Merge pull request #4387 from akohlmey/next_release

Step version strings for next release

.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 +1,58 @@
+# LAMMPS Release Steps
+
+The following notes chronicle the current steps for preparing and publishing LAMMPS releases.
+For definition of what LAMMPS versions and the different kinds of releases mean, please
+refer to [the corresponding section in the LAMMPS manual](https://docs.lammps.org/Manual_version.html).
+
+## 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.
+
+### 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"
+
+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.
+
+## 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()
@@ -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)
@@ -515,22 +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)
-option(WITH_CURL "Enable libcurl support" ${CURL_FOUND})
-if(WITH_CURL)
-  target_compile_definitions(lammps PRIVATE -DLAMMPS_CURL)
-
-  # need to use pkgconfig for fully static bins to find custom static libs
-  if (CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
-    include(FindPkgConfig)
-    pkg_check_modules(CURL IMPORTED_TARGET libcurl libssl libcrypto)
-    target_link_libraries(lammps PUBLIC PkgConfig::CURL)
-  else()
-    find_package(CURL REQUIRED)
-    target_link_libraries(lammps PRIVATE CURL::libcurl)
-  endif()
-endif()
-
 # tweak jpeg library names to avoid linker errors with MinGW cross-compilation
 set(JPEG_NAMES libjpeg libjpeg-62)
 find_package(JPEG QUIET)
@@ -588,7 +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()
@@ -603,13 +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)   #
 ########################################################################
@@ -838,9 +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)
@@ -981,6 +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}")
@@ -999,6 +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}")
@@ -1086,15 +1078,12 @@ if(BUILD_TOOLS)
   message(STATUS "<<< Building Tools >>>")
 endif()
 if(BUILD_LAMMPS_GUI)
-  message(STATUS "<<< Building LAMMPS-GUI >>>")
+  message(STATUS "<<< Building LAMMPS GUI >>>")
   if(LAMMPS_GUI_USE_PLUGIN)
     message(STATUS "Loading LAMMPS library as plugin at run time")
   else()
     message(STATUS "Linking LAMMPS library at compile time")
   endif()
-  if(BUILD_WHAM)
-    message(STATUS "<<< Building WHAM >>>")
-  endif()
 endif()
 if(ENABLE_TESTING)
   message(STATUS "<<< Building Unit Tests >>>")

cmake/Modules/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/GPU.cmake

@@ -189,7 +189,7 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   add_executable(nvc_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
-  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR -DLAMMPS_${LAMMPS_SIZES})
+  target_compile_definitions(nvc_get_devices PRIVATE -DUCL_CUDADR)
   target_link_libraries(nvc_get_devices PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
@@ -489,7 +489,7 @@ else()
   target_link_libraries(gpu PRIVATE mpi_stubs)
 endif()
 
-set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
 target_compile_definitions(gpu PRIVATE -DLAMMPS_${LAMMPS_SIZES})
+set_target_properties(gpu PROPERTIES OUTPUT_NAME lammps_gpu${LAMMPS_MACHINE})
 target_sources(lammps PRIVATE ${GPU_SOURCES})
 target_include_directories(lammps PRIVATE ${GPU_SOURCES_DIR})

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/ML-PACE.cmake

@@ -40,13 +40,6 @@ else()
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
   )
   get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
-
-  # fixup yaml-cpp/emitterutils.cpp for GCC 15+ until patch is applied
-  file(READ ${lib-pace}/yaml-cpp/src/emitterutils.cpp yaml_emitterutils)
-  string(REPLACE "#include <sstream>" "#include <sstream>\n#include <cinttypes>" yaml_tmp_emitterutils "${yaml_emitterutils}")
-  string(REPLACE "#include <cinttypes>\n#include <cinttypes>" "#include <cinttypes>" yaml_emitterutils "${yaml_tmp_emitterutils}")
-  file(WRITE ${lib-pace}/yaml-cpp/src/emitterutils.cpp "${yaml_emitterutils}")
-
 endif()
 
 add_subdirectory(${lib-pace} build-pace)

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/Modules/Packages/VTK.cmake

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

cmake/packaging/linux_wrapper.sh

@@ -7,11 +7,6 @@ export LC_ALL=C
 BASEDIR="$(dirname "$0")"
 EXENAME="$(basename "$0")"
 
-# save old settings (for restoring them later)
-OLDPATH="${PATH}"
-OLDLDLIB="${LD_LIBRARY_PATH}"
-
-# prepend path to find our custom executables
 PATH="${BASEDIR}/bin:${PATH}"
 
 # append to LD_LIBRARY_PATH to prefer local (newer) libs
@@ -20,8 +15,6 @@ LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:${BASEDIR}/lib"
 # set some environment variables for LAMMPS etc.
 LAMMPS_POTENTIALS="${BASEDIR}/share/lammps/potentials"
 MSI2LMP_LIBRARY="${BASEDIR}/share/lammps/frc_files"
-
-# export everything
-export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH OLDPATH OLDLDLIB
+export LD_LIBRARY_PATH LAMMPS_POTENTIALS MSI2LMP_LIBRARY PATH
 
 exec "${BASEDIR}/bin/${EXENAME}" "$@"

cmake/packaging/xdg-open

@@ -33,14 +33,6 @@
 #
 #---------------------------------------------
 
-# restore previously saved environment variables, if available
-if [ -n "${OLDPATH}" ]
-then
-    PATH="${OLDPATH}"
-    LD_LIBRARY_PATH="${OLDLDLIB}"
-    export PATH LD_LIBRARY_PATH
-fi
-
 NEW_LIBRARY_PATH="/usr/local/lib64"
 for s in $(echo $LD_LIBRARY_PATH | sed -e 's/:/ /g')
 do \

cmake/presets/kokkos-cuda.cmake

@@ -1,8 +1,10 @@
 # preset that enables KOKKOS and selects CUDA compilation with OpenMP
-# enabled as well. The GPU architecture *must* match your hardware (If not manually set, Kokkos will try to autodetect it).
+# enabled as well. This preselects CC 5.0 as default GPU arch, since
+# that is compatible with all higher CC, but not the default CC 3.5
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
+set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 get_filename_component(NVCC_WRAPPER_CMD ${CMAKE_CURRENT_SOURCE_DIR}/../lib/kokkos/bin/nvcc_wrapper ABSOLUTE)
 set(CMAKE_CXX_COMPILER ${NVCC_WRAPPER_CMD} CACHE FILEPATH "" FORCE)

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_basics.rst

@@ -502,8 +502,6 @@ using CMake or Make.
                                       # chain.x, micelle2d.x, msi2lmp, phana,
                                       # stl_bin2txt
          -D BUILD_LAMMPS_GUI=value    # yes or no (default). Build LAMMPS-GUI
-         -D BUILD_WHAM=value          # yes (default). Download and build WHAM;
-                                      # only available for BUILD_LAMMPS_GUI=yes
 
       The generated binaries will also become part of the LAMMPS installation
       (see below).

doc/src/Build_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_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/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_lammps_gui.rst

@@ -1,45 +1,44 @@
 Using LAMMPS-GUI
 ================
 
-.. image:: JPG/lammps-gui-banner.png
-   :align: center
-   :scale: 75%
-
-LAMMPS-GUI is a graphical text editor programmed using the `Qt Framework
-<https://www.qt.io/>`_ and customized for editing and running LAMMPS
-input files.  It is linked to the :ref:`LAMMPS library <lammps_c_api>`
-and thus can run LAMMPS directly using the contents of the editor's text
-buffer as input and without having to launch the LAMMPS executable.
-
-It *differs* from other known interfaces to LAMMPS in that it can
-retrieve and display information from LAMMPS *while it is running*,
-display visualizations created with the :doc:`dump image command
-<dump_image>`, can launch the online LAMMPS documentation for known
-LAMMPS commands and styles, and directly integrates with a collection
-of LAMMPS tutorials (:ref:`Gravelle1 <Gravelle1>`).
-
-This document describes **LAMMPS-GUI version 1.7**.
+This document describes **LAMMPS-GUI version 1.6**.
 
 -----
 
-.. contents::
+LAMMPS-GUI is a graphical text editor customized for editing LAMMPS
+input files that is linked to the :ref:`LAMMPS library <lammps_c_api>`
+and thus can run LAMMPS directly using the contents of the editor's text
+buffer as input.  It can retrieve and display information from LAMMPS
+while it is running, display visualizations created with the :doc:`dump
+image command <dump_image>`, and is adapted specifically for editing
+LAMMPS input files through text completion and reformatting, and linking
+to the online LAMMPS documentation for known LAMMPS commands and styles.
 
-----
+.. note::
 
-LAMMPS-GUI aims to provide the traditional experience of running LAMMPS
-using a text editor, a command-line window, and launching the LAMMPS
-text-mode executable printing output to the screen, but just integrated
-into a single application:
+   Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
+   (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
+   Sur or later), and Windows (version 10 or later) :ref:`are available
+   <lammps_gui_install>` for download.  Non-MPI LAMMPS executables (as
+   ``lmp``) for running LAMMPS from the command line and :doc:`some
+   LAMMPS tools <Tools>` compiled executables are also included.
 
-- Write and edit LAMMPS input files using the built-in text editor.
-- Run LAMMPS on those input file with command-line flags to enable a
-  specific accelerator package (or none).
-- Extract data from the created files (like trajectory files, log files
-  with thermodynamic data, or images) and visualize it using external
-  software.
+   The source code for LAMMPS-GUI is included in the LAMMPS source code
+   distribution and can be found in the ``tools/lammps-gui`` folder.  It
+   can be compiled alongside LAMMPS when :doc:`compiling with CMake
+   <Build_cmake>`.
 
-That traditional procedure is effective for people proficient in using the
-command-line, as it allows them to use the tools for the individual steps
+LAMMPS-GUI tries to provide an experience similar to what people
+traditionally would have running LAMMPS using a command line window and
+the console LAMMPS executable but just rolled into a single executable:
+
+- writing & editing LAMMPS input files with a text editor
+- run LAMMPS on those input file with selected command line flags
+- extract data from the created files and visualize it with and
+  external software
+
+That procedure is quite effective for people proficient in using the
+command line, as that allows them to use tools for the individual steps
 that they are most comfortable with.  In fact, it is often *required* to
 adopt this workflow when running LAMMPS simulations on high-performance
 computing facilities.
@@ -50,69 +49,32 @@ window or using external programs, let alone writing scripts to extract
 data from the generated output.  It also integrates well with graphical
 desktop environments where the `.lmp` filename extension can be
 registered with LAMMPS-GUI as the executable to launch when double
-clicking on such files using a file manager.  LAMMPS-GUI also has
-support for 'drag and drop' for opening inputs: an input file can
-be selected and then moved and dropped on the LAMMPS-GUI executable;
-LAMMPS-GUI will launch and read the file into its buffer.  Input files
-also can be dropped into the editor window of the running LAMMPS-GUI
-application, which will close the current file and open the new file.
-In many cases LAMMPS-GUI will be integrated into the graphical desktop
-environment and can be launched just like any other applications from
-the graphical interface.
+clicking on such files.  Also, LAMMPS-GUI has support for drag-n-drop,
+i.e.  an input file can be selected and then moved and dropped on the
+LAMMPS-GUI executable, and LAMMPS-GUI will launch and read the file into
+its buffer.  In many cases LAMMPS-GUI will be integrated into the
+graphical desktop environment and can be launched like other
+applications.
 
 LAMMPS-GUI thus makes it easier for beginners to get started running
-LAMMPS and is well-suited for LAMMPS tutorials, since you only need to
-work with a single, ready-to-use program for most of the tasks.  Plus it
-is available for download as pre-compiled package for popular operating
-systems (Linux, macOS, Windows).  This saves time and allows users to
-focus on learning LAMMPS itself, without the need to learn how to
-compile LAMMPS, learn how to use the command line, or learn how to use a
-separate text editor.
-
+simple LAMMPS simulations.  It is very suitable for tutorials on LAMMPS
+since you only need to learn how to use a single program for most tasks
+and thus time can be saved and people can focus on learning LAMMPS.
 The tutorials at https://lammpstutorials.github.io/ are specifically
-updated for use with LAMMPS-GUI and their tutorial materials can be
-downloaded and edited directly from within the GUI while automatically
-loading the matching tutorial instructions into a webbrowser.
+updated for use with LAMMPS-GUI.
 
-Yet the basic control flow remains similar to running LAMMPS from the
-command line, so the barrier for replacing parts of the functionality of
-LAMMPS-GUI with external tools is low.  That said, LAMMPS-GUI offer some
-unique features that are not easily found elsewhere:
+Another design goal is to keep the barrier low when replacing part of
+the functionality of LAMMPS-GUI with external tools.  That said, LAMMPS-GUI
+has some unique functionality that is not found elsewhere:
 
 - auto-adapting to features available in the integrated LAMMPS library
-- auto-completion for available LAMMPS commands and options only
-- context-sensitive online help for known LAMMPS commands
-- start and stop of simulations via mouse or keyboard
-- monitoring of simulation progress and CPU use
-- interactive visualization using the LAMMPS :doc:`dump image feature <dump_image>`
+- interactive visualization using the :doc:`dump image <dump_image>`
   command with the option to copy-paste the resulting settings
-- automatic slide show generation from dump image output at runtime
-- automatic plotting of thermodynamic data at runtime
+- automatic slide show generation from dump image out at runtime
+- automatic plotting of thermodynamics data at runtime
 - inspection of binary restart files
-- integration will a set of LAMMPS tutorials
 
-.. admonition:: Download LAMMPS-GUI for your platform
-   :class: Hint
-
-   Pre-compiled, ready-to-use LAMMPS-GUI executables for Linux x86\_64
-   (Ubuntu 20.04LTS or later and compatible), macOS (version 11 aka Big
-   Sur or later), and Windows (version 10 or later) :ref:`are available
-   <lammps_gui_install>` for download.  Non-MPI LAMMPS executables (as
-   ``lmp``) for running LAMMPS from the command-line and :doc:`some
-   LAMMPS tools <Tools>` compiled executables are also included.  Also,
-   the pre-compiled LAMMPS-GUI packages include the WHAM executables
-   from http://membrane.urmc.rochester.edu/content/wham/ for use with
-   LAMMPS tutorials documented in this paper (:ref:`Gravelle1
-   <Gravelle1>`).
-
-   The source code for LAMMPS-GUI is included in the LAMMPS source code
-   distribution and can be found in the ``tools/lammps-gui`` folder.  It
-   can be compiled alongside LAMMPS when :doc:`compiling with CMake
-   <Build_cmake>`.
-
------
-
-The following text provides a documentation of the features and
+The following text provides a detailed tour of the features and
 functionality of LAMMPS-GUI.  Suggestions for new features and
 reports of bugs are always welcome.  You can use the :doc:`the same
 channels as for LAMMPS itself <Errors_bugs>` for that purpose.
@@ -122,12 +84,9 @@ channels as for LAMMPS itself <Errors_bugs>` for that purpose.
 Installing Pre-compiled LAMMPS-GUI Packages
 -------------------------------------------
 
-LAMMPS-GUI is available for download as pre-compiled binary packages for
-Linux x86\_64 (Ubuntu 20.04LTS or later and compatible), macOS (version
-11 aka Big Sur or later), and Windows (version 10 or later) from the
-`LAMMPS release pages on GitHub <https://github.com/lammps/lammps/releases/>`_.
-A backup download location is at https://download.lammps.org/static/
-Alternately, LAMMPS-GUI can be compiled from source when building LAMMPS.
+LAMMPS-GUI is available as pre-compiled binary packages for Linux
+x86\_64, macOS 11 and later, and Windows 10 and later.  Alternately, it
+can be compiled from source.
 
 Windows 10 and later
 ^^^^^^^^^^^^^^^^^^^^
@@ -141,11 +100,10 @@ MacOS 11 and later
 ^^^^^^^^^^^^^^^^^^
 
 After downloading the ``LAMMPS-macOS-multiarch-GUI-<version>.dmg``
-application bundle disk image, you need to double-click it and then, in
-the window that opens, drag the app bundle as indicated into the
-"Applications" folder.  Afterwards, the disk image can be unmounted.
-Then follow the instructions in the "README.txt" file to get access to
-the other included command-line executables.
+installer package, you need to double-click it and then, in the window
+that opens, drag the app bundle as indicated into the "Applications"
+folder.  The follow the instructions in the "README.txt" file to
+get access to the other included executables.
 
 Linux on x86\_64
 ^^^^^^^^^^^^^^^^
@@ -159,25 +117,15 @@ into the "LAMMPS_GUI" folder and execute "./lammps-gui" directly.
 
 The second variant uses `flatpak <https://www.flatpak.org>`_ and
 requires the flatpak management and runtime software to be installed.
-After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``
+After downloading the ``LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``
 flatpak bundle, you can install it with ``flatpak install --user
-LAMMPS-GUI-Linux-x86_64-GUI-<version>.flatpak``.  After installation,
+LAMMPS-GUI-Linux-x86_64-GUI-<version>.tar.gz``.  After installation,
 LAMMPS-GUI should be integrated into your desktop environment under
 "Applications > Science" but also can be launched from the console with
 ``flatpak run org.lammps.lammps-gui``.  The flatpak bundle also includes
 the console LAMMPS executable ``lmp`` which can be launched to run
-simulations with, for example with:
-
-.. code-block:: sh
-
-   flatpak run --command=lmp org.lammps.lammps-gui -in in.melt
-
-Other bundled command-line executables are run the same way and can be
-listed with:
-
-.. code-block:: sh
-
-   ls $(flatpak info --show-location org.lammps.lammps-gui )/files/bin
+simulations with, for example: ``flatpak run --command=lmp
+org.lammps.lammps-gui -in in.melt``.
 
 
 Compiling from Source
@@ -217,9 +165,9 @@ window is stored when exiting and restored when starting again.
 Opening Files
 ^^^^^^^^^^^^^
 
-The LAMMPS-GUI application can be launched without command-line arguments
+The LAMMPS-GUI application can be launched without command line arguments
 and then starts with an empty buffer in the *Editor* window.  If arguments
-are given LAMMPS will use first command-line argument as the file name for
+are given LAMMPS will use first command line argument as the file name for
 the *Editor* buffer and reads its contents into the buffer, if the file
 exists.  All further arguments are ignored.  Files can also be opened via
 the *File* menu, the `Ctrl-O` (`Command-O` on macOS) keyboard shortcut
@@ -249,8 +197,8 @@ editor buffer, which may contain multiple :doc:`run <run>` or
 
 LAMMPS runs in a separate thread, so the GUI stays responsive and is
 able to interact with the running calculation and access data it
-produces.  It is important to note that running LAMMPS this way is using
-the contents of the input buffer for the run (via the
+produces.  It is important to note that running LAMMPS this way is
+using the contents of the input buffer for the run (via the
 :cpp:func:`lammps_commands_string()` function of the LAMMPS C-library
 interface), and **not** the original file it was read from.  Thus, if
 there are unsaved changes in the buffer, they *will* be used.  As an
@@ -259,55 +207,28 @@ of a file from the *Run LAMMPS from File* menu entry or with
 `Ctrl-Shift-Enter`.  This option may be required in some rare cases
 where the input uses some functionality that is not compatible with
 running LAMMPS from a string buffer.  For consistency, any unsaved
-changes in the buffer must be either saved to the file or undone before
-LAMMPS can be run from a file.
-
-The line number of the currently executed command is highlighted in
-green in the line number display for the *Editor* Window.
+changes in the buffer must be either saved to the file or undone
+before LAMMPS can be run from a file.
 
 .. image:: JPG/lammps-gui-running.png
    :align: center
    :scale: 75%
 
-While LAMMPS is running, the contents of the status bar change.  The
-text fields that normally show "Ready." and the current working
-directory, change into an area showing the CPU utilization in percent.
-Nest to it is a text indicating that LAMMPS is running, which also
-indicates the number of active threads (in case thread-parallel
-acceleration was selected in the *Preferences* dialog).  On the right
+While LAMMPS is running, the contents of the status bar change.  On
+the left side there is a text indicating that LAMMPS is running, which
+also indicates the number of active threads, when thread-parallel
+acceleration was selected in the *Preferences* dialog.  On the right
 side, a progress bar is shown that displays the estimated progress for
 the current :doc:`run <run>` or :doc:`minimize <minimize>` command.
 
-.. admonition:: CPU Utilization
-   :class: note
-
-   The CPU Utilization should ideally be close to 100% times the number
-   of threads like in the screenshot image above.  Since the GUI is
-   running as a separate thread, the CPU utilization can be higher, for
-   example when the GUI needs to work hard to keep up with the
-   simulation.  This can be caused by having frequent thermo output or
-   running a simulation of a small system.  In the *Preferences* dialog,
-   the polling interval for updating the the *Output* and *Charts*
-   windows can be set. The intervals may need to be lowered to not miss
-   data between *Charts* data updates or to avoid stalling when the
-   thermo output is not transferred to the *Output* window fast enough.
-   It is also possible to reduce the amount of data by increasing the
-   :doc:`thermo interval <thermo>`.  LAMMPS-GUI detects, if the
-   associated I/O buffer is by a significant percentage and will print a
-   warning after the run with suggested adjustments.  The utilization
-   can also be lower, e.g.  when the simulation is slowed down by the
-   GUI or other processes also running on the host computer and
-   competing with LAMMPS-GUI for GPU resources.
-
-   .. image:: JPG/lammps-gui-buffer-warn.png
-      :align: center
-      :scale: 75%
+Also, the line number of the currently executed command is highlighted
+in green.
 
 If an error occurs (in the example below the command :doc:`label
 <label>` was incorrectly capitalized as "Label"), an error message
 dialog is shown and the line of the input which triggered the error is
-highlighted in red.  The state of LAMMPS in the status bar is set to
-"Failed."  instead of "Ready."
+highlighted.  The state of LAMMPS in the status bar is set to "Failed."
+instead of "Ready."
 
 .. image:: JPG/lammps-gui-run-error.png
    :align: center
@@ -340,21 +261,14 @@ Output Window
 
 By default, when starting a run, an *Output* window opens that displays
 the screen output of the running LAMMPS calculation, as shown below.
-This text would normally be seen in the command-line window.
+This text would normally be seen in the command line window.
 
 .. image:: JPG/lammps-gui-log.png
    :align: center
    :scale: 50%
 
 LAMMPS-GUI captures the screen output from LAMMPS as it is generated and
-updates the *Output* window regularly during a run.  If there are any
-warnings or errors in the LAMMPS output, they are highlighted by using
-bold text colored in red.  There is a small panel at the bottom center
-of the *Output* window showing how many warnings and errors were
-detected and how many lines the entire output has.  By clicking on the
-button on the right with the warning symbol or by using the keyboard
-shortcut `Ctrl-N` (`Command-N` on macOS), you can jump to the next
-line with a warning or error.
+updates the *Output* window regularly during a run.
 
 By default, the *Output* window is replaced each time a run is started.
 The runs are counted and the run number for the current run is displayed
@@ -394,28 +308,27 @@ plot of thermodynamic output of the LAMMPS calculation as shown below.
    :align: center
    :scale: 33%
 
-The "Data:" drop down menu on the top right allows selection of
-different properties that are computed and written as thermodynamic
-output to the output window.  Only one property can be shown at a time.
-The plots are updated regularly with new data as the run progresses, so
-they can be used to visually monitor the evolution of available
-properties.  The update interval can be set in the *Preferences* dialog.
-By default, the raw data for the selected property is plotted as a blue
-graph.  From the "Plot:" drop menu on the second row and on the left,
-you can select whether to plot only raw data graph, only a smoothed data
-graph, or both graphs on top of each other.  The smoothing process uses
-a `Savitzky-Golay convolution filter
-<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_.  The
-convolution window width (left) and order (right) parameters can be set
-in the boxes next to the drop down menu.  Default settings are 10 and 4
-which means that the smoothing window includes 10 points each to the
-left and the right of the current data point for a total of 21 points
-and a fourth order polynomial is fitted to the data in the window.
+The drop down menu on the top right allows selection of different
+properties that are computed and written to thermo output.  Only one
+property can be shown at a time.  The plots are updated regularly with
+new data as the run progresses, so they can be used to visually monitor
+the evolution of available properties.  The update interval can be set
+in the *Preferences* dialog.  By default, the raw data for the selected
+property is plotted as a blue graph. As soon as there are a sufficient
+number of data points, there will be a second graph shown in red with a
+smoothed version of the data.  From the drop down menu on the top left,
+you can select whether to plot only the raw data, only the smoothed
+data or both.  The smoothing uses a `Savitzky-Golay convolution filter
+<https://en.wikipedia.org/wiki/Savitzky%E2%80%93Golay_filter>`_ The
+window width (left) and order (right) parameters can be set in the boxes
+next to the drop down menu.  Default settings are 10 and 4 which means
+that the smoothing window includes 10 points each to the left and the
+right of the current data point and a fourth order polynomial is fit to
+the data in the window.
 
-The "Title:" and "Y:" input boxes allow to edit the text shown as the
-plot title and the y-axis label, respectively.  The text entered in the
-"Title:" box is applied to *all* charts, while the "Y:" text changes
-only the y-axis label of the currently *selected* plot.
+You can use the mouse to zoom into the graph (hold the left button and
+drag to mark an area) or zoom out (right click) and you can reset the
+view with a click to the "lens" button next to the data drop down menu.
 
 The window title shows the current run number that this chart window
 corresponds to.  Same as for the *Output* window, the chart window is
@@ -443,40 +356,6 @@ here you get the compounded data set starting with the last change of
 output fields or timestep setting, while the export from the log will
 contain *all* YAML output but *segmented* into individual runs.
 
-The *Preferences* dialog has a *Charts* tab, where you can configure
-multiple chart-related settings, like the default title, colors for the
-graphs, default choice of the raw / smooth graph selection, and the
-default chart graph size.
-
-
-
-.. admonition:: Slowdown of Simulations from Charts Data Processing
-   :class: warning
-
-   Using frequent thermo output during long simulations can result in a
-   significant slowdown of that simulation since it is accumulating many
-   data points for each of the thermo properties in the chart window to
-   be redrawn with every update.  The updates are consuming additional
-   CPU time when smoothing enabled.  This slowdown can be confirmed when
-   an increasing percentage of the total run time is spent in the
-   "Output" or "Other" sections of the :doc:`MPI task timing breakdown
-   <Run_output>`.  It is thus recommended to use a large enough value as
-   argument `N` for the :doc:`thermo command <thermo>` and to select
-   plotting only the "Raw" data in the *Charts Window* during such
-   simulations.  It is always possible to switch between the different
-   display styles for charts during the simulation and after it has
-   finished.
-
-   .. versionchanged:: 1.7
-
-      As of LAMMPS-GUI version 1.7 the chart data processing is
-      significantly optimized compared to older versions of LAMMPS-GUI.
-      The general problem of accumulating excessive amounts of data
-      and the overhead of too frequently polling LAMMPS for new data
-      cannot be optimized away, though.  If necessary, the command
-      line LAMMPS executable needs to be used and the output accumulated
-      of a very fast disk (e.g. a high-performance SSD).
-
 Image Slide Show
 ----------------
 
@@ -519,7 +398,7 @@ below.
 Like for the *Output* and *Charts* windows, its content is continuously
 updated during a run.  It will show "(none)" if there are no variables
 defined.  Note that it is also possible to *set* :doc:`index style
-variables <variable>`, that would normally be set via command-line
+variables <variable>`, that would normally be set via command line
 flags, via the "Set Variables..." dialog from the *Run* menu.
 LAMMPS-GUI automatically defines the variable "gui_run" to the current
 value of the run counter.  That way it is possible to automatically
@@ -556,11 +435,11 @@ correspond to (via their mass) and then colorize them in the image and
 set their atom diameters accordingly.  If this is not possible, for
 instance when using reduced (= 'lj') :doc:`units <units>`, then
 LAMMPS-GUI will check the current pair style and if it is a
-Lennard-Jones type potential, it will extract the *sigma* parameter for
-each atom type and assign atom diameters from those numbers.  For cases
-where atom diameters are not auto-detected, the *Atom size* field can be
-edited and a suitable value set manually. The default value is inferred
-from the x-direction lattice spacing.
+Lennard-Jones type potential, it will extract the *sigma* parameter
+for each atom type and assign atom diameters from those numbers.
+For cases where atom diameters are not auto-detected, the *Atom size* field
+can be edited and a suitable value set manually. The default value
+is inferred from the x-direction lattice spacing.
 
 If elements cannot be detected the default sequence of colors of the
 :doc:`dump image <dump_image>` command is assigned to the different atom
@@ -575,31 +454,22 @@ types.
 |gui-image1|  |gui-image2|
 
 The default image size, some default image quality settings, the view
-style and some colors can be changed in the *Preferences* dialog window.
-From the image viewer window further adjustments can be made: actual
-image size, high-quality (SSAO) rendering, anti-aliasing, view style,
-display of box or axes, zoom factor.  The view of the system can be
-rotated horizontally and vertically.
-
-It is also possible to display only the atoms within a :doc:`group
-defined in the input script <group>` (default is "all").  The available
-groups can be selected from the drop down list next to the "Group:"
-label.  Similarly, if there are :doc:`molecules defined in the input
-<molecule>`, it is possible to select one of them (default is "none")
-and visualize it (it will be shown at the center of the simulation box).
-While a molecule is selected, the group selection is disabled.  It can
-be restored by selecting the molecule "none".
-
-The image can also be re-centered on the center of mass of the selected
-group.  After each change, the image is rendered again and the display
-updated.  The small palette icon on the top left is colored while LAMMPS
-is running to render the new image; it is grayed out when LAMMPS is
-finished.  When there are many atoms to render and high quality images
-with anti-aliasing are requested, re-rendering may take several seconds.
-From the *File* menu of the image window, the current image can be saved
-to a file (keyboard shortcut `Ctrl-S`) or copied to the clipboard
-(keyboard shortcut `Ctrl-C`) for pasting the image into another
-application.
+style and some colors can be changed in the *Preferences* dialog
+window.  From the image viewer window further adjustments can be made:
+actual image size, high-quality (SSAO) rendering, anti-aliasing, view
+style, display of box or axes, zoom factor.  The view of the system can
+be rotated horizontally and vertically.  It is also possible to only
+display the atoms within a group defined in the input script (default is
+"all").  The image can also be re-centered on the center of mass of the
+selected group.  After each change, the image is rendered again and the
+display updated.  The small palette icon on the top left is colored
+while LAMMPS is running to render the new image; it is grayed out when
+LAMMPS is finished.  When there are many atoms to render and high
+quality images with anti-aliasing are requested, re-rendering may take
+several seconds.  From the *File* menu of the image window, the
+current image can be saved to a file (keyboard shortcut `Ctrl-S`) or
+copied to the clipboard (keyboard shortcut `Ctrl-C`) for pasting the
+image into another application.
 
 From the *File* menu it is also possible to copy the current
 :doc:`dump image <dump_image>` and :doc:`dump_modify <dump_image>`
@@ -708,27 +578,13 @@ generated with a :doc:`write_data command <write_data>`.  The third
 window is a :ref:`Snapshot Image Viewer <snapshot_viewer>` containing a
 visualization of the system in the restart.
 
-.. |inspect1| image:: JPG/lammps-gui-inspect-data.png
-   :width: 32%
-
-.. |inspect2| image:: JPG/lammps-gui-inspect-info.png
-   :width: 32%
-
-.. |inspect3| image:: JPG/lammps-gui-inspect-image.png
-   :width: 32%
-
-|inspect1|  |inspect2|  |inspect3|
-
-.. admonition:: Large Restart Files
-   :class: warning
-
-   If the restart file is larger than 250 MBytes, a dialog will ask for
-   confirmation before continuing, since large restart files may require
-   large amounts of RAM since the entire system must be read into RAM.
-   Thus restart file for large simulations that have been run on an HPC
-   cluster may overload a laptop or local workstation. The *Show
-   Details...* button will display a rough estimate of the additional
-   memory required.
+If the restart file is larger than 250 MBytes, a dialog will ask
+for confirmation before continuing, since large restart files
+may require large amounts of RAM since the entire system must
+be read into RAM.  Thus restart file for large simulations that
+have been run on an HPC cluster may overload a laptop or local
+workstation. The *Show Details...* button will display a rough
+estimate of the additional memory required.
 
 Menu
 ----
@@ -800,12 +656,6 @@ timestep.  The *Stop LAMMPS* entry will do this by calling the
 :cpp:func:`lammps_force_timeout` library function, which is equivalent
 to a :doc:`timer timeout 0 <timer>` command.
 
-The *Relaunch LAMMPS Instance* will destroy the current LAMMPS thread
-and free its data and then create a new thread with a new LAMMPS
-instance.  This is usually not needed, since LAMMPS-GUI tries to detect
-when this is needed and does it automatically.  This is available
-in case it missed something and LAMMPS behaves in unexpected ways.
-
 The *Set Variables...* entry opens a dialog box where
 :doc:`index style variables <variable>` can be set. Those variables
 are passed to the LAMMPS instance when it is created and are thus
@@ -844,26 +694,6 @@ output, charts, slide show, variables, or snapshot images.  The
 default settings for their visibility can be changed in the
 *Preferences* dialog.
 
-Tutorials
-^^^^^^^^^
-
-The *Tutorials* menu is to support the set of LAMMPS tutorials for
-beginners and intermediate LAMMPS users documented in (:ref:`Gravelle1
-<Gravelle1>`).  From the drop down menu you can select which of the
-eight currently available tutorial sessions you want to begin.  This
-opens a 'wizard' dialog where you can choose in which folder you want to
-work, whether you want that folder to be wiped from *any* files, whether
-you want to download the solutions files (which can be large) to a
-``solution`` sub-folder, and whether you want the corresponding
-tutorial's online version opened in your web browser.  The dialog will
-then start downloading the files requested (download progress is
-reported in the status line) and load the first input file for the
-selected session into LAMMPS-GUI.
-
-.. image:: JPG/lammps-gui-tutorials.png
-   :align: center
-   :scale: 50%
-
 About
 ^^^^^
 
@@ -927,32 +757,29 @@ look of LAMMPS-GUI.  The settings are grouped and each group is
 displayed within a tab.
 
 .. |guiprefs1| image:: JPG/lammps-gui-prefs-general.png
-   :width: 19%
+   :width: 24%
 
 .. |guiprefs2| image:: JPG/lammps-gui-prefs-accel.png
-   :width: 19%
+   :width: 24%
 
 .. |guiprefs3| image:: JPG/lammps-gui-prefs-image.png
-   :width: 19%
+   :width: 24%
 
 .. |guiprefs4| image:: JPG/lammps-gui-prefs-editor.png
-   :width: 19%
+   :width: 24%
 
-.. |guiprefs5| image:: JPG/lammps-gui-prefs-charts.png
-   :width: 19%
-
-|guiprefs1|  |guiprefs2|  |guiprefs3|  |guiprefs4|  |guiprefs5|
+|guiprefs1|  |guiprefs2|  |guiprefs3|  |guiprefs4|
 
 General Settings:
 ^^^^^^^^^^^^^^^^^
 
 - *Echo input to log:* when checked, all input commands, including
   variable expansions, are echoed to the *Output* window. This is
-  equivalent to using `-echo screen` at the command-line.  There is no
+  equivalent to using `-echo screen` at the command line.  There is no
   log *file* produced by default, since LAMMPS-GUI uses `-log none`.
 - *Include citation details:* when checked full citation info will be
   included to the log window.  This is equivalent to using `-cite
-  screen` on the command-line.
+  screen` on the command line.
 - *Show log window by default:* when checked, the screen output of a
   LAMMPS run will be collected in a log window during the run
 - *Show chart window by default:* when checked, the thermodynamic
@@ -970,12 +797,13 @@ General Settings:
 - *Replace image window on new render:* when checked, an existing
   chart window will be replaced when a new snapshot image is requested,
   otherwise each command will create a new image window.
-- *Download tutorial solutions enabled* this controls whether the
-  "Download solutions" option is enabled by default when setting up
-  a tutorial.
-- *Open tutorial webpage enabled* this controls whether the "Open
-  tutorial webpage in web browser" option is enabled by default when
-  setting up a tutorial.
+- *Path to LAMMPS Shared Library File:* this option is only visible
+  when LAMMPS-GUI was compiled to load the LAMMPS library at run time
+  instead of being linked to it directly.  With the *Browse..* button
+  or by changing the text, a different shared library file with a
+  different compilation of LAMMPS with different settings or from a
+  different version can be loaded.  After this setting was changed,
+  LAMMPS-GUI needs to be re-launched.
 - *Select Default Font:* Opens a font selection dialog where the type
   and size for the default font (used for everything but the editor and
   log) of the application can be set.
@@ -994,36 +822,16 @@ General Settings:
   the plots in the *Charts* window in milliseconds.  The default is to
   redraw the plots every 500 milliseconds.  This is just for the drawing,
   data collection is managed with the previous setting.
-- *HTTPS proxy setting:* Allows to enter a URL for an HTTPS proxy.  This
-  may be needed when the LAMMPS input contains :doc:`geturl commands <geturl>`
-  or for downloading tutorial files from the *Tutorials* menu.  If the
-  ``https_proxy`` environment variable was set externally, its value is
-  displayed but cannot be changed.
-- *Path to LAMMPS Shared Library File:* this option is only visible
-  when LAMMPS-GUI was compiled to load the LAMMPS library at run time
-  instead of being linked to it directly.  With the *Browse..* button
-  or by changing the text, a different shared library file with a
-  different compilation of LAMMPS with different settings or from a
-  different version can be loaded.  After this setting was changed,
-  LAMMPS-GUI needs to be re-launched.
 
 Accelerators:
 ^^^^^^^^^^^^^
 
-This tab enables selection of an accelerator package and modify some of
-its settings to use for running LAMMPS and is equivalent to using the
-:doc:`-sf <suffix>` and :doc:`-pk <package>` flags :doc:`on the
-command-line <Run_options>`.  Only settings supported by the LAMMPS
-library and local hardware are available.  The `Number of threads` field
-allows setting the number of threads for the accelerator packages that
-support using threads (OPENMP, INTEL, KOKKOS, and GPU).  Furthermore,
-the choice of precision mode (double, mixed, or single) for the INTEL
-package can be selected and for the GPU package, whether the neighbor
-lists are built on the GPU or the host (required for :doc:`pair style
-hybrid <pair_hybrid>`) and whether only pair styles should be
-accelerated (i.e. run PPPM entirely on the CPU, which sometimes leads
-to better overall performance).  Whether settings can be changed depends
-on which accelerator package is chosen (or "None").
+This tab enables selection of an accelerator package for LAMMPS to use
+and is equivalent to using the `-suffix` and `-package` flags on the
+command line.  Only settings supported by the LAMMPS library and local
+hardware are available.  The `Number of threads` field allows setting
+the maximum number of threads for the accelerator packages that use
+threads.
 
 Snapshot Image:
 ^^^^^^^^^^^^^^^
@@ -1050,7 +858,7 @@ lists to select the background and box colors.
 Editor Settings:
 ^^^^^^^^^^^^^^^^
 
-This tab allows tweaking settings of the editor window.  Specifically,
+This tab allows tweaking settings of the editor window.  Specifically
 the amount of padding to be added to LAMMPS commands, types or type
 ranges, IDs (e.g. for fixes), and names (e.g. for groups).  The value
 set is the minimum width for the text element and it can be chosen in
@@ -1062,16 +870,6 @@ the completion pop-up window, and whether auto-save mode is enabled.
 In auto-save mode the editor buffer is saved before a run or before
 exiting LAMMPS-GUI.
 
-Charts Settings:
-----------------
-
-This tab allows tweaking settings of the *Charts* window.  Specifically,
-one can set the default chart title (if the title contains '%f' it will
-be replaced with the name of the current input file), one can select
-whether by default the raw data, the smoothed data or both will be
-plotted, one can set the colors for the two lines, the default smoothing
-parameters, and the default size of the chart graph in pixels.
-
 -----------
 
 Keyboard Shortcuts
@@ -1152,21 +950,10 @@ available (On macOS use the Command key instead of Ctrl/Control).
      - Ctrl+Shift+T
      - LAMMPS Tutorial
 
-Further keybindings of the editor window `are documented with the Qt
-documentation
+Further editing keybindings `are documented with the Qt documentation
 <https://doc.qt.io/qt-5/qplaintextedit.html#editing-key-bindings>`_.  In
 case of conflicts the list above takes precedence.
 
 All other windows only support a subset of keyboard shortcuts listed
 above.  Typically, the shortcuts `Ctrl-/` (Stop Run), `Ctrl-W` (Close
 Window), and `Ctrl-Q` (Quit Application) are supported.
-
--------------
-
-.. _Gravelle1:
-
-**(Gravelle1)** Gravelle, Gissinger, Kohlmeyer, `arXiv:2503.14020 \[physics.comp-ph\] <https://doi.org/10.48550/arXiv.2503.14020>`_ (2025)
-
-.. _Gravelle2:
-
-**(Gravelle2)** Gravelle https://lammpstutorials.github.io/

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/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_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_msd.rst

@@ -111,10 +111,7 @@ distance\ :math:`^2` :doc:`units <units>`.
 Restrictions
 """"""""""""
 
-Compute *msd* cannot be used with a dynamic group and the number of
-atoms in the compute group must not be changed by some fixes like,
-for example, :doc:`fix deposit <fix_deposit>` or
-:doc:`fix evaporate <fix_evaporate>`.
+Compute *msd* cannot be used with a dynamic group.
 
 Related commands
 """"""""""""""""

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

@@ -87,7 +87,7 @@ values in the vector.  The *sumsq* option sums the square of the
 values in the vector into a global total.  The *avesq* setting does
 the same as *sumsq*, then divides the sum of squares by the number of
 values.  The last two options can be useful for calculating the
-variance of some quantity (e.g., variance = *avesq* :math:`-` *ave*\
+variance of some quantity (e.g., variance = sumsq :math:`-` ave\
 :math:`^2`).  The *sumabs* option sums the absolute values in the
 vector into a global total.  The *aveabs* setting does the same as
 *sumabs*, then divides the sum of absolute values by the number of
@@ -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_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_ave_time.rst

@@ -345,7 +345,9 @@ Restart, fix_modify, output, run start/stop, minimize info
 .. versionadded:: 4May2022
 
 No information about this fix is written to :doc:`binary restart files
-<restart>`.
+<restart>`.  The :doc:`fix_modify colname <fix_modify>` option can be
+used to change the name of the column in the output file.  When writing
+a YAML format file this name will be in the list of keywords.
 
 This fix produces a global scalar or global vector or global array
 which can be accessed by various :doc:`output commands <Howto_output>`.

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
 """"""""""