        nuget install MSMPIsdk
-        nuget install MSMPIDIST
-        cmake -C cmake/presets/windows.cmake \
-              -D DOWNLOAD_POTENTIALS=off \
-              -D PKG_PYTHON=on \
-              -D WITH_PNG=off \
-              -D WITH_JPEG=off \
-              -S cmake -B build \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_EXCEPTIONS=on \
-              -D ENABLE_TESTING=on
-        cmake --build build --config Release --parallel 2
+        cmake -C cmake\presets\windows.cmake -D CMAKE_CXX_COMPILER=cl -D CMAKE_CXX_COMPILER_LAUNCHER=ccache -D CMAKE_C_COMPILER=cl -D CMAKE_C_COMPILER_LAUNCHER=ccache -D CMAKE_Fortran_COMPILER="" -D DOWNLOAD_POTENTIALS=off -D PKG_PYTHON=on -D WITH_PNG=off -D WITH_JPEG=off -S cmake -B build -D BUILD_SHARED_LIBS=on -D ENABLE_TESTING=on -D CMAKE_BUILD_TYPE=Release -G Ninja
+        cmake --build build
+        ccache -s
 
     - name: Run LAMMPS executable
-      shell: bash
       run: |
-        ./build/Release/lmp.exe -h
-        ./build/Release/lmp.exe -in bench/in.lj
+        build\lmp.exe -h
+        build\lmp.exe -in bench\in.lj
 
     - name: Run Unit Tests
       working-directory: build
-      shell: bash
-      run: ctest -V -C Release -E FixTimestep:python_move_nve
+      run: ctest -V -E FixTimestep:python_move_nve

.github/workflows/full-regression.yml

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

.github/workflows/kokkos-regression.yaml

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

.github/workflows/quick-regression.yml

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

.github/workflows/style-check.yml

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

.github/workflows/unittest-linux.yml

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

.github/workflows/unittest-macos.yml

@@ -11,6 +11,10 @@ on:
 
   workflow_dispatch:
 
+concurrency:
+  group: ${{ github.event_name }}-${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{github.event_name == 'pull_request'}}
+
 jobs:
   build:
     name: MacOS Unit Test

cmake/CMakeLists.txt

@@ -118,7 +118,7 @@ endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
+  set(CMAKE_TUNE_DEFAULT "-fp-model precise -Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
@@ -141,7 +141,7 @@ endif()
 
 # silence nvcc warnings
 if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
-  set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
+  set(CMAKE_TUNE_DEFAULT "${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)
@@ -165,6 +165,7 @@ if(MSVC)
     add_compile_options(/wd4267)
     add_compile_options(/wd4250)
     add_compile_options(/EHsc)
+    add_compile_options(/utf-8)
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -474,13 +475,13 @@ if(BUILD_OMP)
   if(CMAKE_VERSION VERSION_LESS 3.28)
     get_filename_component(_exe "${CMAKE_CXX_COMPILER}" NAME)
     if((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (_exe STREQUAL "crayCC"))
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
     endif()
   else()
     if(CMAKE_CXX_COMPILER_ID STREQUAL "CrayClang")
-      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE} -fopenmp")
-      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE} -fopenmp")
+      set(CMAKE_SHARED_LINKER_FLAGS_${BTYPE} "${CMAKE_SHARED_LINKER_FLAGS_${BTYPE}} -fopenmp")
+      set(CMAKE_STATIC_LINKER_FLAGS_${BTYPE} "${CMAKE_STATIC_LINKER_FLAGS_${BTYPE}} -fopenmp")
     endif()
   endif()
 endif()
@@ -497,7 +498,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_STANDARD GREATER_EQUA
           PROPERTIES COMPILE_OPTIONS "-std=c++14")
 endif()
 
-if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_TOOLS)
+if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR PKG_RHEO OR BUILD_TOOLS)
   enable_language(C)
   if (NOT USE_INTERNAL_LINALG)
     find_package(LAPACK)
@@ -515,14 +516,6 @@ if(PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_ELECTRODE OR BUILD_T
   endif()
 endif()
 
-find_package(CURL QUIET COMPONENTS HTTP HTTPS)
-option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
-if(WITH_CURL)
-  find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
-  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
-  target_link_libraries(lammps PRIVATE CURL::libcurl)
-endif()
-
 # tweak jpeg library names to avoid linker errors with MinGW cross-compilation
 set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
@@ -580,7 +573,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON RHEO)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM COMPRESS ML-PACE LEPTON EXTRA-COMMAND)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -595,13 +588,8 @@ endif()
 
 set(CMAKE_TUNE_FLAGS "${CMAKE_TUNE_DEFAULT}" CACHE STRING "Compiler and machine specific optimization flags (compilation only)")
 separate_arguments(CMAKE_TUNE_FLAGS)
-foreach(_FLAG ${CMAKE_TUNE_FLAGS})
-  target_compile_options(lammps PRIVATE ${_FLAG})
-  # skip these flags when linking the main executable
-  if(NOT (("${_FLAG}" STREQUAL "-Xcudafe") OR (("${_FLAG}" STREQUAL "--diag_suppress=unrecognized_pragma"))))
-    target_compile_options(lmp PRIVATE ${_FLAG})
-  endif()
-endforeach()
+target_compile_options(lammps PRIVATE ${CMAKE_TUNE_FLAGS})
+target_compile_options(lmp PRIVATE ${CMAKE_TUNE_FLAGS})
 ########################################################################
 # Basic system tests (standard libraries, headers, functions, types)   #
 ########################################################################
@@ -830,9 +818,15 @@ foreach(_DEF ${LAMMPS_DEFINES})
   set(LAMMPS_API_DEFINES "${LAMMPS_API_DEFINES} -D${_DEF}")
 endforeach()
 if(BUILD_SHARED_LIBS)
-  install(TARGETS lammps EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+  install(TARGETS lammps EXPORT LAMMPS_Targets
+          LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+          RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   if(NOT BUILD_MPI)
-    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR})
+    install(TARGETS mpi_stubs EXPORT LAMMPS_Targets
+            LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+            RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
   endif()
   configure_file(pkgconfig/liblammps.pc.in ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc @ONLY)
   install(FILES ${CMAKE_CURRENT_BINARY_DIR}/liblammps${LAMMPS_MACHINE}.pc DESTINATION ${CMAKE_INSTALL_LIBDIR}/pkgconfig)
@@ -973,6 +967,9 @@ message(STATUS "<<< Compilers and Flags: >>>
       C++ Standard:  ${CMAKE_CXX_STANDARD}
       C++ Flags:    ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_${BTYPE}}
       Defines:       ${DEFINES}")
+if(CMAKE_CXX_COMPILER_LAUNCHER)
+  message(STATUS "      Launcher:      ${CMAKE_CXX_COMPILER_LAUNCHER}")
+endif()
 get_target_property(OPTIONS lammps COMPILE_OPTIONS)
 if(OPTIONS)
   message("      Options:       ${OPTIONS}")
@@ -991,6 +988,9 @@ if(_index GREATER -1)
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
       C Flags:      ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${BTYPE}}")
+  if(CMAKE_C_COMPILER_LAUNCHER)
+    message(STATUS "      Launcher:      ${CMAKE_C_COMPILER_LAUNCHER}")
+  endif()
 endif()
 message(STATUS "<<< Linker flags: >>>")
 message(STATUS "Executable name:  ${LAMMPS_BINARY}")

cmake/Modules/Documentation.cmake

@@ -4,6 +4,8 @@
 option(BUILD_DOC "Build LAMMPS HTML documentation" OFF)
 
 if(BUILD_DOC)
+  option(BUILD_DOC_VENV "Build LAMMPS documentation virtual environment" ON)
+  mark_as_advanced(BUILD_DOC_VENV)
   # Current Sphinx versions require at least Python 3.8
   # use default (or custom) Python executable, if version is sufficient
   if(Python_VERSION VERSION_GREATER_EQUAL 3.8)
@@ -18,14 +20,6 @@ if(BUILD_DOC)
   find_package(Doxygen 1.8.10 REQUIRED)
   file(GLOB DOC_SOURCES CONFIGURE_DEPENDS ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
-  add_custom_command(
-    OUTPUT docenv
-    COMMAND ${VIRTUALENV} docenv
-  )
-
-  set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
-  set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
-
   set(SPHINX_CONFIG_DIR ${LAMMPS_DOC_DIR}/utils/sphinx-config)
   set(SPHINX_CONFIG_FILE_TEMPLATE ${SPHINX_CONFIG_DIR}/conf.py.in)
   set(SPHINX_STATIC_DIR  ${SPHINX_CONFIG_DIR}/_static)
@@ -44,14 +38,32 @@ if(BUILD_DOC)
   # configure paths in conf.py, since relative paths change when file is copied
   configure_file(${SPHINX_CONFIG_FILE_TEMPLATE} ${DOC_BUILD_CONFIG_FILE})
 
-  add_custom_command(
-    OUTPUT ${DOC_BUILD_DIR}/requirements.txt
-    DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
-    COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
-  )
+  if(BUILD_DOC_VENV)
+    add_custom_command(
+      OUTPUT docenv
+      COMMAND ${VIRTUALENV} docenv
+    )
+
+    set(DOCENV_BINARY_DIR ${CMAKE_BINARY_DIR}/docenv/bin)
+    set(DOCENV_REQUIREMENTS_FILE ${LAMMPS_DOC_DIR}/utils/requirements.txt)
+
+    add_custom_command(
+      OUTPUT ${DOC_BUILD_DIR}/requirements.txt
+      DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
+      COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+      COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    )
+
+    set(DOCENV_DEPS docenv ${DOC_BUILD_DIR}/requirements.txt)
+    if(NOT TARGET Sphinx::sphinx-build)
+      add_executable(Sphinx::sphinx-build IMPORTED GLOBAL)
+      set_target_properties(Sphinx::sphinx-build PROPERTIES IMPORTED_LOCATION "${DOCENV_BINARY_DIR}/sphinx-build")
+    endif()
+  else()
+    find_package(Sphinx)
+  endif()
 
   set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
   set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
@@ -97,8 +109,9 @@ if(BUILD_DOC)
   endif()
   add_custom_command(
     OUTPUT html
-    DEPENDS ${DOC_SOURCES} docenv ${DOC_BUILD_DIR}/requirements.txt ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
-    COMMAND ${DOCENV_BINARY_DIR}/sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
+    DEPENDS ${DOC_SOURCES} ${DOCENV_DEPS} ${DOXYGEN_XML_DIR}/index.xml ${BUILD_DOC_CONFIG_FILE}
+    COMMAND ${Python3_EXECUTABLE} ${LAMMPS_DOC_DIR}/utils/make-globbed-tocs.py -d ${LAMMPS_DOC_DIR}/src
+    COMMAND Sphinx::sphinx-build ${SPHINX_EXTRA_OPTS} -b html -c ${DOC_BUILD_DIR} -d ${DOC_BUILD_DIR}/doctrees ${LAMMPS_DOC_DIR}/src ${DOC_BUILD_DIR}/html
     COMMAND ${CMAKE_COMMAND} -E create_symlink Manual.html ${DOC_BUILD_DIR}/html/index.html
     COMMAND ${CMAKE_COMMAND} -E copy_directory ${LAMMPS_DOC_DIR}/src/PDF ${DOC_BUILD_DIR}/html/PDF
     COMMAND ${CMAKE_COMMAND} -E remove -f ${DOXYGEN_XML_DIR}/run.stamp

cmake/Modules/FindSphinx.cmake

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

cmake/Modules/FindVORO.cmake

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

cmake/Modules/Packages/EXTRA-COMMAND.cmake

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

cmake/Modules/Packages/H5MD.cmake

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

cmake/Modules/Packages/KOKKOS.cmake

@@ -8,8 +8,24 @@ endif()
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
-  message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
-  set(Kokkos_ENABLE_CUDA_LAMBDA ON CACHE BOOL "" FORCE)
+  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.
@@ -18,6 +34,15 @@ if(Kokkos_ENABLE_OPENMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   endif()
 endif()
+
+if(Kokkos_ENABLE_SERIAL)
+  if(NOT (Kokkos_ENABLE_OPENMP OR Kokkos_ENABLE_THREADS OR
+    Kokkos_ENABLE_CUDA OR Kokkos_ENABLE_HIP OR Kokkos_ENABLE_SYCL
+    OR Kokkos_ENABLE_OPENMPTARGET))
+  option(Kokkos_ENABLE_ATOMICS_BYPASS "Disable atomics for Kokkos Serial Backend" ON)
+  mark_as_advanced(Kokkos_ENABLE_ATOMICS_BYPASS)
+  endif()
+endif()
 ########################################################################
 
 option(EXTERNAL_KOKKOS "Build against external kokkos library" OFF)
@@ -45,8 +70,8 @@ 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/4.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "243de871b3dc2cf3990c1c404032df83" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  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")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
@@ -71,7 +96,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 4.3.01 REQUIRED CONFIG)
+  find_package(Kokkos 4.4.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
@@ -105,6 +130,7 @@ 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
@@ -127,7 +153,7 @@ if(PKG_KSPACE)
                                  ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   set(FFT_KOKKOS "KISS" CACHE STRING "FFT library for Kokkos-enabled KSPACE package")
-  set(FFT_KOKKOS_VALUES KISS FFTW3 MKL HIPFFT CUFFT)
+  set(FFT_KOKKOS_VALUES KISS FFTW3 MKL NVPL HIPFFT CUFFT MKL_GPU)
   set_property(CACHE FFT_KOKKOS PROPERTY STRINGS ${FFT_KOKKOS_VALUES})
   validate_option(FFT_KOKKOS FFT_KOKKOS_VALUES)
   string(TOUPPER ${FFT_KOKKOS} FFT_KOKKOS)
@@ -137,10 +163,8 @@ if(PKG_KSPACE)
       message(FATAL_ERROR "The CUDA backend of Kokkos requires either KISS FFT or CUFFT.")
     elseif(FFT_KOKKOS STREQUAL "KISS")
       message(WARNING "Using KISS FFT with the CUDA backend of Kokkos may be sub-optimal.")
-      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_KISS)
     elseif(FFT_KOKKOS STREQUAL "CUFFT")
       find_package(CUDAToolkit REQUIRED)
-      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_CUFFT)
       target_link_libraries(lammps PRIVATE CUDA::cufft)
     endif()
   elseif(Kokkos_ENABLE_HIP)
@@ -152,10 +176,21 @@ if(PKG_KSPACE)
     elseif(FFT_KOKKOS STREQUAL "HIPFFT")
       include(DetectHIPInstallation)
       find_package(hipfft REQUIRED)
-      target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_HIPFFT)
       target_link_libraries(lammps PRIVATE hip::hipfft)
     endif()
+  elseif(FFT_KOKKOS STREQUAL "MKL_GPU")
+    if(NOT Kokkos_ENABLE_SYCL)
+      message(FATAL_ERROR "Using MKL_GPU FFT currently requires the SYCL backend of Kokkos.")
+    endif()
+    find_package(MKL REQUIRED)
+    target_link_libraries(lammps PRIVATE mkl_sycl_dft mkl_intel_ilp64 mkl_tbb_thread mkl_core tbb)
+  elseif(FFT_KOKKOS STREQUAL "MKL")
+    find_package(MKL REQUIRED)
+  elseif(FFT_KOKKOS STREQUAL "NVPL")
+      find_package(nvpl_fft REQUIRED)
+      target_link_libraries(lammps PRIVATE nvpl::fftw)
   endif()
+  target_compile_definitions(lammps PRIVATE -DFFT_KOKKOS_${FFT_KOKKOS})
 endif()
 
 if(PKG_ML-IAP)

cmake/Modules/Packages/KSPACE.cmake

@@ -10,7 +10,7 @@ if(${FFTW}_FOUND)
 else()
   set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
 endif()
-set(FFT_VALUES KISS FFTW3 MKL)
+set(FFT_VALUES KISS FFTW3 MKL NVPL)
 set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
 validate_option(FFT FFT_VALUES)
 string(TOUPPER ${FFT} FFT)
@@ -41,6 +41,10 @@ elseif(FFT STREQUAL "MKL")
     target_compile_definitions(lammps PRIVATE -DFFT_MKL_THREADS)
   endif()
   target_link_libraries(lammps PRIVATE MKL::MKL)
+elseif(FFT STREQUAL "NVPL")
+  find_package(nvpl_fft REQUIRED)
+  target_compile_definitions(lammps PRIVATE -DFFT_NVPL)
+  target_link_libraries(lammps PRIVATE nvpl::fftw)
 else()
   # last option is KISSFFT
   target_compile_definitions(lammps PRIVATE -DFFT_KISS)

cmake/Modules/Packages/PLUMED.cmake

@@ -32,9 +32,9 @@ 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/v2.9.1/plumed-src-2.9.1.tgz"
+set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.9.2/plumed-src-2.9.2.tgz"
   CACHE STRING "URL for PLUMED tarball")
-set(PLUMED_MD5 "c3b2d31479c1e9ce211719d40e9efbd7" CACHE STRING "MD5 checksum of PLUMED tarball")
+set(PLUMED_MD5 "04862602a372c1013bdfee2d6d03bace" CACHE STRING "MD5 checksum of PLUMED tarball")
 
 mark_as_advanced(PLUMED_URL)
 mark_as_advanced(PLUMED_MD5)

cmake/Modules/Packages/RHEO.cmake

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

cmake/Modules/Packages/VORONOI.cmake

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

cmake/presets/kokkos-sycl-intel.cmake

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

cmake/presets/mingw-cross.cmake

@@ -67,6 +67,7 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SMTBQ

cmake/presets/most.cmake

@@ -60,6 +60,7 @@ set(ALL_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SPH

cmake/presets/oneapi.cmake

@@ -3,26 +3,9 @@
 set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
-set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
-
 set(MPI_CXX "icpx" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
-unset(HAVE_OMP_H_INCLUDE CACHE)
-set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp;-qopenmp-simd" CACHE STRING "" FORCE)
-set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
+# force using internal BLAS/LAPCK since external ones may not be ABI compatible
+set(USE_INTERNAL_LINALG ON CACHE BOOL "" FORCE)
 

cmake/presets/windows.cmake

@@ -60,6 +60,7 @@ set(WIN_PACKAGES
   REACTION
   REAXFF
   REPLICA
+  RHEO
   RIGID
   SHOCK
   SMTBQ

doc/.gitignore

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

doc/Makefile

@@ -83,7 +83,10 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+globbed-tocs:
+	$(PYTHON) $(BUILDDIR)/utils/make-globbed-tocs.py -d $(RSTDIR)
+
+html: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -113,7 +116,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+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
@@ -132,7 +135,7 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf fasthtml/PDF/.[sg]*
 	@echo "Fast HTML build finished. The HTML pages are in doc/fasthtml."
 
-spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen globbed-tocs $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; \
@@ -143,7 +146,7 @@ spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives
 	)
 	@echo "Spell check finished."
 
-epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+epub: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p epub/JPG
@@ -166,7 +169,7 @@ mobi: epub
 	@ebook-convert LAMMPS.epub LAMMPS.mobi
 	@echo "Conversion finished. The MOBI manual file is created."
 
-pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
+pdf: xmlgen globbed-tocs $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi

doc/documentation_conventions.md

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

doc/github-development-workflow.md

@@ -6,7 +6,9 @@ choices the LAMMPS developers have agreed on. Git and GitHub provide the
 tools, but do not set policies, so it is up to the developers to come to
 an agreement as to how to define and interpret policies. This document
 is likely to change as our experiences and needs change, and we try to
-adapt it accordingly. Last change 2023-02-10.
+adapt it accordingly.
+
+Last change: 2023-02-10
 
 ## Table of Contents
 
@@ -72,7 +74,7 @@ be assigned to signal urgency to merge this pull request quickly.
 People can be assigned to review a pull request in two ways:
 
   * They can be assigned manually to review a pull request
-    by the submitter or a LAMMPS developer
+    by the submitter or a LAMMPS developer.
   * They can be automatically assigned, because a developer's GitHub
     handle matches a file pattern in the `.github/CODEOWNERS` file,
     which associates developers with the code they contributed and
@@ -86,9 +88,9 @@ required before merging, in addition to passing all automated
 compilation and unit tests.  Merging counts as implicit approval, so
 does submission of a pull request (by a LAMMPS developer). So the person
 doing the merge may not also submit an approving review.  The GitHub
-feature, that reviews from code owners are "hard" reviews (i.e. they
-must all approve before merging is allowed), is currently disabled.
-It is in the discretion of the merge maintainer to assess when a
+feature that reviews from code owners are "hard" reviews (i.e. they
+must all approve before merging is allowed) is currently disabled.
+It is at the discretion of the merge maintainer to assess when a
 sufficient degree of approval has been reached, especially from external
 collaborators.  Reviews may be (automatically) dismissed, when the
 reviewed code has been changed. Review may be requested a second time.
@@ -147,7 +149,8 @@ only contain bug fixes, feature additions to peripheral functionality,
 and documentation updates.  In between stable releases, bug fixes and
 infrastructure updates are back-ported from the "develop" branch to the
 "maintenance" branch and occasionally merged into "stable" and published
-as update releases.
+as update releases. Further explanation of LAMMPS versions can be found
+[in the documentation](https://docs.lammps.org/Manual_version.html).
 
 ## Project Management
 

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "29 August 2024" "2024-08-29"
+.TH LAMMPS "1" "19 November 2024" "2024-11-19"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 29 August 2024
+\- Molecular Dynamics Simulator.  Version 19 November 2024
 
 .SH SYNOPSIS
 .B lmp

doc/msi2lmp.1

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

doc/src/Build_development.rst

@@ -138,12 +138,27 @@ during development:
 The status of this automated testing can be viewed on `https://ci.lammps.org
 <https://ci.lammps.org>`_.
 
-The scripts and inputs for integration, run, and regression testing
-are maintained in a
-`separate repository <https://github.com/lammps/lammps-testing>`_
-of the LAMMPS project on GitHub.  A few tests are also run as GitHub
-Actions and their configuration files are in the ``.github/workflows/``
-folder of the LAMMPS git tree.
+The scripts and inputs for integration, run, and legacy regression
+testing are maintained in a `separate repository
+<https://github.com/lammps/lammps-testing>`_ of the LAMMPS project on
+GitHub.  A few tests are also run as GitHub Actions and their
+configuration files are in the ``.github/workflows/`` folder of the
+LAMMPS git tree.
+
+Regression tests can also be performed locally with the :ref:`regression
+tester tool <regression>`.  The tool checks if a given LAMMPS binary run
+with selected input examples produces thermo output that is consistent
+with the provided log files.  The script can be run in one pass over all
+available input files, but it can also first create multiple lists of
+inputs or folders that can then be run with multiple workers
+concurrently to speed things up.  Another mode allows to do a quick
+check of inputs that contain commands that have changes in the current
+checkout branch relative to a git branch.  This works similar to the two
+pass mode, but will select only shorter runs and no more than 100 inputs
+that are chosen randomly.  This ensures that this test runs
+significantly faster compared to the full test run.  These test runs can
+also be performed with instrumented LAMMPS binaries (see previous
+section).
 
 The unit testing facility is integrated into the CMake build process of
 the LAMMPS source code distribution itself.  It can be enabled by
@@ -630,11 +645,35 @@ The following target are available for both, GNU make and CMake:
 GitHub command line interface
 -----------------------------
 
-GitHub is developing a `tool for the command line
-<https://cli.github.com>`_ that interacts with the GitHub website via a
-command called ``gh``.  This can be extremely convenient when working
-with a Git repository hosted on GitHub (like LAMMPS).  It is thus highly
-recommended to install it when doing LAMMPS development.
+GitHub has developed a `command line tool <https://cli.github.com>`_
+to interact with the GitHub website via a command called ``gh``.
+This is extremely convenient when working with a Git repository hosted
+on GitHub (like LAMMPS).  It is thus highly recommended to install it
+when doing LAMMPS development.  To use ``gh`` you must be within a git
+checkout of a repository and you must obtain an authentication token
+to connect your checkout with a GitHub user.  This is done with the
+command: ``gh auth login`` where you then have to follow the prompts.
+Here are some examples:
 
-The capabilities of the ``gh`` command is continually expanding, so
-please see the documentation at https://cli.github.com/manual/
+.. list-table::
+   :header-rows: 1
+   :widths: 34 66
+
+   * - Command
+     - Description
+   * - ``gh pr list``
+     - List currently open pull requests
+   * - ``gh pr checks 404``
+     - Shows the status of all checks for pull request #404
+   * - ``gh pr view 404``
+     - Shows the description and recent comments for pull request #404
+   * - ``gh co 404``
+     - Check out the branch from pull request #404; set up for pushing changes
+   * - ``gh issue list``
+     - List currently open issues
+   * - ``gh issue view 430 --comments``
+     - Shows the description and all comments for issue #430
+
+The capabilities of the ``gh`` command are continually expanding, so
+for more details please see the documentation at https://cli.github.com/manual/
+or use ``gh --help`` or ``gh <command> --help`` for embedded help.

doc/src/Build_extras.rst

@@ -7,6 +7,8 @@ in addition to
 .. list-table::
    :align: center
    :header-rows: 1
+   :widths: 50 50
+   :width: 80%
 
    * - CMake build
      - Traditional make
@@ -115,7 +117,7 @@ GPU package
 
 To build with this package, you must choose options for precision and
 which GPU hardware to build for. The GPU package currently supports
-three different types of backends: OpenCL, CUDA and HIP.
+three different types of back ends: OpenCL, CUDA and HIP.
 
 CMake build
 ^^^^^^^^^^^
@@ -205,7 +207,7 @@ necessary for ``hipcc`` and the linker to work correctly.
 .. versionadded:: 3Aug2022
 
 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 backends. To use
+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,
 the use of HIP for Intel GPUs is experimental. You should only use this
@@ -751,14 +753,27 @@ This list was last updated for version 4.3.0 of the Kokkos library.
       platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on
       NVIDIA GPUs.
 
-      To simplify compilation, five preset files are included in the
+      For Intel GPUs using SYCL, set these variables:
+
+      .. code-block:: bash
+
+         -D Kokkos_ARCH_HOSTARCH=yes   # HOSTARCH = HOST from list above
+         -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
+         -D Kokkos_ENABLE_SYCL=yes
+         -D Kokkos_ENABLE_OPENMP=yes
+         -D FFT_KOKKOS=MKL_GPU
+
+      This will enable FFTs on the GPU using the oneMKL library.
+
+      To simplify compilation, six preset files are included in the
       ``cmake/presets`` folder, ``kokkos-serial.cmake``,
       ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
-      ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``.  They will enable
-      the KOKKOS package and enable some hardware choices.  For GPU
-      support those preset files must be customized to match the
-      hardware used. So to compile with CUDA device parallelization with
-      some common packages enabled, you can do the following:
+      ``kokkos-hip.cmake``, ``kokkos-sycl-nvidia.cmake``, and
+      ``kokkos-sycl-intel.cmake``.  They will enable the KOKKOS
+      package and enable some hardware choices.  For GPU support those
+      preset files must be customized to match the hardware used. So
+      to compile with CUDA device parallelization with some common
+      packages enabled, you can do the following:
 
       .. code-block:: bash
 
@@ -830,6 +845,18 @@ This list was last updated for version 4.3.0 of the Kokkos library.
          FFT_INC = -DFFT_HIPFFT          # enable use of hipFFT (optional)
          FFT_LIB = -lhipfft              # link to hipFFT library
 
+      For Intel GPUs using SYCL:
+
+      .. code-block:: make
+
+         KOKKOS_DEVICES = SYCL
+         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is
+                                         #            hosting the GPU
+                                         # GPUARCH = GPU from list above
+         FFT_INC = -DFFT_KOKKOS_MKL_GPU  # enable use of oneMKL for Intel GPUs (optional)
+                                         # link to oneMKL FFT library
+         FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -mkl_core -ltbb
+
 Advanced KOKKOS compilation settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -2224,28 +2251,38 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 RHEO package
 ------------
 
-To build with this package you must have the `GNU Scientific Library
-(GSL) <https://www.gnu.org/software/gsl/>` installed in locations that
-are accessible in your environment.  The GSL library should be at least
-version 2.7.
+This package depends on the BPM package.
 
 .. tabs::
 
    .. tab:: CMake build
 
-      If CMake cannot find the GSL library or include files, you can set:
-
       .. code-block:: bash
 
-         -D GSL_ROOT_DIR=path    # path to root of GSL installation
+         -D PKG_RHEO=yes               # enable the package itself
+         -D PKG_BPM=yes                # the RHEO package requires BPM
+         -D USE_INTERNAL_LINALG=value  # prefer internal LAPACK if true
+
+      Some features in the RHEO package are dependent on code in the BPM
+      package so the latter one *must* be enabled as well.
+
+      The RHEO package also requires LAPACK (and BLAS) and CMake
+      can identify their locations and pass that info to the RHEO
+      build script.  But on some systems this may cause problems when
+      linking or the dependency is not desired.  By using the setting
+      ``-D USE_INTERNAL_LINALG=yes`` when running the CMake
+      configuration, you will select compiling and linking the bundled
+      linear algebra library and work around the limitations.
 
    .. tab:: Traditional make
 
-      LAMMPS will try to auto-detect the GSL compiler and linker flags
-      from the corresponding ``pkg-config`` file (``gsl.pc``), otherwise
-      you can edit the file ``lib/rheo/Makefile.lammps``
-      to specify the paths and library names where indicated by comments.
-      This must be done **before** the package is installed.
+      The RHEO package requires LAPACK (and BLAS) which can be either
+      a system provided library or the bundled "linalg" library. This
+      is a subset of LAPACK translated to C++.  For that, one of the
+      provided ``Makefile.lammps.<config>`` files needs to be copied
+      to ``Makefile.lammps`` and edited as needed.  The default file
+      uses the bundled "linalg" library, which can be built by
+      ``make lib-linalg args='-m serial'`` in the ``src`` folder.
 
 ----------
 

doc/src/Build_settings.rst

@@ -67,10 +67,10 @@ libraries and better pipelining for packing and communication.
 
       .. code-block:: bash
 
-         -D FFT=value              # FFTW3 or MKL or KISS, default is FFTW3 if found,
-                                   # else KISS
-         -D FFT_KOKKOS=value       # FFTW3 or MKL or KISS or CUFFT or HIPFFT,
-                                   # default is KISS
+         -D FFT=value              # FFTW3 or MKL or NVPL or KISS,
+                                   # default is FFTW3 if found, else KISS
+         -D FFT_KOKKOS=value       # FFTW3 or MKL or NVPL or KISS or CUFFT
+                                   # or HIPFFT or MKL_GPU, default is KISS
          -D FFT_SINGLE=value       # yes or no (default), no = double precision
          -D FFT_PACK=value         # array (default) or pointer or memcpy
          -D FFT_USE_HEFFTE=value   # yes or no (default), yes links to heFFTe
@@ -103,6 +103,8 @@ libraries and better pipelining for packing and communication.
          -D FFT_HEFFTE_BACKEND=value # FFTW or MKL or empty/undefined for the stock
                                      # heFFTe back end
          -D Heffte_ROOT=path         # path to an existing heFFTe installation
+         -D nvpl_fft_INCLUDE_DIR=path # path to NVPL FFT include files
+         -D nvpl_fft_LIBRARY_DIR=path # path to NVPL FFT libraries
 
       .. note::
 
@@ -121,9 +123,10 @@ libraries and better pipelining for packing and communication.
       .. code-block:: make
 
          FFT_INC = -DFFT_<NAME>        # where <NAME> is KISS (default), FFTW3,
-                                       # FFTW (same as FFTW3), or MKL
+                                       # FFTW (same as FFTW3), NVPL, or MKL
          FFT_INC = -DFFT_KOKKOS_<NAME> # where <NAME> is KISS (default), FFTW3,
-                                       # FFTW (same as FFTW3), MKL, CUFFT, or HIPFFT
+                                       # FFTW (same as FFTW3), NVPL, MKL, CUFFT,
+                                       # HIPFFT, or MKL_GPU
          FFT_INC = -DFFT_SINGLE       # do not specify for double precision
          FFT_INC = -DFFT_FFTW_THREADS # enable using threaded FFTW3 libraries
          FFT_INC = -DFFT_MKL_THREADS  # enable using threaded FFTs with MKL libraries
@@ -141,6 +144,9 @@ libraries and better pipelining for packing and communication.
          # cuFFT either precision
          FFT_LIB =  -lcufft
 
+         # MKL_GPU either precision
+         FFT_LIB = -lmkl_sycl_dft -lmkl_intel_ilp64 -lmkl_tbb_thread -lmkl_core -ltbb
+
          # FFTW3 double precision
          FFT_LIB =  -lfftw3
 
@@ -165,6 +171,10 @@ libraries and better pipelining for packing and communication.
          # MKL with automatic runtime selection of interface libs
          FFT_LIB =  -lmkl_rt
 
+         # threaded NVPL FFT
+         FFT_LIB =  -lnvpl_fftw
+
+
       As with CMake, you do not need to set paths in ``FFT_INC`` or
       ``FFT_PATH``, if the compiler can find the FFT header and library
       files in its default search path.  You must specify ``FFT_LIB``
@@ -218,10 +228,15 @@ The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
+The NVIDIA Performance Libraries (NVPL) FFT library is optimized for NVIDIA
+Grace Armv9.0 architecture. You can download it from https://docs.nvidia.com/nvpl/
+
 The cuFFT and hipFFT FFT libraries are packaged with NVIDIA's CUDA and
 AMD's HIP installations, respectively. These FFT libraries require the
 Kokkos acceleration package to be enabled and the Kokkos back end to be
-GPU-resident (i.e., HIP or CUDA).
+GPU-resident (i.e., HIP or CUDA). Similarly, GPU offload of FFTs on
+Intel GPUs with oneMKL currently requires the Kokkos acceleration
+package to be enabled with the SYCL back end.
 
 Performing 3d FFTs in parallel can be time-consuming due to data access
 and required communication.  This cost can be reduced by performing

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>`

doc/src/Commands_fix.rst

@@ -43,7 +43,7 @@ OPT.
    * :doc:`brownian/asphere <fix_brownian>`
    * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`charge/regulation <fix_charge_regulation>`
-   * :doc:`cmap <fix_cmap>`
+   * :doc:`cmap (k) <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
    * :doc:`controller <fix_controller>`
    * :doc:`damping/cundall <fix_damping_cundall>`
@@ -134,7 +134,7 @@ OPT.
    * :doc:`nve/dot <fix_nve_dot>`
    * :doc:`nve/dotc/langevin <fix_nve_dotc_langevin>`
    * :doc:`nve/eff <fix_nve_eff>`
-   * :doc:`nve/limit <fix_nve_limit>`
+   * :doc:`nve/limit (k) <fix_nve_limit>`
    * :doc:`nve/line <fix_nve_line>`
    * :doc:`nve/manifold/rattle <fix_nve_manifold_rattle>`
    * :doc:`nve/noforce <fix_nve_noforce>`
@@ -178,6 +178,7 @@ OPT.
    * :doc:`python/move <fix_python_move>`
    * :doc:`qbmsst <fix_qbmsst>`
    * :doc:`qeq/comb (o) <fix_qeq_comb>`
+   * :doc:`qeq/ctip <fix_qeq>`
    * :doc:`qeq/dynamic <fix_qeq>`
    * :doc:`qeq/fire <fix_qeq>`
    * :doc:`qeq/point <fix_qeq>`
@@ -186,10 +187,11 @@ OPT.
    * :doc:`qeq/slater <fix_qeq>`
    * :doc:`qmmm <fix_qmmm>`
    * :doc:`qtb <fix_qtb>`
+   * :doc:`qtpie/reaxff <fix_qtpie_reaxff>`
    * :doc:`rattle <fix_shake>`
    * :doc:`reaxff/bonds (k) <fix_reaxff_bonds>`
    * :doc:`reaxff/species (k) <fix_reaxff_species>`
-   * :doc:`recenter <fix_recenter>`
+   * :doc:`recenter (k) <fix_recenter>`
    * :doc:`restrain <fix_restrain>`
    * :doc:`rheo <fix_rheo>`
    * :doc:`rheo/oxidation <fix_rheo_oxidation>`
@@ -267,7 +269,7 @@ OPT.
    * :doc:`wall/piston <fix_wall_piston>`
    * :doc:`wall/reflect (k) <fix_wall_reflect>`
    * :doc:`wall/reflect/stochastic <fix_wall_reflect_stochastic>`
-   * :doc:`wall/region <fix_wall_region>`
+   * :doc:`wall/region (k) <fix_wall_region>`
    * :doc:`wall/region/ees <fix_wall_ees>`
    * :doc:`wall/srd <fix_wall_srd>`
    * :doc:`wall/table <fix_wall>`

doc/src/Commands_pair.rst

@@ -44,7 +44,7 @@ OPT.
    * :doc:`born/coul/wolf/cs (g) <pair_cs>`
    * :doc:`born/gauss <pair_born_gauss>`
    * :doc:`bpm/spring <pair_bpm_spring>`
-   * :doc:`brownian (o) <pair_brownian>`
+   * :doc:`brownian (ko) <pair_brownian>`
    * :doc:`brownian/poly (o) <pair_brownian>`
    * :doc:`buck (giko) <pair_buck>`
    * :doc:`buck/coul/cut (giko) <pair_buck>`
@@ -59,6 +59,7 @@ OPT.
    * :doc:`comb (o) <pair_comb>`
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
+   * :doc:`coul/ctip <pair_coul>`
    * :doc:`coul/cut (gko) <pair_coul>`
    * :doc:`coul/cut/dielectric <pair_dielectric>`
    * :doc:`coul/cut/global (o) <pair_coul>`

doc/src/Developer_write.rst

@@ -12,3 +12,4 @@ details are provided for writing code for LAMMPS.
 
    Developer_write_pair
    Developer_write_fix
+   Developer_write_command

doc/src/Developer_write_command.rst

@@ -0,0 +1,348 @@
+Writing a new command style
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Command styles allow to do system manipulations or interfaces to the
+operating system.
+
+In the text below, we will discuss the implementation of one example.  As
+shown on the page for :doc:`writing or extending command styles
+<Modify_command>`, in order to implement a new command style, a new class
+must be written that is either directly or indirectly derived from the
+``Command`` class.  There is just one method that must be implemented:
+``Command::command()``.  In addition, a custom constructor is needed to get
+access to the members of the ``LAMMPS`` class like the ``Error`` class to
+print out error messages.  The ``Command::command()`` method processes the
+arguments passed to the command in the input and executes it.  Any other
+methods would be for the convenience of implementation of the new command.
+
+In general, new command styles should be added to the :ref:`EXTRA-COMMAND
+package <PKG-EXTRA-COMMAND>`.  If you feel that your contribution should be
+added to a different package, please consult with the :doc:`LAMMPS
+developers <Intro_authors>` first.  The contributed code needs to support
+the :doc:`traditional GNU make build process <Build_make>` **and** the
+:doc:`CMake build process <Build_cmake>`.
+
+----
+
+Case 1: Implementing the geturl command
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+In this section, we will describe the procedure of adding a simple command
+style to LAMMPS: the :doc:`geturl command <geturl>` that allows to download
+files directly without having to rely on an external program like "wget" or
+"curl".  The complete implementation can be found in the files
+``src/EXTRA-COMMAND/geturl.cpp`` and ``src/EXTRA-COMMAND/geturl.h`` of the
+LAMMPS source code.
+
+Interfacing the *libcurl* library
+"""""""""""""""""""""""""""""""""
+
+Rather than implementing the various protocols for downloading files, we
+rely on an external library: `libcurl library <https:://curl.se/libcurl/>`_.
+This requires that the library and its headers are installed.  For the
+traditional GNU make build system, this simply requires edits to the machine
+makefile to add compilation flags like for other libraries.  For the CMake
+based build system, we need to add some lines to the file
+``cmake/Modules/Packages/EXTRA-COMMAND.cmake``:
+
+.. code-block:: cmake
+
+   find_package(CURL QUIET COMPONENTS HTTP HTTPS)
+   option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
+   if(WITH_CURL)
+     find_package(CURL REQUIRED COMPONENTS HTTP HTTPS)
+     target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
+     target_link_libraries(lammps PRIVATE CURL::libcurl)
+   endif()
+
+The first ``find_package()`` command uses a built-in CMake module to find
+an existing *libcurl* installation with development headers and support for
+using the HTTP and HTTPS protocols.  The "QUIET" flag ensures that there is
+no screen output and no error if the search fails.  The status of the search
+is recorded in the "${CURL_FOUND}" variable.  That variable sets the default
+of the WITH_CURL option, which toggles whether support for *libcurl* is included
+or not.
+
+The second ``find_package()`` uses the "REQUIRED" flag to produce an error
+if the WITH_CURL option was set to ``True``, but no suitable *libcurl*
+implementation with development support was found.  This construct is used
+so that the CMake script code inside the ``if(WITH_CURL)`` and ``endif()``
+block can be expanded later to download and compile *libcurl* as part of the
+LAMMPS build process, if it is not found locally.  The
+``target_compile_definitions()`` function added the define ``-DLAMMPS_CURL``
+to the compilation flags when compiling objects for the LAMMPS library.
+This allows to always compile the :doc:`geturl command <geturl>`, but use
+pre-processing to compile in the interface to *libcurl* only when it is
+present and usable and otherwise stop with an error message about the
+unavailability of *libcurl* to execute the functionality of the command.
+
+Header file
+"""""""""""
+
+The first segment of any LAMMPS source should be the copyright and
+license statement.  Note the marker in the first line to indicate to
+editors like emacs that this file is a C++ source, even though the .h
+extension suggests a C source (this is a convention inherited from the
+very beginning of the C++ version of LAMMPS).
+
+.. code-block:: c++
+
+   /* -*- c++ -*- ----------------------------------------------------------
+      LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+      https://www.lammps.org/, Sandia National Laboratories
+      LAMMPS development team: developers@lammps.org
+
+      Copyright (2003) Sandia Corporation.  Under the terms of Contract
+      DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+      certain rights in this software.  This software is distributed under
+      the GNU General Public License.
+
+      See the README file in the top-level LAMMPS directory.
+   ------------------------------------------------------------------------- */
+
+Every command style must be registered in LAMMPS by including the following
+lines of code in the second part of the header after the copyright
+message and before the include guards for the class definition:
+
+.. code-block:: c++
+
+   #ifdef COMMAND_CLASS
+   // clang-format off
+   CommandStyle(geturl,GetURL);
+   // clang-format on
+   #else
+
+This block between ``#ifdef COMMAND_CLASS`` and ``#else`` will be
+included by the ``Input`` class in ``input.cpp`` to build a map of
+"factory functions" that will create an instance of a Command class
+and call its ``command()`` method.  The map connects the name of the
+command ``geturl`` with the name of the class ``GetURL``.  During
+compilation, LAMMPS constructs a file ``style_command.h`` that contains
+``#include`` statements for all "installed" command styles.  Before
+including ``style_command.h`` into ``input.cpp``, the ``COMMAND_CLASS``
+define is set and the ``CommandStyle(name,class)`` macro defined.  The
+code of the macro adds the installed command styles to the "factory map"
+which enables the ``Input`` to execute the command.
+
+The list of header files to include in ``style_command.h`` is automatically
+updated by the build system if there are new files, so the presence of the
+new header file in the ``src/EXTRA-COMMAND`` folder and the enabling of the
+EXTRA-COMMAND package will trigger LAMMPS to include the new command style
+when it is (re-)compiled.  The "// clang-format" format comments are needed
+so that running :ref:`clang-format <clang-format>` on the file will not
+insert unwanted blanks which would break the ``CommandStyle`` macro.
+
+The third part of the header file is the actual class definition of the
+``GetURL`` class.  This has the custom constructor and the ``command()``
+method implemented by this command style.  For the constructor there is
+nothing to do but to pass the ``lmp`` pointer to the base class.  Since the
+``command()`` method is labeled "virtual" in the base class, it must be
+given the "override" property.
+
+.. code-block:: c++
+
+   #ifndef LMP_GETURL_H
+   #define LMP_GETURL_H
+
+   #include "command.h"
+
+   namespace LAMMPS_NS {
+
+   class GetURL : public Command {
+    public:
+     GetURL(class LAMMPS *lmp) : Command(lmp) {};
+     void command(int, char **) override;
+   };
+   }    // namespace LAMMPS_NS
+   #endif
+   #endif
+
+The "override" property helps to detect unexpected mismatches because
+compilation will stop with an error in case the signature of a function
+is changed in the base class without also changing it in all derived
+classes.
+
+Implementation file
+"""""""""""""""""""
+
+We move on to the implementation of the ``GetURL`` class in the
+``geturl.cpp`` file.  This file also starts with a LAMMPS copyright and
+license header.  Below that notice is typically the space where comments may
+be added with additional information about this specific file, the
+author(s), affiliation(s), and email address(es).  This way the contributing
+author(s) can be easily contacted, when there are questions about the
+implementation later.  Since the file(s) may be around for a long time, it
+is beneficial to use some kind of "permanent" email address, if possible.
+
+.. code-block:: c++
+
+   /* ----------------------------------------------------------------------
+      LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+      https://www.lammps.org/, Sandia National Laboratories
+      LAMMPS development team: developers@lammps.org
+
+      Copyright (2003) Sandia Corporation.  Under the terms of Contract
+      DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+      certain rights in this software.  This software is distributed under
+      the GNU General Public License.
+
+      See the README file in the top-level LAMMPS directory.
+   ------------------------------------------------------------------------- */
+
+   /* ----------------------------------------------------------------------
+      Contributing authors:  Axel Kohlmeyer (Temple U),
+   ------------------------------------------------------------------------- */
+
+   #include "geturl.h"
+
+   #include "comm.h"
+   #include "error.h"
+
+   #if defined(LAMMPS_CURL)
+   #include <curl/curl.h>
+   #endif
+
+   using namespace LAMMPS_NS;
+
+The second section of the implementation file has various include
+statements.  The include file for the class header has to come first, then a
+couple of LAMMPS classes (sorted alphabetically) followed by the header for
+the *libcurl* interface.  This is wrapped into an ``#ifdef`` block so that
+LAMMPS will compile this file without error when the *libcurl* header is not
+available and thus the define not set.  The final statement of this segment
+imports the ``LAMMPS_NS::`` namespace globally for this file.  This way, all
+LAMMPS specific functions and classes do not have to be prefixed with
+``LAMMPS_NS::``.
+
+The command() function (required)
+"""""""""""""""""""""""""""""""""
+
+Since the required custom constructor is trivial and implemented in the
+header, there is only one function that must be implemented for a command
+style and that is the ``command()`` function.
+
+.. code-block:: c++
+
+   void GetURL::command(int narg, char **arg)
+   {
+   #if !defined(LAMMPS_CURL)
+     error->all(FLERR, "LAMMPS has not been compiled with libcurl support");
+   #else
+     if (narg < 1) utils::missing_cmd_args(FLERR, "geturl", error);
+     int verify = 1;
+     int overwrite = 1;
+     int verbose = 0;
+
+This first part also has the ``#ifdef`` block depending on the LAMMPS_CURL
+define.  This way the command will simply print an error, if *libcurl* is
+not available but will not fail to compile.  Furthermore, it sets the
+defaults for the following optional arguments.
+
+.. code-block:: c++
+
+     // process arguments
+
+     std::string url = arg[0];
+
+     // sanity check
+
+     if ((url.find(':') == std::string::npos) || (url.find('/') == std::string::npos))
+       error->all(FLERR, "URL '{}' is not a supported URL", url);
+
+     std::string output = url.substr(url.find_last_of('/') + 1);
+     if (output.empty()) error->all(FLERR, "URL '{}' must end in a file string", url);
+
+This block stores the positional, i.e. non-optional argument of the URL to
+be downloaded and adds a couple of sanity checks on the string to make sure it is
+a valid URL.  Also it derives the default name of the output file from the URL.
+
+.. code-block:: c++
+
+     int iarg = 1;
+     while (iarg < narg) {
+       if (strcmp(arg[iarg], "output") == 0) {
+         if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl output", error);
+         output = arg[iarg + 1];
+         ++iarg;
+       } else if (strcmp(arg[iarg], "overwrite") == 0) {
+         if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl overwrite", error);
+         overwrite = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+         ++iarg;
+       } else if (strcmp(arg[iarg], "verify") == 0) {
+         if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verify", error);
+         verify = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+         ++iarg;
+       } else if (strcmp(arg[iarg], "verbose") == 0) {
+         if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "geturl verbose", error);
+         verbose = utils::logical(FLERR, arg[iarg + 1], false, lmp);
+         ++iarg;
+       } else {
+         error->all(FLERR, "Unknown geturl keyword: {}", arg[iarg]);
+       }
+       ++iarg;
+     }
+
+This block parses the optional arguments following the URL and stops with an
+error if there are arguments missing or an unknown argument is encountered.
+
+.. code-block:: c++
+
+     // only download files from rank 0
+
+     if (comm->me != 0) return;
+
+     if (!overwrite && platform::file_is_readable(output)) return;
+
+     // open output file for writing
+
+     FILE *out = fopen(output.c_str(), "wb");
+     if (!out)
+       error->all(FLERR, "Cannot open output file {} for writing: {}", output, utils::getsyserror());
+
+Here all MPI ranks other than 0 will return, so that the URL download will
+only happen from a single MPI rank. For that rank the output file is opened
+for writing using the C library function ``fopen()``.
+
+.. code-block:: c++
+
+     // initialize curl and perform download
+
+     CURL *curl;
+     curl_global_init(CURL_GLOBAL_DEFAULT);
+     curl = curl_easy_init();
+     if (curl) {
+       (void) curl_easy_setopt(curl, CURLOPT_URL, url.c_str());
+       (void) curl_easy_setopt(curl, CURLOPT_WRITEDATA, (void *) out);
+       (void) curl_easy_setopt(curl, CURLOPT_FILETIME, 1L);
+       (void) curl_easy_setopt(curl, CURLOPT_FAILONERROR, 1L);
+       if (verbose && screen) {
+         (void) curl_easy_setopt(curl, CURLOPT_VERBOSE, 1L);
+         (void) curl_easy_setopt(curl, CURLOPT_STDERR, (void *) screen);
+       }
+       if (!verify) {
+         (void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYPEER, 0L);
+         (void) curl_easy_setopt(curl, CURLOPT_SSL_VERIFYHOST, 0L);
+       }
+       auto res = curl_easy_perform(curl);
+       if (res != CURLE_OK) {
+         long response = 0L;
+         curl_easy_getinfo(curl, CURLINFO_RESPONSE_CODE, &response);
+         error->one(FLERR, "Download of {} failed with: {} {}", output, curl_easy_strerror(res),
+                    response);
+       }
+       curl_easy_cleanup(curl);
+
+This block now implements the actual URL download with the selected options
+via the "easy" interface of *libcurl*.  For the details of what these
+function calls do, please have a look at the `*libcurl documentation
+<https://curl.se/libcurl/c/allfuncs.html>`_.
+
+ .. code-block:: c++
+
+     }
+     curl_global_cleanup();
+     fclose(out);
+   #endif
+   }
+
+Finally, the previously opened file is closed and the command is complete.

doc/src/Developer_write_pair.rst

@@ -160,7 +160,7 @@ message and before the include guards for the class definition:
 
    #endif
 
-This block of between ``#ifdef PAIR_CLASS`` and ``#else`` will be
+This block between ``#ifdef PAIR_CLASS`` and ``#else`` will be
 included by the ``Force`` class in ``force.cpp`` to build a map of
 "factory functions" that will create an instance of these classes and
 return a pointer to it.  The map connects the name of the pair style,

doc/src/Errors_details.rst

@@ -54,3 +54,26 @@ 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.
+
+.. _err0003:
+
+Illegal variable command: expected X arguments but found Y
+----------------------------------------------------------
+
+This error indicates that there are the wrong number of arguments for a
+specific variable command, but a common reason for that is a variable
+expression that 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, 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 then pass that string as
+"word" to the variable command.
+
+Thus missing quotes or accidental extra whitespace will lead to the
+error shown in the header because the unquoted whitespace will result
+in the text being broken into more "words", i.e. the variable expression
+being split.

doc/src/Howto_bioFF.rst

@@ -1,5 +1,5 @@
-CHARMM, AMBER, COMPASS, and DREIDING force fields
-=================================================
+CHARMM, AMBER, COMPASS, DREIDING, and OPLS force fields
+=======================================================
 
 A compact summary of the concepts, definitions, and properties of
 force fields with explicit bonded interactions (like the ones discussed
@@ -236,6 +236,40 @@ documentation for the formula it computes.
 
 * :doc:`special_bonds <special_bonds>` dreiding
 
+OPLS
+----
+
+OPLS (Optimized Potentials for Liquid Simulations) is a general force
+field for atomistic simulation of organic molecules in solvent.  It was
+developed by the `Jorgensen group
+<https://traken.chem.yale.edu/oplsaam.html>`_ at Purdue University and
+later at Yale University.  Multiple versions of the OPLS parameters
+exist for united atom representations (OPLS-UA) and for all-atom
+representations (OPLS-AA).
+
+This force field is based on atom types mapped to specific functional
+groups in organic and biological molecules.  Each atom includes a
+static, partial atomic charge reflecting the oxidation state of the
+element derived from its bonded neighbors :ref:`(Jorgensen)
+<howto-jorgensen>` and computed based on increments determined by the
+atom type of the atoms bond to it.
+
+The interaction styles listed below compute force field formulas that
+are fully or in part consistent with the OPLS style force fields.  See
+each command's documentation for the formula it computes.  Some are only
+compatible with a subset of OPLS interactions.
+
+* :doc:`bond_style <bond_harmonic>` harmonic
+* :doc:`angle_style <angle_harmonic>` harmonic
+* :doc:`dihedral_style <dihedral_opls>` opls
+* :doc:`improper_style <improper_cvff>` cvff
+* :doc:`improper_style <improper_fourier>` fourier
+* :doc:`improper_style <improper_harmonic>` harmonic
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/cut
+* :doc:`pair_style <pair_lj_cut_coul>` lj/cut/coul/long
+* :doc:`pair_modify <pair_modify>` geometric
+* :doc:`special_bonds <special_bonds>` lj/coul 0.0 0.0 0.5
+
 ----------
 
 .. _Typelabel2:
@@ -266,3 +300,6 @@ documentation for the formula it computes.
 
 **(Mayo)** Mayo, Olfason, Goddard III (1990). J Phys Chem, 94, 8897-8909. https://doi.org/10.1021/j100389a010
 
+.. _howto-Jorgensen:
+
+**(Jorgensen)** Jorgensen, Tirado-Rives (1988). J Am Chem Soc, 110, 1657-1666. https://doi.org/10.1021/ja00214a001

doc/src/Howto_bpm.rst

@@ -5,7 +5,11 @@ The BPM package implements bonded particle models which can be used to
 simulate mesoscale solids.  Solids are constructed as a collection of
 particles, which each represent a coarse-grained region of space much
 larger than the atomistic scale.  Particles within a solid region are
-then connected by a network of bonds to provide solid elasticity.
+then connected by a network of bonds to model solid elasticity.
+There are many names for methods that are based on similar (or
+equivalent) capabilities to those in this package, including, but not
+limited to, cohesive beam models, bonded DEMs, lattice spring models,
+mass spring models, and lattice particle methods.
 
 Unlike traditional bonds in molecular dynamics, the equilibrium bond
 length can vary between bonds. Bonds store the reference state.  This
@@ -42,7 +46,8 @@ Currently, there are two 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. Alternatively, the second bond style, :doc:`bond bpm/rotational
+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
 <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
@@ -55,8 +60,9 @@ orientation similar to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
 In addition to bond styles, a new pair style :doc:`pair bpm/spring
 <pair_bpm_spring>` was added to accompany the bpm/spring bond
-style. This pair style is simply a hookean repulsion with similar
-velocity damping as its sister bond style.
+style. By default, this pair style is simply a hookean repulsion with
+similar velocity damping as its sister bond style, but optional
+arguments can be used to modify the force.
 
 ----------
 

doc/src/Howto_chunk.rst

@@ -58,28 +58,30 @@ chunk ID for an individual atom can also be static (e.g. a molecule
 ID), or dynamic (e.g. what spatial bin an atom is in as it moves).
 
 Note that this compute allows the per-atom output of other
-:doc:`computes <compute>`, :doc:`fixes <fix>`, and
-:doc:`variables <variable>` to be used to define chunk IDs for each
-atom.  This means you can write your own compute or fix to output a
-per-atom quantity to use as chunk ID.  See the :doc:`Modify <Modify>`
-doc pages for info on how to do this.  You can also define a :doc:`per-atom variable <variable>` in the input script that uses a formula to
-generate a chunk ID for each atom.
+:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`variables
+<variable>` to be used to define chunk IDs for each atom.  This means
+you can write your own compute or fix to output a per-atom quantity to
+use as chunk ID.  See the :doc:`Modify <Modify>` doc pages for info on
+how to do this.  You can also define a :doc:`per-atom variable
+<variable>` in the input script that uses a formula to generate a chunk
+ID for each atom.
 
 Fix ave/chunk command:
 ----------------------
 
-This fix takes the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  For each chunk,
-it then sums one or more specified per-atom values over the atoms in
-each chunk.  The per-atom values can be any atom property, such as
-velocity, force, charge, potential energy, kinetic energy, stress,
-etc.  Additional keywords are defined for per-chunk properties like
-density and temperature.  More generally any per-atom value generated
-by other :doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom variables <variable>`, can be summed over atoms in each chunk.
+This fix takes the ID of a :doc:`compute chunk/atom
+<compute_chunk_atom>` command as input.  For each chunk, it then sums
+one or more specified per-atom values over the atoms in each chunk.  The
+per-atom values can be any atom property, such as velocity, force,
+charge, potential energy, kinetic energy, stress, etc.  Additional
+keywords are defined for per-chunk properties like density and
+temperature.  More generally any per-atom value generated by other
+:doc:`computes <compute>`, :doc:`fixes <fix>`, and :doc:`per-atom
+variables <variable>`, can be summed over atoms in each chunk.
 
 Similar to other averaging fixes, this fix allows the summed per-chunk
 values to be time-averaged in various ways, and output to a file.  The
-fix produces a global array as output with one row of values per
-chunk.
+fix produces a global array as output with one row of values per chunk.
 
 Compute \*/chunk commands:
 --------------------------
@@ -97,17 +99,20 @@ category:
 * :doc:`compute torque/chunk <compute_vcm_chunk>`
 * :doc:`compute vcm/chunk <compute_vcm_chunk>`
 
-They each take the ID of a :doc:`compute chunk/atom <compute_chunk_atom>` command as input.  As their names
-indicate, they calculate the center-of-mass, radius of gyration,
-moments of inertia, mean-squared displacement, temperature, torque,
-and velocity of center-of-mass for each chunk of atoms.  The :doc:`compute property/chunk <compute_property_chunk>` command can tally the
-count of atoms in each chunk and extract other per-chunk properties.
+They each take the ID of a :doc:`compute chunk/atom
+<compute_chunk_atom>` command as input.  As their names indicate, they
+calculate the center-of-mass, radius of gyration, moments of inertia,
+mean-squared displacement, temperature, torque, and velocity of
+center-of-mass for each chunk of atoms.  The :doc:`compute
+property/chunk <compute_property_chunk>` command can tally the count of
+atoms in each chunk and extract other per-chunk properties.
 
-The reason these various calculations are not part of the :doc:`fix ave/chunk command <fix_ave_chunk>`, is that each requires a more
+The reason these various calculations are not part of the :doc:`fix
+ave/chunk command <fix_ave_chunk>`, is that each requires a more
 complicated operation than simply summing and averaging over per-atom
-values in each chunk.  For example, many of them require calculation
-of a center of mass, which requires summing mass\*position over the
-atoms and then dividing by summed mass.
+values in each chunk.  For example, many of them require calculation of
+a center of mass, which requires summing mass\*position over the atoms
+and then dividing by summed mass.
 
 All of these computes produce a global vector or global array as
 output, with one or more values per chunk.  The output can be used in
@@ -118,9 +123,10 @@ various ways:
 * As input to the :doc:`fix ave/histo <fix_ave_histo>` command to
   histogram values across chunks.  E.g. a histogram of cluster sizes or
   molecule diffusion rates.
-* As input to special functions of :doc:`equal-style variables <variable>`, like sum() and max() and ave().  E.g. to
-  find the largest cluster or fastest diffusing molecule or average
-  radius-of-gyration of a set of molecules (chunks).
+* As input to special functions of :doc:`equal-style variables
+  <variable>`, like sum() and max() and ave().  E.g. to find the largest
+  cluster or fastest diffusing molecule or average radius-of-gyration of
+  a set of molecules (chunks).
 
 Other chunk commands:
 ---------------------
@@ -138,9 +144,10 @@ spatially average per-chunk values calculated by a per-chunk compute.
 
 The :doc:`compute reduce/chunk <compute_reduce_chunk>` command reduces a
 peratom value across the atoms in each chunk to produce a value per
-chunk.  When used with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can
-create peratom values that induce a new set of chunks with a second
-:doc:`compute chunk/atom <compute_chunk_atom>` command.
+chunk.  When used with the :doc:`compute chunk/spread/atom
+<compute_chunk_spread_atom>` command it can create peratom values that
+induce a new set of chunks with a second :doc:`compute chunk/atom
+<compute_chunk_atom>` command.
 
 Example calculations with chunks
 --------------------------------

doc/src/Howto_cmake.rst

@@ -348,7 +348,7 @@ Some common LAMMPS specific variables
    * - ``FFT``
      - select which FFT library to use: ``FFTW3``, ``MKL``, ``KISS`` (default, unless FFTW3 is found)
    * - ``FFT_KOKKOS``
-     - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``KISS`` (default)
+     - select which FFT library to use in Kokkos-enabled styles: ``FFTW3``, ``MKL``, ``HIPFFT``, ``CUFFT``, ``MKL_GPU``, ``KISS`` (default)
    * - ``FFT_SINGLE``
      - select whether to use single precision FFTs (default: ``off``)
    * - ``WITH_JPEG``

doc/src/Howto_pylammps.rst

@@ -39,16 +39,18 @@ lammps.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 original :py:class:`ctypes based interface <lammps.lammps>`
+* 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
 -----------

doc/src/Intro_authors.rst

@@ -56,7 +56,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
      - SNL
      - jmgoff at sandia.gov
      - machine learned potentials, QEq solvers, Python
-   * - Megan McCarthy
+   * - Meg McCarthy
      - SNL
      - megmcca at sandia.gov
      - alloys, micro-structure, machine learned potentials
@@ -67,7 +67,7 @@ lammps.org".  General questions about LAMMPS should be posted in the
    * - `Trung Nguyen <tn_>`_
      - U Chicago
      - ndactrung at gmail.com
-     - soft matter, GPU package
+     - soft matter, GPU package, DIELECTRIC package, regression testing
 
 .. _rb:  https://rbberger.github.io/
 .. _gc:  https://enthalpiste.fr/

doc/src/Intro_portability.rst

@@ -31,18 +31,19 @@ Operating systems
 ^^^^^^^^^^^^^^^^^
 
 The primary development platform for LAMMPS is Linux.  Thus, the chances
-for LAMMPS to compile without problems on Linux machines are the best.
+for LAMMPS to compile without problems are the best on Linux machines.
 Also, compilation and correct execution on macOS and Windows (using
-Microsoft Visual C++) is checked automatically for largest part of the
-source code.  Some (optional) features are not compatible with all
+Microsoft Visual C++) is checked automatically for the largest part of
+the source code.  Some (optional) features are not compatible with all
 operating systems, either through limitations of the corresponding
-LAMMPS source code or through source code or build system
-incompatibilities of required libraries.
+LAMMPS source code or through incompatibilities of source code or
+build system of required external libraries or packages.
 
 Executables for Windows may be created natively using either Cygwin or
 Visual Studio or with a Linux to Windows MinGW cross-compiler.
 
-Additionally, FreeBSD and Solaris have been tested successfully.
+Additionally, FreeBSD and Solaris have been tested successfully to
+run LAMMPS and produce results consistent with those on Linux.
 
 Compilers
 ^^^^^^^^^

doc/src/Library_atoms.rst

@@ -4,6 +4,7 @@ Per-atom properties
 This section documents the following functions:
 
 - :cpp:func:`lammps_extract_atom_datatype`
+- :cpp:func:`lammps_extract_atom_size`
 - :cpp:func:`lammps_extract_atom`
 
 -----------------------
@@ -13,6 +14,11 @@ This section documents the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_extract_atom_size
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_extract_atom
    :project: progguide
 

doc/src/Packages_details.rst

@@ -880,7 +880,7 @@ groups of atoms that interact with the remaining atoms as electrolyte.
 
 **Authors:** The ELECTRODE package is written and maintained by Ludwig
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
-Robert Meissner (TUHH, Hamburg, Germany).
+Robert Meissner (Helmholtz-Zentrum Hereon, Geesthacht and TUHH, Hamburg, Germany).
 
 .. versionadded:: 4May2022
 

doc/src/Run_windows.rst

@@ -3,71 +3,70 @@ Running LAMMPS on Windows
 
 To run a serial (non-MPI) executable, follow these steps:
 
-* Get a command prompt by going to Start->Run... ,
-  then typing "cmd".
-* Move to the directory where you have your input script,
+* Install a LAMMPS installer package from https://packages.lammps.org/windows.html
+* Open the "Command Prompt" or "Terminal" app.
+* Change to the directory where you have your input script,
   (e.g. by typing: cd "Documents").
-* At the command prompt, type "lmp -in in.file", where
-  in.file is the name of your LAMMPS input script.
+* At the command prompt, type "lmp -in in.file.lmp", where
+  ``in.file.lmp`` is the name of your LAMMPS input script.
 
 Note that the serial executable includes support for multi-threading
-parallelization from the styles in the OPENMP packages.  To run with
-4 threads, you can type this:
+parallelization from the styles in the OPENMP and KOKKOS packages.
+To run with 4 threads, you can type this:
 
 .. code-block:: bash
 
-   lmp -in in.lj -pk omp 4 -sf omp
+   lmp -in in.lj.lmp -pk omp 4 -sf omp
+   lmp -in in.lj.lmp -k on t 4 -sf kk
+
+Alternately, you can also install a package with LAMMPS-GUI included and
+open the LAMMPS-GUI app (the package includes the command line version
+of LAMMPS as well) and open the input file in the GUI and run it from
+there.  For details on LAMMPS-GUI, see :doc:`Howto_lammps_gui`.
 
 ----------
 
-For the MPI executable, which allows you to run LAMMPS under Windows
-in parallel, follow these steps.
+For the MS-MPI executables, which allow you to run LAMMPS under Windows
+in parallel using MPI rather than multi-threading, follow these steps.
 
-Download and install a compatible MPI library binary package:
-
-* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
-* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
-
-The LAMMPS Windows installer packages will automatically adjust your
-path for the default location of this MPI package. After the
-installation of the MPICH2 software, it needs to be integrated into
-the system.  For this you need to start a Command Prompt in
-*Administrator Mode* (right click on the icon and select it). Change
-into the MPICH2 installation directory, then into the subdirectory
-**bin** and execute **smpd.exe -install**\ . Exit the command window.
-
-* Get a new, regular command prompt by going to Start->Run... ,
-  then typing "cmd".
-* Move to the directory where you have your input file
-  (e.g. by typing: cd "Documents").
+Download and install the MS-MPI runtime package ``msmpisetup.exe`` from
+https://www.microsoft.com/en-us/download/details.aspx?id=105289 (Note
+that the ``msmpisdk.msi`` is **only** required for **compilation** of
+LAMMPS from source on Windows using Microsoft Visual Studio). After
+installation of MS-MPI perform a reboot.
 
 Then you can run the executable in serial like in the example above
 or in parallel using MPI with one of the following commands:
 
 .. code-block:: bash
 
-   mpiexec -localonly 4 lmp -in in.file
-   mpiexec -np 4 lmp -in in.file
+   mpiexec -localonly 4 lmp -in in.file.lmp
+   mpiexec -np 4 lmp -in in.file.lmp
 
-where in.file is the name of your LAMMPS input script. For the latter
-case, you may be prompted to enter the password that you set during
-installation of the MPI library software.
+where ``in.file.lmp`` is the name of your LAMMPS input script. For the
+latter case, you may be prompted to enter the password that you set
+during installation of the MPI library software.
 
 In this mode, output may not immediately show up on the screen, so if
 your input script takes a long time to execute, you may need to be
 patient before the output shows up.
 
-The parallel executable can also run on a single processor by typing
-something like this:
+Note that the parallel executable also includes OpenMP multi-threading
+through both the OPENMP and the KOKKOS package, which can be combined
+with MPI using something like:
 
 .. code-block:: bash
 
-   lmp -in in.lj
+   mpiexec -localonly 2 lmp -in in.lj.lmp -pk omp 2 -sf omp
+   mpiexec -localonly 2 lmp -in in.lj.lmp -kokkos on t 2 -sf kk
 
-Note that the parallel executable also includes OpenMP
-multi-threading, which can be combined with MPI using something like:
-
-.. code-block:: bash
-
-   mpiexec -localonly 2 lmp -in in.lj -pk omp 2 -sf omp
+-------------
 
+MPI parallelization will work for *all* functionality in LAMMPS and in
+many cases the MPI parallelization is more efficient than
+multi-threading since LAMMPS was designed from ground up for MPI
+parallelization using domain decomposition.  Multi-threading is only
+available for selected styles and implemented on top of the MPI
+parallelization.  Multi-threading is most useful for systems with large
+load imbalances when using domain decomposition and a smaller number
+of threads (<= 8).

doc/src/Tools.rst

@@ -1022,7 +1022,7 @@ regression tests with a given LAMMPS binary.  The tool launches the
 LAMMPS binary with any given input script under one of the `examples`
 subdirectories, and compares the thermo output in the generated log file
 with those in the provided log file with the same number of processors
-ub the same subdirectory. If the differences between the actual and
+in the same subdirectory. If the differences between the actual and
 reference values are within specified tolerances, the test is considered
 passed.  For each test batch, that is, a set of example input scripts,
 the mpirun command, the LAMMPS command line arguments, and the

doc/src/angles.rst

@@ -1,8 +0,0 @@
-Angle Styles
-############
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   angle_*

doc/src/bond_bpm_spring.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_style bpm/spring keyword value attribute1 attribute2 ...
 
-* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break*
+* optional keyword = *overlay/pair* or *store/local* or *smooth* or *break* or *volume/factor*
 
   .. parsed-literal::
 
@@ -36,6 +36,9 @@ Syntax
        *break* value = *yes* or *no*
           indicates whether bonds break during a run
 
+       *volume/factor* value = *yes* or *no*
+          indicates whether forces include the volumetric contribution
+
 Examples
 """"""""
 
@@ -44,6 +47,9 @@ Examples
    bond_style bpm/spring
    bond_coeff 1 1.0 0.05 0.1
 
+   bond_style bpm/spring volume/factor yes
+   bond_coeff 1 1.0 0.05 0.1 0.5
+
    bond_style bpm/spring myfix 1000 time id1 id2
    dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
    dump_modify 1 write_header no
@@ -97,15 +103,6 @@ approach the critical strain
 
    w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right)^8 .
 
-The following coefficients must be defined for each bond type via the
-:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
-the data file or restart files read by the :doc:`read_data
-<read_data>` or :doc:`read_restart <read_restart>` commands:
-
-* :math:`k`             (force/distance units)
-* :math:`\epsilon_c`    (unit less)
-* :math:`\gamma`        (force/velocity units)
-
 If the *normalize* keyword is set to *yes*, the elastic bond force will be
 normalized by :math:`r_0` such that :math:`k` must be given in force units.
 
@@ -123,6 +120,43 @@ during a simulation run. This will prevent some unnecessary calculation.
 However, if a bond reaches a strain greater than :math:`\epsilon_c`,
 it will trigger an error.
 
+.. versionadded:: TBD
+
+The *volume/factor* keyword toggles whether an additional multibody
+contribution is added to he force using the formulation in
+:ref:`(Clemmer2) <multibody-Clemmer>`,
+
+.. math::
+
+   \alpha_v \left(\left[\frac{V_i + V_j}{V_{0,i} + V_{0,j}}\right]^{1/3} - \frac{r_{ij}}{r_{0,ij}}\right)
+
+where :math:`\alpha_v` is a user specified coefficient and :math:`V_i`
+and :math:`V_{0,i}` are estimates of the current and local volume
+of atom :math:`i`. These volumes are calculated as the sum of current
+or initial bond lengths cubed. In 2D, the volume is replaced with an area
+calculated using bond lengths squared and the cube root in the above equation
+is accordingly replaced with a square root. This approximation assumes bonds
+are evenly distributed on a spherical surface and neglects constant prefactors
+which are irrelevant since only the ratio of volumes matters. This term may be
+used to adjust the Poisson's ratio.
+
+If a bond is broken (or created), :math:`V_{0,i}` is updated by subtracting
+(or adding) that bond's contribution.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* :math:`k`             (force/distance units)
+* :math:`\epsilon_c`    (unit less)
+* :math:`\gamma`        (force/velocity units)
+
+Additionally, if *volume/factor* is set to *yes*, a fourth coefficient
+must be provided:
+
+* :math:`a_v`           (force units)
+
 If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
@@ -213,7 +247,7 @@ Related commands
 Default
 """""""
 
-The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, and *break* = *yes*
+The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *no*, *break* = *yes*, and *volume/factor* = *no*
 
 ----------
 
@@ -224,3 +258,7 @@ The option defaults are *overlay/pair* = *no*, *smooth* = *yes*, *normalize* = *
 .. _Groot4:
 
 **(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
+
+.. _multibody-Clemmer:
+
+**(Clemmer2)** Clemmer, Monti, Lechman, Soft Matter, 20, 1702 (2024).

doc/src/bonds.rst

@@ -1,8 +0,0 @@
-Bond Styles
-###########
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   bond_*

doc/src/compute.rst

@@ -236,6 +236,7 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
 * :doc:`fep/ta <compute_fep_ta>` - compute free energies for a test area perturbation
 * :doc:`force/tally <compute_tally>` - force between two groups of atoms via the tally callback mechanism
 * :doc:`fragment/atom <compute_cluster_atom>` - fragment ID for each atom
+* :doc:`gaussian/grid/local <compute_gaussian_grid_local>` - local array of Gaussian atomic contributions on a regular grid
 * :doc:`global/atom <compute_global_atom>` - assign global values to each atom from arrays of global values
 * :doc:`group/group <compute_group_group>` - energy/force between two groups of atoms
 * :doc:`gyration <compute_gyration>` - radius of gyration of group of atoms

doc/src/compute_angle_local.rst

@@ -78,7 +78,7 @@ system and output the statistics in various ways:
    compute 2 all angle/local eng theta v_cos v_cossq set theta t
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[3] mode vector file tmp.histo

doc/src/compute_bond_local.rst

@@ -139,7 +139,7 @@ output the statistics in various ways:
    compute 2 all bond/local engpot dist v_dsq set dist d
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 0 6 20 c_2[3] mode vector file tmp.histo

doc/src/compute_composition_atom.rst

@@ -88,6 +88,10 @@ too frequently.
 
 ----------
 
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/compute_dihedral_local.rst

@@ -76,7 +76,7 @@ angle in the system and output the statistics in various ways:
    compute 2 all dihedral/local phi v_cos v_cossq set phi p
    dump 1 all local 100 tmp.dump c_1[*] c_2[*]
 
-   compute 3 all reduce ave c_2[*]
+   compute 3 all reduce ave c_2[*] inputs local
    thermo_style custom step temp press c_3[*]
 
    fix 10 all ave/histo 10 10 100 -1 1 20 c_2[2] mode vector file tmp.histo

doc/src/compute_gaussian_grid_local.rst

@@ -0,0 +1,97 @@
+.. index:: compute gaussian/grid/local
+.. index:: compute gaussian/grid/local/kk
+
+compute gaussian/grid/local command
+===================================
+
+Accelerator Variants: *gaussian/grid/local/kk*
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   compute ID group-ID gaussian/grid/local grid nx ny nz rcutfac  R_1 R_2 ... sigma_1 sigma_2
+
+* ID, group-ID are documented in :doc:`compute <compute>` command
+* gaussian/grid/local = style name of this compute command
+* *grid* values = nx, ny, nz, number of grid points in x, y, and z directions (positive integer)
+* *rcutfac* = scale factor applied to all cutoff radii (positive real)
+* *R_1, R_2,...* = list of cutoff radii, one for each type (distance units)
+* *sigma_1, sigma_2,...* = Gaussian widths, one for each type (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+    compute mygrid all gaussian/grid/local grid 40 40 40 4.0 0.5 0.5 0.4 0.4
+
+Description
+"""""""""""
+
+Define a computation that calculates a Gaussian representation of the ionic
+structure. This representation is used for the efficient evaluation
+of quantities related to the structure factor in a grid-based workflow,
+such as the ML-DFT workflow MALA :ref:`(Ellis) <Ellis2021b>`, for which it was originally
+implemented. Usage of the workflow is described in a separate publication :ref:`(Fiedler) <Fiedler2023>`.
+
+For each LAMMPS type, a separate sum of Gaussians is calculated, using
+a separate Gaussian broadening per type. The computation
+is always performed on the numerical grid, no atom-based version of this
+compute exists. The Gaussian representation can only be executed in a local
+fashion, thus the output array only contains rows for grid points
+that are local to the processor subdomain. The layout of the grid is the same
+as for the see :doc:`sna/grid/local <compute_sna_atom>` command.
+
+Namely, the array contains one row for each of the
+local grid points, looping over the global index *ix* fastest,
+then *iy*, and *iz* slowest.  Each row of the array contains
+the global indexes *ix*, *iy*, and *iz* first, followed by the *x*, *y*,
+and *z* coordinates of the grid point, followed by the values of the Gaussians
+(one floating point number per type per grid point).
+
+----------
+
+
+.. include:: accel_styles.rst
+
+	     
+
+----------
+
+Output info
+"""""""""""
+
+Compute *gaussian/grid/local* evaluates a local array.
+The array contains one row for each of the
+local grid points, looping over the global index *ix* fastest,
+then *iy*, and *iz* slowest.  The array contains math :math:`ntypes+6` columns,
+where *ntypes* is the number of LAMMPS types. The first three columns are
+the global indexes *ix*, *iy*, and *iz*, followed by the *x*, *y*,
+and *z* coordinates of the grid point, followed by the *ntypes* columns
+containing the values of the Gaussians for each type.
+
+Restrictions
+""""""""""""
+
+These computes are part of the ML-SNAP package.  They are only enabled
+if LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`compute sna/grid/local <compute_sna_atom>`
+
+----------
+
+.. _Ellis2021b:
+
+**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, `Phys. Rev. B, 104, 035120, (2021) <https://doi.org/10.1103/PhysRevB.104.035120>`_
+
+.. _Fiedler2023:
+
+**(Fiedler)** Fiedler, Modine, Schmerler, Vogel, Popoola, Thompson, Rajamanickam, and Cangi,
+`npj Comp. Mater., 9, 115 (2023) <https://doi.org/10.1038/s41524-023-01070-z>`_
+

doc/src/compute_pressure.rst

@@ -125,10 +125,6 @@ where thermo_temp is the ID of a similarly defined compute of style
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Output info
 """""""""""
 

doc/src/compute_reduce.rst

@@ -206,11 +206,13 @@ IDs and the bond stretch will be printed with thermodynamic output.
 
 The *inputs* keyword allows selection of whether all the inputs are
 per-atom or local quantities.  As noted above, all the inputs must be
-the same kind (per-atom or local).  Per-atom is the default setting.
-If a compute or fix is specified as an input, it must produce per-atom
-or local data to match this setting.  If it produces both, e.g. for
+the same kind (per-atom or local).  Per-atom is the default setting.  If
+a compute or fix is specified as an input, it must produce per-atom or
+local data to match this setting.  If it produces both, like for example
 the :doc:`compute voronoi/atom <compute_voronoi_atom>` command, then
-this keyword selects between them.
+this keyword selects between them.  If a compute *only* produces local
+data, like for example the :doc:`compute bond/local command
+<compute_bond_local>`, the setting "inputs local" is *required*.
 
 ----------
 

doc/src/compute_reduce_chunk.rst

@@ -37,55 +37,57 @@ Description
 
 Define a calculation that reduces one or more per-atom vectors into
 per-chunk values.  This can be useful for diagnostic output.  Or when
-used in conjunction with the :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>` command it can be
-used to create per-atom values that induce a new set of chunks with a
-second :doc:`compute chunk/atom <compute_chunk_atom>` command.  An
-example is given below.
+used in conjunction with the :doc:`compute chunk/spread/atom
+<compute_chunk_spread_atom>` command it can be used to create per-atom
+values that induce a new set of chunks with a second :doc:`compute
+chunk/atom <compute_chunk_atom>` command.  An example is given below.
 
-In LAMMPS, chunks are collections of atoms defined by a :doc:`compute chunk/atom <compute_chunk_atom>` command, which assigns each atom
-to a single chunk (or no chunk).  The ID for this command is specified
-as chunkID.  For example, a single chunk could be the atoms in a
-molecule or atoms in a spatial bin.  See the :doc:`compute chunk/atom <compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>`
-doc pages for details of how chunks can be defined and examples of how
-they can be used to measure properties of a system.
+In LAMMPS, chunks are collections of atoms defined by a :doc:`compute
+chunk/atom <compute_chunk_atom>` command, which assigns each atom to a
+single chunk (or no chunk).  The ID for this command is specified as
+chunkID.  For example, a single chunk could be the atoms in a molecule
+or atoms in a spatial bin.  See the :doc:`compute chunk/atom
+<compute_chunk_atom>` and :doc:`Howto chunk <Howto_chunk>` doc pages for
+details of how chunks can be defined and examples of how they can be
+used to measure properties of a system.
 
 For each atom, this compute accesses its chunk ID from the specified
-*chunkID* compute.  The per-atom value from an input contributes
-to a per-chunk value corresponding the the chunk ID.
+*chunkID* compute.  The per-atom value from an input contributes to a
+per-chunk value corresponding the chunk ID.
 
 The reduction operation is specified by the *mode* setting and is
 performed over all the per-atom values from the atoms in each chunk.
-The *sum* option adds the pre-atom values to a per-chunk total.  The
-*min* or *max* options find the minimum or maximum value of the
-per-atom values for each chunk.
+The *sum* option adds the per-atom values to a per-chunk total.  The
+*min* or *max* options find the minimum or maximum value of the per-atom
+values for each chunk.
 
-Note that only atoms in the specified group contribute to the
-reduction operation.  If the *chunkID* compute returns a 0 for the
-chunk ID of an atom (i.e., the atom is not in a chunk defined by the
-:doc:`compute chunk/atom <compute_chunk_atom>` command), that atom will
-also not contribute to the reduction operation.  An input that is a
-compute or fix may define its own group which affects the quantities
-it returns.  For example, a compute with return a zero value for atoms
-that are not in the group specified for that compute.
+Note that only atoms in the specified group contribute to the reduction
+operation.  If the *chunkID* compute returns a 0 for the chunk ID of an
+atom (i.e., the atom is not in a chunk defined by the :doc:`compute
+chunk/atom <compute_chunk_atom>` command), that atom will also not
+contribute to the reduction operation.  An input that is a compute or
+fix may define its own group which affects the quantities it returns.
+For example, a compute will return a zero value for atoms that are not
+in the group specified for that compute.
 
 Each listed input is operated on independently.  Each input can be the
-result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the evaluation
-of an atom-style :doc:`variable <variable>`.
+result of a :doc:`compute <compute>` or :doc:`fix <fix>` or the
+evaluation of an atom-style :doc:`variable <variable>`.
 
-Note that for values from a compute or fix, the bracketed index I can
-be specified using a wildcard asterisk with the index to effectively
+Note that for values from a compute or fix, the bracketed index I can be
+specified using a wildcard asterisk with the index to effectively
 specify multiple values.  This takes the form "\*" or "\*n" or "m\*" or
-"m\*n".  If :math:`N` is the size of the vector (for *mode* = scalar) or the
-number of columns in the array (for *mode* = vector), then an asterisk
-with no numeric values means all indices from 1 to :math:`N`.  A leading
-asterisk means all indices from 1 to n (inclusive).  A trailing
-asterisk means all indices from n to :math:`N` (inclusive).  A middle asterisk
-means all indices from m to n (inclusive).
+"m\*n".  If :math:`N` is the size of the vector (for *mode* = scalar) or
+the number of columns in the array (for *mode* = vector), then an
+asterisk with no numeric values means all indices from 1 to :math:`N`.
+A leading asterisk means all indices from 1 to n (inclusive).  A
+trailing asterisk means all indices from n to :math:`N` (inclusive).  A
+middle asterisk means all indices from m to n (inclusive).
 
 Using a wildcard is the same as if the individual columns of the array
-had been listed one by one.  For example, the following two compute reduce/chunk
-commands are equivalent, since the
-:doc:`compute property/chunk <compute_property_chunk>` command creates a per-atom
+had been listed one by one.  For example, the following two compute
+reduce/chunk commands are equivalent, since the :doc:`compute
+property/chunk <compute_property_chunk>` command creates a per-atom
 array with 3 columns:
 
 .. code-block:: LAMMPS
@@ -164,13 +166,14 @@ Output info
 """""""""""
 
 This compute calculates a global vector if a single input value is
-specified, otherwise a global array is output.  The number of columns
-in the array is the number of inputs provided.  The length of the
-vector or the number of vector elements or array rows = the number of
-chunks *Nchunk* as calculated by the specified :doc:`compute chunk/atom <compute_chunk_atom>` command.  The vector or array can
-be accessed by any command that uses global values from a compute as
-input.  See the :doc:`Howto output <Howto_output>` page for an
-overview of LAMMPS output options.
+specified, otherwise a global array is output.  The number of columns in
+the array is the number of inputs provided.  The length of the vector or
+the number of vector elements or array rows = the number of chunks
+*Nchunk* as calculated by the specified :doc:`compute chunk/atom
+<compute_chunk_atom>` command.  The vector or array can be accessed by
+any command that uses global values from a compute as input.  See the
+:doc:`Howto output <Howto_output>` page for an overview of LAMMPS output
+options.
 
 The per-atom values for the vector or each column of the array will be
 in whatever :doc:`units <units>` the corresponding input value is in.
@@ -183,7 +186,9 @@ Restrictions
 Related commands
 """"""""""""""""
 
-:doc:`compute chunk/atom <compute_chunk_atom>`, :doc:`compute reduce <compute_reduce>`, :doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
+:doc:`compute chunk/atom <compute_chunk_atom>`,
+:doc:`compute reduce <compute_reduce>`,
+:doc:`compute chunk/spread/atom <compute_chunk_spread_atom>`
 
 Default
 """""""

doc/src/compute_rheo_property_atom.rst

@@ -81,7 +81,7 @@ includes *xx*, *xy*, *yx*, and *yy*. In 3D, this includes *xx*, *xy*, *xz*,
 Many properties require their respective fixes, listed below in related
 commands, be defined. For instance, the *viscosity* attribute is the
 viscosity of a particle calculated by
-:doc:`fix rheo/viscous <fix_rheo_viscosity>`. The meaning of less obvious
+:doc:`fix rheo/viscosity <fix_rheo_viscosity>`. The meaning of less obvious
 properties is described below.
 
 The *phase* property indicates whether the particle is in a fluid state,

doc/src/compute_sna_atom.rst

@@ -3,7 +3,9 @@
 .. index:: compute snav/atom
 .. index:: compute snap
 .. index:: compute sna/grid
+.. index:: compute sna/grid/kk
 .. index:: compute sna/grid/local
+.. index:: compute sna/grid/local/kk
 
 compute sna/atom command
 ========================
@@ -20,9 +22,14 @@ compute snap command
 compute sna/grid command
 ========================
 
+compute sna/grid/kk command
+===========================
+
 compute sna/grid/local command
 ==============================
 
+Accelerator Variants: *sna/grid/local/kk*
+
 Syntax
 """"""
 
@@ -33,17 +40,17 @@ Syntax
    compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
    compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
    compute ID group-ID snap rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-   compute ID group-ID sna/grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
-   compute ID group-ID sna/grid/local nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID sna/grid grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
+   compute ID group-ID sna/grid/local grid nx ny nz rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
 
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * sna/atom = style name of this compute command
-* rcutfac = scale factor applied to all cutoff radii (positive real)
-* rfac0 = parameter in distance to angle conversion (0 < rcutfac < 1)
-* twojmax = band limit for bispectrum components (non-negative integer)
-* R_1, R_2,... = list of cutoff radii, one for each type (distance units)
-* w_1, w_2,... = list of neighbor weights, one for each type
-* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
+* *rcutfac* = scale factor applied to all cutoff radii (positive real)
+* *rfac0* = parameter in distance to angle conversion (0 < rcutfac < 1)
+* *twojmax* = band limit for bispectrum components (non-negative integer)
+* *R_1, R_2,...* = list of cutoff radii, one for each type (distance units)
+* *w_1, w_2,...* = list of neighbor weights, one for each type
+* *grid* values = nx, ny, nz, number of grid points in x, y, and z directions (positive integer)
 * zero or more keyword/value pairs may be appended
 * keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag* or *nnn* or *wmode* or *delta*
 
@@ -103,7 +110,7 @@ Examples
    compute snap all snap 1.4 0.95 6 2.0 1.0
    compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 chem 2 0 1
    compute snap all snap 1.0 0.99363 6 3.81 3.83 1.0 0.93 switchinnerflag 1 sinner 1.35 1.6 dinner 0.25 0.3
-   compute bgrid all sna/grid/local 200 200 200 1.4 0.95 6 2.0 1.0
+   compute bgrid all sna/grid/local grid 200 200 200 1.4 0.95 6 2.0 1.0
    compute bnnn all sna/atom 9.0 0.99363 8 0.5 1.0 rmin0 0.0 nnn 24 wmode 1 delta 0.2
 
 Description
@@ -252,7 +259,8 @@ for finite-temperature Kohn-Sham density functional theory (:ref:`Ellis
 et al. <Ellis2021>`) Neighbor atoms not in the group do not contribute
 to the bispectrum components of the grid points. The distance cutoff
 :math:`R_{ii'}` assumes that *i* has the same type as the neighbor atom
-*i'*.
+*i'*. Both computes can be hardware accelerated with Kokkos by using the
+*sna/grid/kk* and *sna/grid/local/kk* commands, respectively.
 
 Compute *sna/grid* calculates a global array containing bispectrum
 components for a regular grid of points.
@@ -463,6 +471,12 @@ fluctuations in the resulting local atomic environment fingerprint.  The
 detailed formalism is given in the paper by Lafourcade et
 al. :ref:`(Lafourcade) <Lafourcade2023_2>`.
 
+----------
+
+
+.. include:: accel_styles.rst
+
+	     
 ----------
 
 Output info
@@ -654,7 +668,7 @@ of Angular Momentum, World Scientific, Singapore (1987).
 
 .. _Ellis2021:
 
-**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam,  Phys Rev B, 104, 035120, (2021)
+**(Ellis)** Ellis, Fiedler, Popoola, Modine, Stephens, Thompson, Cangi, Rajamanickam, `Phys. Rev. B, 104, 035120, (2021) <https://doi.org/10.1103/PhysRevB.104.035120>`_
 
 .. _Lafourcade2023_2:
 

doc/src/compute_stress_curvilinear.rst

@@ -87,7 +87,7 @@ This array can be output with :doc:`fix ave/time <fix_ave_time>`,
 
 .. code-block:: LAMMPS
 
-  compute 1 all stress/spherical 0 0 0 0.1 10
+  compute p all stress/spherical 0 0 0 0.1 10
   fix 2 all ave/time 100 1 100 c_p[*] file dump_p.out mode vector
 
 The values calculated by this compute are "intensive".  The stress

doc/src/compute_stress_mop.rst

@@ -129,6 +129,9 @@ package <Build_package>` doc page on for more info.
 The method is implemented for orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
+Contributions from bonds, angles, and dihedrals are not compatible
+with MPI parallel runs.
+
 The method only works with two-body pair interactions, because it
 requires the class method ``Pair::single()`` to be implemented, which is
 not possible for manybody potentials.  In particular, compute

doc/src/compute_temp_deform.rst

@@ -128,6 +128,12 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
 thermostatting.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Output info
 """""""""""
 

doc/src/compute_temp_partial.rst

@@ -46,7 +46,7 @@ degrees of freedom.
 
 A symmetric tensor, stored as a six-element vector, is also calculated
 by this compute for use in the computation of a pressure tensor by the
-:doc:`compute pressue <compute_pressure>` command.  The formula for
+:doc:`compute pressure <compute_pressure>` command.  The formula for
 the components of the tensor is the same as the above expression for
 :math:`E_\mathrm{kin}`, except that the 1/2 factor is NOT included and
 the :math:`v_i^2` is replaced by :math:`v_{i,x} v_{i,y}` for the
@@ -82,12 +82,6 @@ See the :doc:`Howto thermostat <Howto_thermostat>` page for a
 discussion of different ways to compute temperature and perform
 thermostatting.
 
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
 Output info
 """""""""""
 

doc/src/computes.rst

@@ -1,8 +0,0 @@
-Computes
-########
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   compute_*

doc/src/dihedrals.rst

@@ -1,8 +0,0 @@
-Dihedral Styles
-###############
-
-.. toctree::
-   :maxdepth: 1
-   :glob:
-
-   dihedral_*

doc/src/fix.rst

@@ -357,6 +357,7 @@ accelerated styles exist.
 * :doc:`python/move <fix_python_move>` - move particles using a Python function during a simulation run
 * :doc:`qbmsst <fix_qbmsst>` - quantum bath multi-scale shock technique time integrator
 * :doc:`qeq/comb <fix_qeq_comb>` - charge equilibration for COMB potential
+* :doc:`qeq/ctip <fix_qeq>` - charge equilibration for CTIP potential
 * :doc:`qeq/dynamic <fix_qeq>` - charge equilibration via dynamic method
 * :doc:`qeq/fire <fix_qeq>` - charge equilibration via FIRE minimizer
 * :doc:`qeq/point <fix_qeq>` - charge equilibration via point method
@@ -365,6 +366,7 @@ accelerated styles exist.
 * :doc:`qeq/slater <fix_qeq>` - charge equilibration via Slater method
 * :doc:`qmmm <fix_qmmm>` - functionality to enable a quantum mechanics/molecular mechanics coupling
 * :doc:`qtb <fix_qtb>` - implement quantum thermal bath scheme
+* :doc:`qtpie/reaxff <fix_qtpie_reaxff>` - apply QTPIE charge equilibration
 * :doc:`rattle <fix_shake>` - RATTLE constraints on bonds and/or angles
 * :doc:`reaxff/bonds <fix_reaxff_bonds>` - write out ReaxFF bond information
 * :doc:`reaxff/species <fix_reaxff_species>` - write out ReaxFF molecule information

doc/src/fix_acks2_reaxff.rst

@@ -111,7 +111,8 @@ LAMMPS was built with that package. See the :doc:`Build package
 
 This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
-periodic cell dimensions less than :math:`10~\AA`.
+periodic cell dimensions smaller than the non-bonded cutoff radius,
+which is typically :math:`10~\AA` for ReaxFF simulations.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,
@@ -122,7 +123,8 @@ components in non-periodic directions.
 Related commands
 """"""""""""""""
 
-:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
+:doc:`fix qtpi/reaxff <fix_qtpie_reaxff>`
 
 Default
 """""""

doc/src/fix_adapt.rst

@@ -119,6 +119,14 @@ style supports it.  Note that the :doc:`pair_style <pair_style>` and
 to specify these parameters initially; the fix adapt command simply
 overrides the parameters.
 
+.. note::
+
+   Pair_coeff settings must be made **explicitly** in order for fix
+   adapt to be able to change them.  Settings inferred from mixing
+   are not suitable.  If necessary all mixed settings can be output
+   to a file using the :doc:`write_coeff command <write_coeff>` and
+   then the desired mixed pair_coeff settings copied from that file.
+
 The *pstyle* argument is the name of the pair style.  If
 :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
 *pstyle* should be a sub-style name.  If there are multiple
@@ -319,25 +327,36 @@ all types from 1 to :math:`N`.  A leading asterisk means all types from
 :math:`N` (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
-Currently *bond* does not support bond_style hybrid nor bond_style
-hybrid/overlay as bond styles. The bond styles that currently work
-with fix_adapt are
+If :doc:`bond_style hybrid <bond_hybrid>` is used, *bstyle* should be a
+sub-style name. The bond styles that currently work with fix adapt are:
 
-+------------------------------------+------------+------------+
-| :doc:`class2 <bond_class2>`        | r0         | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`fene <bond_fene>`            | k,r0       | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`fene/nm <bond_fene>`         | k,r0       | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`gromos <bond_gromos>`        | k,r0       | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`harmonic <bond_harmonic>`    | k,r0       | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`morse <bond_morse>`          | r0         | type bonds |
-+------------------------------------+------------+------------+
-| :doc:`nonlinear <bond_nonlinear>`  | epsilon,r0 | type bonds |
-+------------------------------------+------------+------------+
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`class2 <bond_class2>`                         | k2,k3,k4,r0               | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`fene <bond_fene>`                             | k,r0                      | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`fene/expand <bond_fene_expand>`               | k,r0,epsilon,sigma,shift  | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`fene/nm <bond_fene>`                          | k,r0                      | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`gaussian <bond_gaussian>`                     | alpha,width,r0            | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`gromos <bond_gromos>`                         | k,r0                      | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`harmonic <bond_harmonic>`                     | k,r0                      | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`harmonic/restrain <bond_harmonic_restrain>`   | k                         | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`harmonic/shift <bond_harmonic_shift>`         | k,r0,r1                   | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`harmonic/shift/cut <bond_harmonic_shift_cut>` | k,r0,r1                   | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`mm3 <bond_mm3>`                               | k,r0                      | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`morse <bond_morse>`                           | d0,alpha,r0               | type bonds |
++-----------------------------------------------------+---------------------------+------------+
+| :doc:`nonlinear <bond_nonlinear>`                   | lamda,epsilon,r0          | type bonds |
++-----------------------------------------------------+---------------------------+------------+
 
 ----------
 
@@ -357,15 +376,40 @@ all types from 1 to :math:`N`.  A leading asterisk means all types from
 :math:`N` (inclusive).  A middle asterisk means all types from m to n
 (inclusive).
 
-Currently *angle* does not support angle_style hybrid nor angle_style
-hybrid/overlay as angle styles. The angle styles that currently work
-with fix_adapt are
+If :doc:`angle_style hybrid <angle_hybrid>` is used, *astyle* should be a
+sub-style name. The angle styles that currently work with fix adapt are:
 
-+------------------------------------+----------+-------------+
-| :doc:`harmonic <angle_harmonic>`   | k,theta0 | type angles |
-+------------------------------------+----------+-------------+
-| :doc:`cosine <angle_cosine>`       | k        | type angles |
-+------------------------------------+----------+-------------+
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`harmonic <angle_harmonic>`                                   | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`charmm <angle_charmm>`                                       | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`class2 <angle_class2>`                                       | k2,k3,k4,theta0    | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`cosine <angle_cosine>`                                       | k                  | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`cosine/delta <angle_cosine_delta>`                           | k                  | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`cosine/periodic <angle_cosine_periodic>`                     | k,b,n              | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`cosine/squared <angle_cosine_squared>`                       | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`cosine/squared/restricted <angle_cosine_squared_restricted>` | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`dipole <angle_dipole>`                                       | k,gamma0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`fourier <angle_fourier>`                                     | k,c0,c1,c2         | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`fourier/simple <angle_fourier_simple>`                       | k,c,n              | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`gaussian <angle_gaussian>`                                   | alpha,width,theta0 | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`mm3 <angle_mm3>`                                             | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`quartic <angle_quartic>`                                     | k2,k3,k4,theta0    | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
+| :doc:`spica <angle_spica>`                                         | k,theta0           | type angles |
++--------------------------------------------------------------------+--------------------+-------------+
 
 Note that internally, theta0 is stored in radians, so the variable
 this fix uses to reset theta0 needs to generate values in radians.

doc/src/fix_adapt_fep.rst

@@ -116,12 +116,22 @@ style supports it.  Note that the :doc:`pair_style <pair_style>` and
 to specify these parameters initially; the fix adapt command simply
 overrides the parameters.
 
-The *pstyle* argument is the name of the pair style.  If :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used, *pstyle* should be
-a sub-style name.  For example, *pstyle* could be specified as "soft"
-or "lubricate".  The *pparam* argument is the name of the parameter to
-change.  This is the current list of pair styles and parameters that
-can be varied by this fix.  See the doc pages for individual pair
-styles and their energy formulas for the meaning of these parameters:
+.. note::
+
+   Pair_coeff settings must be made **explicitly** in order for fix
+   adapt/fep to be able to change them.  Settings inferred from mixing
+   are not suitable.  If necessary all mixed settings can be output
+   to a file using the :doc:`write_coeff command <write_coeff>` and
+   then the desired mixed pair_coeff settings copied from that file.
+
+The *pstyle* argument is the name of the pair style.  If
+:doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` is used,
+*pstyle* should be a sub-style name.  For example, *pstyle* could be
+specified as "soft" or "lubricate".  The *pparam* argument is the name
+of the parameter to change.  This is the current list of pair styles and
+parameters that can be varied by this fix.  See the doc pages for
+individual pair styles and their energy formulas for the meaning of
+these parameters:
 
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |

doc/src/fix_addforce.rst

@@ -115,10 +115,6 @@ correctly, the minimization will not converge properly.
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_atom_swap.rst

@@ -119,15 +119,14 @@ groups of atoms that have different charges, these charges will not be
 changed when the atom types change.
 
 Since this fix computes total potential energies before and after
-proposed swaps, so even complicated potential energy calculations are
-OK, including the following:
+proposed swaps, even complicated potential energy calculations are
+acceptable, including the following:
 
 * long-range electrostatics (:math:`k`-space)
 * many body pair styles
-* hybrid pair styles
-* eam pair styles
+* hybrid pair styles (with restrictions)
+* EAM pair styles
 * triclinic systems
-* need to include potential energy contributions from other fixes
 
 Some fixes have an associated potential energy. Examples of such fixes
 include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
@@ -181,6 +180,10 @@ This fix is part of the MC package.  It is only enabled if LAMMPS was
 built with that package.  See the :doc:`Build package <Build_package>`
 doc page for more info.
 
+When this fix is used with a :doc:`hybrid pair style <pair_hybrid>`
+system, only swaps between atom types of the same sub-style (or
+combination of sub-styles) are permitted.
+
 This fix cannot be used with systems that do not have per-type masses
 (e.g. atom style sphere) since the implemented algorithm pre-computes
 velocity rescaling factors from per-type masses and ignores any per-atom

doc/src/fix_aveforce.rst

@@ -71,10 +71,6 @@ to it.
 
 ----------
 
-.. include:: accel_styles.rst
-
-----------
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_cmap.rst

@@ -1,8 +1,11 @@
 .. index:: fix cmap
+.. index:: fix cmap/kk
 
 fix cmap command
 ================
 
+Accelerator Variants: *cmap/kk*
+
 Syntax
 """"""
 
@@ -141,6 +144,12 @@ outermost level.
    MUST not disable the :doc:`fix_modify <fix_modify>` *energy* option
    for this fix.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/fix_colvars.rst

@@ -1,8 +1,11 @@
 .. index:: fix colvars
+.. index:: fix colvars/kk
 
 fix colvars command
 ===================
 
+Accelerator Variants: *colvars/kk*
+
 Syntax
 """"""
 
@@ -118,6 +121,16 @@ thermostat target temperature.
 The *seed* keyword contains the seed for the random number generator
 that will be used in the colvars module.
 
+----------
+
+.. note::
+
+   Fix colvars/kk is not really ported to KOKKOS, since the colvars
+   library has not been ported to KOKKOS.  It merely has some
+   optimizations to reduce the data transfers between host and device
+   for KOKKOS with GPUs.
+
+----------
 
 Restarting
 """"""""""

doc/src/fix_external.rst

@@ -139,9 +139,9 @@ properties are:
    void set_vector_length(int n);
    void set_vector(int idx, double val);
 
-These allow to set per-atom energy contributions, per-atom stress
-contributions, the length and individual values of a global vector
-of properties that the caller code may want to communicate  to LAMMPS
+These enable setting per-atom energy and  per-atom stress contributions,
+the length and individual values of a global vector of properties that
+the caller code may want to communicate  to LAMMPS
 (e.g. for use in :doc:`fix ave/time <fix_ave_time>` or in
 :doc:`equal-style variables <variable>` or for
 :doc:`custom thermo output <thermo_style>`.
@@ -173,9 +173,19 @@ stress/atom <compute_stress_atom>` commands.  The former can be
 accessed by :doc:`thermodynamic output <thermo_style>`.  The default
 setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
-This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the potential
-energy discussed above.  The scalar stored by this fix is "extensive".
+This fix computes a global scalar, a global vector, and a per-atom array
+which can be accessed by various :doc:`output commands <Howto_output>`.
+The scalar is the potential energy discussed above.  The scalar stored
+by this fix is "extensive".
+The global vector has a custom length and needs to be set by the external
+program using the
+:cpp:func:`lammps_fix_external_set_vector() <lammps_fix_external_set_vector>`
+and :cpp:func:`lammps_fix_external_set_vector_length()
+<lammps_fix_external_set_vector_length>`
+calls of the LAMMPS library interface or the equivalent call of the Python
+or Fortran modules.
+The per-atom array has 3 values for each atom and is the applied external
+force.
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_gcmc.rst

@@ -50,8 +50,8 @@ Syntax
        *intra_energy* value = intramolecular energy (energy units)
        *tfac_insert* value = scale up/down temperature of inserted atoms (unitless)
        *overlap_cutoff* value = maximum pair distance for overlap rejection (distance units)
-       *max* value = Maximum number of molecules allowed in the system
-       *min* value = Minimum number of molecules allowed in the system
+       *max* value = Maximum number of atoms allowed in the fix group (and region)
+       *min* value = Minimum number of atoms allowed in the fix group (and region)
 
 Examples
 """"""""
@@ -380,10 +380,11 @@ an infinite positive energy to all new configurations that place any
 pair of atoms closer than the specified overlap cutoff distance.
 
 The *max* and *min* keywords allow for the restriction of the number of
-atoms in the simulation. They automatically reject all insertion or
-deletion moves that would take the system beyond the set boundaries.
-Should the system already be beyond the boundary, only moves that bring
-the system closer to the bounds may be accepted.
+atoms in the fix group (and region in case the *region* keyword is
+used).  They automatically reject all insertion or deletion moves that
+would take the system beyond the set boundaries.  Should the system
+already be beyond the boundary, only moves that bring the system closer
+to the bounds may be accepted.
 
 The *group* keyword adds all inserted atoms to the :doc:`group <group>`
 of the group-ID value. The *grouptype* keyword adds all inserted atoms

doc/src/fix_halt.rst

@@ -101,7 +101,7 @@ hstyle = bondmax option.
 .. code-block:: LAMMPS
 
    compute         bdist all bond/local dist
-   compute         bmax all reduce max c_bdist
+   compute         bmax all reduce max c_bdist inputs local
    variable        bondmax equal c_bmax
 
 Thus these two versions of a fix halt command will do the same thing:

doc/src/fix_langevin.rst

@@ -231,12 +231,6 @@ the particles.  As described below, this energy can then be printed
 out or added to the potential energy of the system to monitor energy
 conservation.
 
-.. note::
-
-   This accumulated energy does NOT include kinetic energy removed
-   by the *zero* flag. LAMMPS will print a warning when both options are
-   active.
-
 The keyword *zero* can be used to eliminate drift due to the
 thermostat. Because the random forces on different atoms are
 independent, they do not sum exactly to zero.  As a result, this fix

doc/src/fix_nonaffine_displacement.rst

@@ -102,7 +102,6 @@ zeroed. The *update* reference style implies the reference state will be updated
 *nstep* timesteps. The *offset* reference will update the reference state *nstep*
 timesteps before a multiple of *nevery* timesteps.
 
-
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
@@ -129,6 +128,12 @@ This compute is part of the EXTRA-FIX package.  It is only enabled if
 LAMMPS was built with that package.  See the
 :doc:`Build package <Build_package>` page for more info.
 
+As this fix depends on a run including specific reference timesteps, it
+currently does not update peratom values if used in conjunction with the
+:doc:`rerun command <rerun>` since it cannot ensure the necessary reference
+timesteps are included.
+
+
 Related commands
 """"""""""""""""
 

doc/src/fix_nph_body.rst

@@ -79,8 +79,6 @@ It also means that changing attributes of *thermo_temp* or
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_npt_body.rst

@@ -103,8 +103,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_nve_limit.rst

@@ -1,8 +1,11 @@
 .. index:: fix nve/limit
+.. index:: fix nve/limit/kk
 
 fix nve/limit command
 =====================
 
+Accelerator Variants: *nve/limit/kk*
+
 Syntax
 """"""
 
@@ -79,6 +82,12 @@ is "extensive".
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
  none

doc/src/fix_nvt_body.rst

@@ -85,8 +85,6 @@ remaining thermal degrees of freedom, and the bias is added back in.
 
 ----------
 
-.. include:: accel_styles.rst
-
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_pour.rst

@@ -155,6 +155,22 @@ many timesteps until the desired # of particles has been inserted.
    the :doc:`compute_modify dynamic/dof yes <compute_modify>` command
    for the temperature compute you are using.
 
+.. admonition:: Implementation Notes
+  :class: Hint
+
+  The exact insertion procedure depends on many factors (e.g. the range of
+  diameters inserted or whether molecules are being inserted). However, in
+  the simplest scenario of monodisperse atoms, the procedure works as
+  follows. First, the number of timesteps between two insertion events is
+  calculated as the time for a particle to fall through the insertion region,
+  accounting for gravity and any region motion. Next, the target number of
+  particles inserted per event (assuming no failed insertions due to overlaps)
+  is calculated as the product of the volume fraction and the volume of the
+  insertion region divided by the volume of a particle (or area in 2D).
+  Events are repeated until all N particles have been inserted, where
+  the final event is likely interrupted upon reaching N. Estimates of this
+  process are printed to the log/screen at the start of a run.
+
 ----------
 
 All other keywords are optional with defaults as shown below.

doc/src/fix_qeq.rst

@@ -1,6 +1,7 @@
 .. index:: fix qeq/point
 .. index:: fix qeq/shielded
 .. index:: fix qeq/slater
+.. index:: fix qeq/ctip
 .. index:: fix qeq/dynamic
 .. index:: fix qeq/fire
 
@@ -13,6 +14,9 @@ fix qeq/shielded command
 fix qeq/slater command
 ======================
 
+fix qeq/ctip command
+====================
+
 fix qeq/dynamic command
 =======================
 
@@ -27,18 +31,20 @@ Syntax
    fix ID group-ID style Nevery cutoff tolerance maxiter qfile keyword ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/dynamic* or *qeq/fire*
+* style = *qeq/point* or *qeq/shielded* or *qeq/slater* or *qeq/ctip* or *qeq/dynamic* or *qeq/fire*
 * Nevery = perform charge equilibration every this many steps
 * cutoff = global cutoff for charge-charge interactions (distance unit)
 * tolerance = precision to which charges will be equilibrated
 * maxiter = maximum iterations to perform charge equilibration
-* qfile = a filename with QEq parameters or *coul/streitz* or *reaxff*
+* qfile = a filename with QEq parameters or *coul/streitz* or *coul/ctip* or *reaxff*
 * zero or more keyword/value pairs may be appended
-* keyword = *alpha* or *qdamp* or *qstep* or *warn*
+* keyword = *alpha* or *cdamp* or *maxrepeat* or *qdamp* or *qstep* or *warn*
 
   .. parsed-literal::
 
        *alpha* value = Slater type orbital exponent (qeq/slater only)
+       *cdamp* value = damping parameter for Coulomb interactions (qeq/ctip only)
+       *maxrepeat* value = number of equilibration cycles allowed to ensure no atoms cross charge bounds (qeq/ctip only)
        *qdamp* value = damping factor for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
        *qstep* value = time step size for damped dynamics charge solver (qeq/dynamic and qeq/fire only)
        *warn* value = do (=yes) or do not (=no) print a warning when the maximum number of iterations is reached
@@ -51,6 +57,7 @@ Examples
    fix 1 all qeq/point 1 10 1.0e-6 200 param.qeq1
    fix 1 qeq qeq/shielded 1 8 1.0e-6 100 param.qeq2
    fix 1 all qeq/slater 5 10 1.0e-6 100 params alpha 0.2
+   fix 1 all qeq/ctip 1 12 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
    fix 1 qeq qeq/dynamic 1 12 1.0e-3 100 my_qeq
    fix 1 all qeq/fire 1 10 1.0e-3 100 my_qeq qdamp 0.2 qstep 0.1
 
@@ -103,7 +110,7 @@ equalizes the derivative of energy with respect to charge of all the
 atoms) by adjusting the partial charge on individual atoms based on
 interactions with their neighbors within *cutoff*\ .  It requires a few
 parameters in the appropriate units for each atom type which are read
-from a file specified by *qfile*\ .  The file has the following format
+from a file specified by *qfile*\ .  The file has the following format:
 
 .. parsed-literal::
 
@@ -112,20 +119,32 @@ from a file specified by *qfile*\ .  The file has the following format
    ...
    Ntype chi eta gamma zeta qcore
 
+except for fix style *qeq/ctip* where the format is:
+
+.. parsed-literal::
+
+   1 chi eta gamma zeta qcore qmin qmax omega
+   2 chi eta gamma zeta qcore qmin qmax omega
+   ...
+   Ntype chi eta gamma zeta qcore qmin qmax omega
+
 There have to be parameters given for every atom type. Wildcard entries
 are possible using the same type range syntax as for "coeff" commands
 (i.e., n\*m, n\*, \*m, \*). Later entries will overwrite previous ones.
-Empty lines or any text following the pound sign (#) are ignored.
-Each line starts with the atom type followed by five parameters.
-Only a subset of the parameters is used by each QEq style as described
-below, thus the others can be set to 0.0 if desired, but all five
-entries per line are required.
+Empty lines or any text following the pound sign (#) are ignored.  Each
+line starts with the atom type followed by eight parameters.  Only a
+subset of the parameters is used by each QEq style as described below,
+thus the others can be set to 0.0 if desired, but all eight entries per
+line are required.
 
 * *chi* = electronegativity in energy units
 * *eta* = self-Coulomb potential in energy units
 * *gamma* = shielded Coulomb constant defined by :ref:`ReaxFF force field <vanDuin>` in distance units
 * *zeta* = Slater type orbital exponent defined by the :ref:`Streitz-Mintmire <Streitz1>` potential in reverse distance units
 * *qcore* = charge of the nucleus defined by the :ref:`Streitz-Mintmire potential <Streitz1>` potential in charge units
+* *qmin* = lower bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
+* *qmax* = upper bound on the allowed charge defined by the :ref:`CTIP <CTIP1>` potential in charge units
+* *omega* = penalty parameter used to enforce charge bounds defined by the :ref:`CTIP <CTIP1>` potential in energy units
 
 The fix qeq styles will print a warning if the charges are not
 equilibrated within *tolerance* by *maxiter* steps, unless the
@@ -171,6 +190,22 @@ on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
 usually a good number.  Keyword *alpha* can be used to change the Slater
 type orbital exponent.
 
+.. versionadded:: 19Nov2024
+
+The *qeq/ctip* style describes partial charges on atoms in the same way
+as style *qeq/shielded* but also enables the definition of charge
+bounds.  Only the *chi*, *eta*, *gamma*, *qmin*, *qmax*, and *omega*
+parameters from the *qfile* file are used.  When using the string
+*coul/ctip* as filename, these parameters are extracted directly from an
+active *coul/ctip* pair style.  This style solves partial charges on
+atoms via the matrix inversion method.  Keyword *cdamp* can be used to
+change the damping parameter used to calculate Coulomb interactions.
+Keyword *maxrepeat* can be used to adjust the number of equilibration
+cycles allowed to ensure no atoms have crossed the charge bounds.  A
+value of 10 is usually a good choice.  A tolerance between 1.0e-6 and
+1.0e-8 is usually a good choice but should be checked in conjunction
+with the timestep for adequate energy conservation during dynamic runs.
+
 The *qeq/dynamic* style describes partial charges on atoms as point
 charges that interact through 1/r, but the extended Lagrangian method is
 used to solve partial charges on atoms.  Only the *chi* and *eta*
@@ -186,7 +221,7 @@ minimization algorithm to solve for equilibrium charges.  Keyword
 *qdamp* can be used to change the damping factor, while keyword *qstep*
 can be used to change the time step size.
 
-Note that *qeq/point*, *qeq/shielded*, and *qeq/slater* describe
+Note that *qeq/point*, *qeq/shielded*, *qeq/slater*, and *qeq/ctip* describe
 different charge models, whereas the matrix inversion method and the
 extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
 different solvers.
@@ -266,6 +301,11 @@ Chemistry, 95, 3358-3363 (1991).
 **(Streitz-Mintmire)** F. H. Streitz, J. W. Mintmire, Physical Review B, 50,
 16, 11996 (1994)
 
+.. _CTIP1:
+
+**(CTIP)** G. Plummer, J. P. Tavenner, M. I. Mendelev, Z. Wu, J. W. Lawson,
+in preparation
+
 .. _vanDuin:
 
 **(ReaxFF)** A. C. T. van Duin, S. Dasgupta, F. Lorant, W. A. Goddard III, J

doc/src/fix_qeq_reaxff.rst

@@ -124,7 +124,8 @@ LAMMPS was built with that package. See the :doc:`Build package
 
 This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
-periodic cell dimensions less than 10 Angstroms.
+periodic cell dimensions smaller than the non-bonded cutoff radius,
+which is typically :math:`10~\AA` for ReaxFF simulations.
 
 This fix may be used in combination with :doc:`fix efield <fix_efield>`
 and will apply the external electric field during charge equilibration,
@@ -138,7 +139,8 @@ as an atom-style variable using the *potential* keyword for `fix efield`.
 Related commands
 """"""""""""""""
 
-:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/shielded <fix_qeq>`,
+:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix qtpie/reaxff <fix_qtpie_reaxff>`
 
 Default
 """""""

doc/src/fix_qtpie_reaxff.rst

@@ -0,0 +1,200 @@
+.. index:: fix qtpie/reaxff
+
+fix qtpie/reaxff command
+========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   fix ID group-ID qtpie/reaxff Nevery cutlo cuthi tolerance params gfile args
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* qtpie/reaxff = style name of this fix command
+* Nevery = perform QTPIE every this many steps
+* cutlo,cuthi = lo and hi cutoff for Taper radius
+* tolerance = precision to which charges will be equilibrated
+* params = reaxff or a filename
+* gfile = the name of a file containing Gaussian orbital exponents
+* one or more keywords or keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *maxiter*
+       *maxiter* N = limit the number of iterations to *N*
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 reaxff exp.qtpie
+   fix 1 all qtpie/reaxff 1 0.0 10.0 1.0e-6 params.qtpie exp.qtpie maxiter 500
+
+Description
+"""""""""""
+
+.. versionadded:: 19Nov2024
+
+The QTPIE charge equilibration method is an extension of the QEq charge
+equilibration method. With QTPIE, the partial charges on individual atoms
+are computed by minimizing the electrostatic energy of the system in the
+same way as the QEq method but where the absolute electronegativity,
+:math:`\chi_i`, of each atom in the QEq charge equilibration scheme
+:ref:`(Rappe and Goddard) <Rappe3>` is replaced with an effective
+electronegativity given by :ref:`(Chen) <qtpie-Chen>`
+
+.. math::
+   \chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j) S_{ij}}
+                                {\sum_{m=1}^{N}S_{im}},
+
+which acts to penalize long-range charge transfer seen with the QEq charge
+equilibration scheme. In this equation, :math:`N` is the number of atoms in
+the system and :math:`S_{ij}` is the overlap integral between atom :math:`i`
+and atom :math:`j`.
+
+The effect of an external electric field can be incorporated into the QTPIE
+method by modifying the absolute or effective electronegativities of each
+atom :ref:`(Chen) <qtpie-Chen>`. This fix models the effect of an external
+electric field by using the effective electronegativity given in
+:ref:`(Gergs) <Gergs>`:
+
+.. math::
+   \chi_{\mathrm{eff},i} = \frac{\sum_{j=1}^{N} (\chi_i - \chi_j + \phi_i - \phi_j) S_{ij}}
+                                {\sum_{m=1}^{N}S_{im}},
+
+where :math:`\phi_i` and :math:`\phi_j` are the electric
+potentials at the positions of atom :math:`i` and :math:`j`
+due to the external electric field.
+
+This fix is typically used in conjunction with the ReaxFF force
+field model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
+command, but it can be used with any potential in LAMMPS, so long as it
+defines and uses charges on each atom. For more technical details about the
+charge equilibration performed by `fix qtpie/reaxff`, which is the same as in
+:doc:`fix qeq/reaxff <fix_qeq_reaxff>` except for the use of
+:math:`\chi_{\mathrm{eff},i}`, please refer to :ref:`(Aktulga) <qeq-Aktulga2>`.
+To be explicit, this fix replaces :math:`\chi_k` of eq. 3 in
+:ref:`(Aktulga) <qeq-Aktulga2>` with :math:`\chi_{\mathrm{eff},k}`.
+
+This fix requires the absolute electronegativity, :math:`\chi`, in eV, the
+self-Coulomb potential, :math:`\eta`, in eV, and the shielded Coulomb
+constant, :math:`\gamma`, in :math:`\AA^{-1}`. If the *params* setting above
+is the word "reaxff", then these are extracted from the
+:doc:`pair_style reaxff <pair_reaxff>` command and the ReaxFF force field
+file it reads in.  If a file name is specified for *params*, then the
+parameters are taken from the specified file and the file must contain
+one line for each atom type.  The latter form must be used when performing
+QTPIE with a non-ReaxFF potential. Each line should be formatted as follows,
+ensuring that the parameters are given in units of eV, eV, and :math:`\AA^{-1}`,
+respectively:
+
+.. parsed-literal::
+
+   itype chi eta gamma
+
+where *itype* is the atom type from 1 to Ntypes. Note that eta is
+defined here as twice the eta value in the ReaxFF file.
+
+The overlap integrals in the equation for :math:`\chi_{\mathrm{eff},i}`
+are computed by using normalized 1s Gaussian type orbitals. The Gaussian
+orbital exponents, :math:`\alpha`, that are needed to compute the overlap
+integrals are taken from the file given by *gfile*.
+This file must contain one line for each atom type and provide the Gaussian
+orbital exponent for each atom type in units of inverse square Bohr radius.
+Each line should be formatted as follows:
+
+.. parsed-literal::
+
+   itype alpha
+
+Empty lines or any text following the pound sign (#) are ignored. An example
+*gfile* for a system with two atom types is
+
+.. parsed-literal::
+
+    # An example gfile. Exponents are taken from Table 2.2 of Chen, J. (2009).
+    # Theory and applications of fluctuating-charge models.
+    # The units of the exponents are 1 / (Bohr radius)^2 .
+    1  0.2240  # O
+    2  0.5434  # H
+
+The optional *maxiter* keyword allows changing the max number
+of iterations in the linear solver. The default value is 200.
+
+.. note::
+
+   In order to solve the self-consistent equations for electronegativity
+   equalization, LAMMPS imposes the additional constraint that all the
+   charges in the fix group must add up to zero.  The initial charge
+   assignments should also satisfy this constraint.  LAMMPS will print a
+   warning if that is not the case.
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files
+<restart>`.  This fix computes a global scalar (the number of
+iterations) and a per-atom vector (the effective electronegativity), which
+can be accessed by various :doc:`output commands <Howto_output>`.
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.
+
+This fix is invoked during :doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+This fix is part of the REAXFF package.  It is only enabled if
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
+
+This fix does not correctly handle interactions involving multiple
+periodic images of the same atom.  Hence, it should not be used for
+periodic cell dimensions smaller than the non-bonded cutoff radius,
+which is typically :math:`10~\AA` for ReaxFF simulations.
+
+This fix may be used in combination with :doc:`fix efield <fix_efield>`
+and will apply the external electric field during charge equilibration,
+but there may be only one fix efield instance used and the electric field
+must be applied to all atoms in the system. Consequently, `fix efield` must
+be used with *group-ID* all and must not be used with the keyword *region*.
+Equal-style variables can be used for electric field vector
+components without any further settings. Atom-style variables can be used
+for spatially-varying electric field vector components, but the resulting
+electric potential must be specified as an atom-style variable using
+the *potential* keyword for `fix efield`.
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
+:doc:`fix acks2/reaxff <fix_acks2_reaxff>`
+
+Default
+"""""""
+
+maxiter 200
+
+----------
+
+.. _Rappe3:
+
+**(Rappe)** Rappe and Goddard III, Journal of Physical Chemistry, 95,
+3358-3363 (1991).
+
+.. _qtpie-Chen:
+
+**(Chen)** Chen, Jiahao. Theory and applications of fluctuating-charge models.
+University of Illinois at Urbana-Champaign, 2009.
+
+.. _Gergs:
+
+**(Gergs)** Gergs, Dirkmann and Mussenbrock.
+Journal of Applied Physics 123.24 (2018).
+
+.. _qeq-Aktulga2:
+
+**(Aktulga)** Aktulga, Fogarty, Pandit, Grama, Parallel Computing, 38,
+245-259 (2012).

doc/src/fix_recenter.rst

@@ -1,8 +1,11 @@
 .. index:: fix recenter
+.. index:: fix recenter/kk
 
 fix recenter command
 ====================
 
+Accelerator Variants: *recenter/kk*
+
 Syntax
 """"""
 
@@ -113,6 +116,12 @@ The scalar and vector values calculated by this fix are "extensive".
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Restrictions
 """"""""""""
 

doc/src/fix_rheo.rst

@@ -16,8 +16,7 @@ Syntax
 * kstyle = *quintic* or *RK0* or *RK1* or *RK2*
 * zmin = minimal number of neighbors for reproducing kernels
 * zero or more keyword/value pairs may be appended to args
-* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or
-            *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
+* keyword = *thermal* or *interface/reconstruct* or *surface/detection* or *shift* or *rho/sum* or *density* or *self/mass* or *speed/sound*
 
   .. parsed-literal::
 

doc/src/fix_spring_self.rst

@@ -13,7 +13,7 @@ Syntax
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * spring/self = style name of this fix command
-* K = spring constant (force/distance units)
+* K = spring constant (force/distance units), can be a variable (see below)
 * dir = xyz, xy, xz, yz, x, y, or z (optional, default: xyz)
 
 Examples
@@ -22,6 +22,7 @@ Examples
 .. code-block:: LAMMPS
 
    fix tether boundary-atoms spring/self 10.0
+   fix var all spring/self v_kvar
    fix zrest  move spring/self 10.0 z
 
 Description
@@ -42,6 +43,22 @@ directions, but it can be limited to the xy-, xz-, yz-plane and the
 x-, y-, or z-direction, thus restraining the atoms to a line or a
 plane, respectively.
 
+The force constant *k* can be specified as an equal-style or atom-style
+:doc:`variable <variable>`.  If the value is a variable, it should be specified
+as v_name, where name is the variable name.  In this case, the variable
+will be evaluated each time step, and its value(s) will be used as
+force constant for the spring force.
+
+Equal-style variables can specify formulas with various mathematical
+functions and include :doc:`thermo_style <thermo_style>` command
+keywords for the simulation box parameters, time step, and elapsed time.
+Thus, it is easy to specify a time-dependent force field.
+
+Atom-style variables can specify the same formulas as equal-style
+variables but can also include per-atom values, such as atom
+coordinates.  Thus, it is easy to specify a spatially-dependent force
+field with optional time-dependence as well.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
@@ -89,7 +106,9 @@ invoked by the :doc:`minimize <minimize>` command.
 
 Restrictions
 """"""""""""
- none
+
+The KOKKOS version, *fix spring/self/kk* may only be used with a constant
+value of K, not a variable.
 
 Related commands
 """"""""""""""""