Merge branch 'develop' into amoeba-gpu

.gitattributes

@@ -3,6 +3,7 @@
 .github export-ignore
 .lgtm.yml export-ignore
 SECURITY.md export-ignore
+CITATION.cff export-ignore
 *       text=auto
 *.jpg   -text
 *.pdf   -text

.github/CODEOWNERS

@@ -13,20 +13,21 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
+src/AMOEBA/*          @sjplimp
 src/COMPRESS/*        @rbberger
 src/GPU/*             @ndtrung81
 src/KOKKOS/*          @stanmoore1
 src/KIM/*             @ellio167
 src/LATTE/*           @cnegre
-src/MESSAGE/*         @sjplimp
 src/MLIAP/*           @athomps
 src/SNAP/*            @athomps
 src/SPIN/*            @julient31
 src/BROWNIAN/*        @samueljmcameron
 src/CG-DNA/*          @ohenrich
-src/CG-SDK/*          @akohlmey
+src/CG-SPICA/*        @yskmiyazaki
 src/COLVARS/*         @giacomofiorin
 src/DIELECTRIC/*      @ndtrung81
+src/ELECTRODE/*       @ludwig-ahrens
 src/FEP/*             @agiliopadua
 src/ML-HDNNP/*        @singraber
 src/INTEL/*           @wmbrownintel
@@ -133,6 +134,7 @@ tools/coding_standard/* @rbberger
 tools/valgrind/*      @akohlmey
 tools/swig/*          @akohlmey
 tools/offline/*       @rbberger
+tools/vim/*           @hammondkd
 
 # tests
 unittest/*            @akohlmey @rbberger

.github/codecov.yml

@@ -7,7 +7,7 @@ coverage:
         threshold: 10%
         only_pulls: false
         branches:
-          - "master"
+          - "develop"
         flags:
           - "unit"
         paths:
@@ -16,14 +16,14 @@ coverage:
     project:
         default:
             branches:
-              - "master"
+              - "develop"
             paths:
               - "src"
             informational: true
     patch:
         default:
             branches:
-              - "master"
+              - "develop"
             paths:
               - "src"
             informational: true

.github/workflows/compile-msvc.yml

@@ -3,7 +3,11 @@ name: "Native Windows Compilation and Unit Tests"
 
 on:
   push:
-    branches: [develop]
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
 
   workflow_dispatch:
 

.github/workflows/coverity.yml

@@ -0,0 +1,103 @@
+name: "Run Coverity Scan"
+
+on:
+  schedule:
+    - cron: "0 0 * * FRI"
+
+  workflow_dispatch:
+
+jobs:
+  analyze:
+    name: Analyze
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+    container:
+      image: lammps/buildenv:ubuntu20.04
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 2
+
+    - name: Create Build and Download Folder
+      run: mkdir build download
+
+    - name: Cache Coverity
+      id: cache-coverity
+      uses: actions/cache@v3
+      with:
+        path: ./download/
+        key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}
+
+    - name: Download Coverity if necessary
+      if: steps.cache-coverity.outputs.cache-hit != 'true'
+      working-directory: download
+      run: |
+        wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS" -O coverity_tool.tgz
+        wget -nv https://scan.coverity.com/download/linux64 --post-data "token=${{ secrets.COVERITY_TOKEN }}&project=LAMMPS&md5=1" -O coverity_tool.md5
+        echo " coverity_tool.tgz" >> coverity_tool.md5
+        md5sum -c coverity_tool.md5
+
+    - name: Setup Coverity
+      run: |
+        tar xzf download/coverity_tool.tgz
+        ln -s cov-analysis-linux64-* coverity
+
+    - name: Configure LAMMPS via CMake
+      shell: bash
+      working-directory: build
+      run: |
+        cmake \
+        -C ../cmake/presets/clang.cmake \
+        -C ../cmake/presets/most.cmake \
+        -C ../cmake/presets/kokkos-openmp.cmake \
+        -D CMAKE_BUILD_TYPE="RelWithDebug" \
+        -D CMAKE_TUNE_FLAGS="-Wall -Wextra -Wno-unused-result" \
+        -D BUILD_MPI=on \
+        -D BUILD_OMP=on \
+        -D BUILD_SHARED_LIBS=on \
+        -D LAMMPS_SIZES=SMALLBIG \
+        -D LAMMPS_EXCEPTIONS=off \
+        -D PKG_MESSAGE=on \
+        -D PKG_MPIIO=on \
+        -D PKG_ATC=on \
+        -D PKG_AWPMD=on \
+        -D PKG_BOCS=on \
+        -D PKG_EFF=on \
+        -D PKG_H5MD=on \
+        -D PKG_INTEL=on \
+        -D PKG_LATBOLTZ=on \
+        -D PKG_MANIFOLD=on \
+        -D PKG_MGPT=on \
+        -D PKG_ML-PACE=on \
+        -D PKG_ML-RANN=on \
+        -D PKG_MOLFILE=on \
+        -D PKG_NETCDF=on \
+        -D PKG_PTM=on \
+        -D PKG_QTB=on \
+        -D PKG_SMTBQ=on \
+        -D PKG_TALLY=on \
+        ../cmake
+
+    - name: Run Coverity Scan
+      shell: bash
+      working-directory: build
+      run: |
+        export PATH=$GITHUB_WORKSPACE/coverity/bin:$PATH
+        cov-build --dir cov-int cmake --build . --parallel 2
+
+    - name: Create tarball with scan results
+      shell: bash
+      working-directory: build
+      run: tar czf lammps.tgz cov-int
+
+    - name: Upload scan result to Coverity
+      shell: bash
+      run: |
+        curl --form token=${{ secrets.COVERITY_TOKEN }} \
+             --form email=${{ secrets.COVERITY_EMAIL }} \
+             --form file=@build/lammps.tgz \
+             --form version=${{ github.sha }} \
+             --form description="LAMMPS automated build" \
+             https://scan.coverity.com/builds?project=LAMMPS

.github/workflows/unittest-macos.yml

@@ -3,7 +3,11 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches: [develop]
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
 
   workflow_dispatch:
 
@@ -39,6 +43,7 @@ jobs:
       working-directory: build
       run: |
         ccache -z
+        python3 -m pip install numpy
         python3 -m pip install pyyaml
         cmake -C ../cmake/presets/clang.cmake \
               -C ../cmake/presets/most.cmake \

CITATION.cff

@@ -0,0 +1,91 @@
+# YAML 1.2
+---
+cff-version: 1.2.0
+title: "LAMMPS: Large-scale Atomic/Molecular Massively Parallel Simulator"
+type: software
+authors:
+  - family-names: "Plimpton"
+    given-names: "Steven J."
+  - family-names: "Kohlmeyer"
+    given-names: "Axel"
+    orcid: "https://orcid.org/0000-0001-6204-6475"
+  - family-names: "Thompson"
+    given-names: "Aidan P."
+    orcid: "https://orcid.org/0000-0002-0324-9114"
+  - family-names: "Moore"
+    given-names: "Stan G."
+  - family-names: "Berger"
+    given-names: "Richard"
+    orcid: "https://orcid.org/0000-0002-3044-8266"
+doi: 10.5281/zenodo.3726416
+license: GPL-2.0-only
+url: https://www.lammps.org
+repository-code: https://github.com/lammps/lammps/
+keywords:
+  - "Molecular Dynamics"
+  - "Materials Modeling"
+message: "If you are referencing LAMMPS in a publication, please cite the paper below."
+preferred-citation:
+  type: article
+  doi: "10.1016/j.cpc.2021.108171"
+  url: "https://www.sciencedirect.com/science/article/pii/S0010465521002836"
+  authors:
+  - family-names: "Thompson"
+    given-names: "Aidan P."
+    orcid: "https://orcid.org/0000-0002-0324-9114"
+  - family-names: "Aktulga"
+    given-names: "H. Metin"
+  - family-names: "Berger"
+    given-names: "Richard"
+    orcid: "https://orcid.org/0000-0002-3044-8266"
+  - family-names: "Bolintineanu"
+    given-names: "Dan S."
+  - family-names: "Brown"
+    given-names: "W. Michael"
+  - family-names: "Crozier"
+    given-names: "Paul S."
+  - family-names: "in 't Veld"
+    given-names: "Pieter J."
+  - family-names: "Kohlmeyer"
+    given-names: "Axel"
+    orcid: "https://orcid.org/0000-0001-6204-6475"
+  - family-names: "Moore"
+    given-names: "Stan G."
+  - family-names: "Nguyen"
+    given-names: "Trung Dac"
+  - family-names: "Shan"
+    given-names: "Ray"
+  - family-names: "Stevens"
+    given-names: "Mark J."
+  - family-names: "Tranchida"
+    given-names: "Julien"
+  - family-names: "Trott"
+    given-names: "Christian"
+  - family-names: "Plimpton"
+    given-names: "Steven J."
+  title: "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales"
+  journal: "Computer Physics Communications"
+  keywords:
+   - Molecular dynamics
+   - Materials modeling
+   - Parallel algorithms
+   - LAMMPS
+  month: 2
+  volume: 271
+  issn: 0010-4655
+  pages: 108171
+  year: 2022
+references:
+ - title: "Fast Parallel Algorithms for Short-Range Molecular Dynamics"
+   type: article
+   journal: Journal of Computational Physics
+   volume: 117
+   number: 1
+   pages: "1-19"
+   year: 1995
+   issn: 0021-9991
+   doi: 10.1006/jcph.1995.1039
+   url: https://www.sciencedirect.com/science/article/pii/S002199918571039X
+   authors:
+   - family-names: "Plimpton"
+     given-names: "Steve"

SECURITY.md

@@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
 behavior from calling functions in one of those libraries.
 
 Thus is is quite easy to crash LAMMPS through malicious input and do all
-kinds of filesystem manipulations.  And because of that LAMMPS should
+kinds of file system manipulations.  And because of that LAMMPS should
 **NEVER** be compiled or **run** as superuser, either from a "root" or
 "administrator" account directly or indirectly via "sudo" or "su".
 
 Therefore what could be seen as a security vulnerability is usually
-either a user mistake or a bug in the code.  Bugs can be reported in
+either a user mistake or a bug in the code.  Bugs can be reported in the
-the LAMMPS project
+LAMMPS project [issue tracker on
-[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+GitHub](https://github.com/lammps/lammps/issues).
 
 To mitigate issues with using homoglyphs or bidirectional reordering in
 unicode, which have been demonstrated as a vector to obfuscate and hide
@@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep all
+LAMMPS follows continuous release development model.  We aim to keep to
-release versions (stable or patch) fully functional and employ a variety
+keep the development version (develop branch) always fully functional
-of automatic testing procedures to detect failures of existing
+and employ a variety of automatic testing procedures to detect failures
-functionality from adding new features before releases are made.  Thus
+of existing functionality from adding or modifying features.  Most of
-bugfixes and updates are only integrated into the current development
+those tests are run on pull requests *before* merging to the development
-branch and thus the next (patch) release and users are recommended to
+branch.  The develop branch is protected, so all changes *must* be
-update regularly.
+submitted as a pull request and thus cannot avoid the automated tests.
+
+Additional tests are run *after* merging.  Before releases are made
+*all* tests must have cleared.  Then a release tag is applied and the
+release branch fast-forwarded to that tag.  Bug fixes and updates are
+applied to the current development branch and thus will be available in
+the next (patch) release.  For stable releases, selected bug fixes are
+back-ported and occasionally published as update releases.  There are
+only updates to the latest stable release.

cmake/CMakeLists.txt

@@ -135,13 +135,11 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 # and prints lots of pointless warnings about "unsafe" functions
 if(MSVC)
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    if(LAMMPS_EXCEPTIONS)
+    add_compile_options(/EHsc)
-      add_compile_options(/EHsc)
-    endif()
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -154,6 +152,19 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
+# set path to python interpreter and thus enforcing python version if
+# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
+if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
+  if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
+  else()
+    set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/bin/python")
+  endif()
+  set(Python_EXECUTABLE "${PYTHON_EXECUTABLE}")
+  message(STATUS "Running in virtual environment: $ENV{VIRTUAL_ENV}\n"
+    "   Setting Python interpreter to: ${PYTHON_EXECUTABLE}")
+endif()
+
 set(LAMMPS_MACHINE "" CACHE STRING "Suffix to append to lmp binary (WON'T enable any features automatically")
 mark_as_advanced(LAMMPS_MACHINE)
 if(LAMMPS_MACHINE)
@@ -203,7 +214,7 @@ set(STANDARD_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -366,6 +377,7 @@ pkg_depends(DIELECTRIC EXTRA-PAIR)
 pkg_depends(CG-DNA MOLECULE)
 pkg_depends(CG-DNA ASPHERE)
 pkg_depends(ELECTRODE KSPACE)
+pkg_depends(EXTRA-MOLECULE MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
@@ -405,9 +417,11 @@ endif()
 
 if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
-  find_package(LAPACK)
+  if (NOT USE_INTERNAL_LINALG)
-  find_package(BLAS)
+    find_package(LAPACK)
-  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+    find_package(BLAS)
+  endif()
+  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
     include(CheckGeneratorSupport)
     if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
       status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
@@ -636,7 +650,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -783,9 +797,13 @@ if(BUILD_SHARED_LIBS)
     set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
-        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
     endif()
   else()
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(BUILD_IS_MULTI_CONFIG)
@@ -818,11 +836,17 @@ endif()
 ###############################################################################
 if(BUILD_SHARED_LIBS OR PKG_PYTHON)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
-        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
     endif()
   else()
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(Python_EXECUTABLE)

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -6,6 +6,9 @@ if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
     "Please remove CMakeCache.txt and CMakeFiles first.")
 endif()
 
+set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty"
+  CACHE STRING "URL for thirdparty package downloads")
+
 # global LAMMPS/plugin build settings
 set(LAMMPS_SOURCE_DIR ""  CACHE PATH "Location of LAMMPS sources folder")
 if(NOT LAMMPS_SOURCE_DIR)
@@ -78,6 +81,13 @@ function(get_newest_file path variable)
   set(${variable} ${_bestfile} PARENT_SCOPE)
 endfunction()
 
+# get LAMMPS version date
+function(get_lammps_version version_header variable)
+    file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
+    string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1\\2\\3" date "${line}")
+    set(${variable} "${date}" PARENT_SCOPE)
+endfunction()
+
 #################################################################################
 # LAMMPS C++ interface. We only need the header related parts except on windows.
 add_library(lammps INTERFACE)
@@ -89,6 +99,7 @@ endif()
 ################################################################################
 # MPI configuration
 if(NOT CMAKE_CROSSCOMPILING)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
   find_package(MPI QUIET)
   option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
 else()

cmake/Modules/LAMMPSUtils.cmake

@@ -110,14 +110,16 @@ function(FetchPotentials pkgfolder potfolder)
       math(EXPR plusone "${blank}+1")
       string(SUBSTRING ${line} 0 ${blank} pot)
       string(SUBSTRING ${line} ${plusone} -1 sum)
-      if(EXISTS ${LAMMPS_POTENTIALS_DIR}/${pot})
+      if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
         file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
       endif()
       if(NOT sum STREQUAL oldsum)
-        message(STATUS "Checking external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+        string(MD5 TMP_EXT "${CMAKE_BINARY_DIR}")
+        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
           EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
-        file(COPY "${CMAKE_BINARY_DIR}/${pot}" DESTINATION ${LAMMPS_POTENTIALS_DIR})
+        file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
+        file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
       endif()
     endforeach()
   endif()

cmake/Modules/Packages/GPU.cmake

@@ -238,7 +238,8 @@ elseif(GPU_API STREQUAL "OPENCL")
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
-          set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
+          message(FATAL_ERROR "GPU_API=HIP requires HIP_PATH to be defined.\n"
+          "Either pass the HIP_PATH as a CMake option via -DHIP_PATH=... or set the HIP_PATH environment variable.")
       else()
           set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
       endif()
@@ -266,6 +267,8 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
+  elseif(HIP_PLATFORM STREQUAL "spirv")
+    set(HIP_ARCH "spirv" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
     set(HIP_ARCH "sm_50" CACHE STRING "HIP primary CUDA architecture (e.g. sm_60)")
@@ -345,7 +348,14 @@ elseif(GPU_API STREQUAL "HIP")
           VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
           DEPENDS ${CU_FILE}
           COMMENT "Generating ${CU_NAME}.cubin")
-    endif()
+    elseif(HIP_PLATFORM STREQUAL "spirv")
+      configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
+
+      add_custom_command(OUTPUT ${CUBIN_FILE}
+        VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} -c -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+        DEPENDS ${CU_CPP_FILE}
+        COMMENT "Gerating ${CU_NAME}.cubin")
+      endif()
 
     add_custom_command(OUTPUT ${CUBIN_H_FILE}
       COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR} -D VARNAME=${CU_NAME} -D HEADER_FILE=${CUBIN_H_FILE} -D SOURCE_FILE=${CUBIN_FILE} -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateBinaryHeader.cmake

cmake/Modules/Packages/KOKKOS.cmake

@@ -47,8 +47,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "b5c44ea961031795f434002cd7b31c20" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -72,7 +72,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.6.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.6.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()

cmake/Modules/Packages/LATTE.cmake

@@ -23,8 +23,9 @@ if(DOWNLOAD_LATTE)
   # CMake cannot pass BLAS or LAPACK library variable to external project if they are a list
   list(LENGTH BLAS_LIBRARIES} NUM_BLAS)
   list(LENGTH LAPACK_LIBRARIES NUM_LAPACK)
-  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
+    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
+                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
   endif()
 
   include(ExternalProject)

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)
@@ -26,8 +26,21 @@ if(DOWNLOAD_MDI)
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(NOT PYTHON_VERSION_STRING)
+      set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+      # search for interpreter first, so we have a consistent library
+      find_package(PythonInterp) # Deprecated since version 3.12
+      if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      endif()
+    endif()
+    # search for the library matching the selected interpreter
+    set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
     find_package(PythonLibs QUIET) # Deprecated since version 3.12
     if(PYTHONLIBS_FOUND)
+      if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+        message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+      endif()
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   else()
@@ -44,7 +57,7 @@ if(DOWNLOAD_MDI)
   ExternalProject_Add(mdi_build
     URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
-    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    CMAKE_ARGS
     -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
     -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
@@ -54,6 +67,7 @@ if(DOWNLOAD_MDI)
     -Dlanguage=C
     -Dlibtype=STATIC
     -Dmpi=${MDI_USE_MPI}
+    -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
     INSTALL_COMMAND ""

cmake/Modules/Packages/MISC.cmake

@@ -0,0 +1,13 @@
+# pair style and fix srp/react depend on the fixes bond/break and bond/create from the MC package
+if(NOT PKG_MC)
+  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
+  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.h)
+  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
+  get_property(LAMMPS_PAIR_HEADERS GLOBAL PROPERTY PAIR)
+  list(REMOVE_ITEM LAMMPS_PAIR_HEADERS ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.h)
+  set_property(GLOBAL PROPERTY PAIR "${LAMMPS_PAIR_HEADERS}")
+  get_target_property(LAMMPS_SOURCES lammps SOURCES)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/fix_srp_react.cpp)
+  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MISC/pair_srp_react.cpp)
+  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
+endif()

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -44,7 +44,9 @@ if(DOWNLOAD_N2P2)
   else()
     # get path to MPI include directory
     get_target_property(N2P2_MPI_INCLUDE MPI::MPI_CXX INTERFACE_INCLUDE_DIRECTORIES)
-    set(N2P2_PROJECT_OPTIONS "-I${N2P2_MPI_INCLUDE}")
+    foreach (_INCL ${N2P2_MPI_INCLUDE})
+      set(N2P2_PROJECT_OPTIONS "${N2P2_PROJECT_OPTIONS} -I${_INCL}")
+    endforeach()
   endif()
 
   # prefer GNU make, if available. N2P2 lib seems to need it.
@@ -75,7 +77,7 @@ if(DOWNLOAD_N2P2)
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""
     PATCH_COMMAND sed -i -e "s/\\(MPI_\\(P\\|Unp\\)ack(\\)/\\1(void *) /" src/libnnpif/LAMMPS/InterfaceLammps.cpp
-    BUILD_COMMAND ${N2P2_MAKE} -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
+    BUILD_COMMAND ${N2P2_MAKE} -C <SOURCE_DIR>/src -f makefile libnnpif ${N2P2_BUILD_OPTIONS}
     BUILD_ALWAYS YES
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE 1

cmake/Modules/Packages/ML-IAP.cmake

@@ -25,16 +25,18 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
-  get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
-  add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+  foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
-          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
-          COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+            COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          COMMENT "Generating C++ sources with cythonize...")
+            WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
+            COMMENT "Generating C++ sources with cythonize...")
+    target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  endforeach()
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
-  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()

cmake/Modules/Packages/PYTHON.cmake

@@ -1,8 +1,28 @@
 if(CMAKE_VERSION VERSION_LESS 3.12)
+  if(NOT PYTHON_VERSION_STRING)
+    set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+    # search for interpreter first, so we have a consistent library
+    find_package(PythonInterp) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+  endif()
+  # search for the library matching the selected interpreter
+  set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
   find_package(PythonLibs REQUIRED) # Deprecated since version 3.12
+  if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+    message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+  endif()
   target_include_directories(lammps PRIVATE ${PYTHON_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE ${PYTHON_LIBRARIES})
 else()
+  if(NOT Python_INTERPRETER)
+    # backward compatibility
+    if(PYTHON_EXECUTABLE)
+      set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+    find_package(Python COMPONENTS Interpreter)
+  endif()
   find_package(Python REQUIRED COMPONENTS Interpreter Development)
   target_link_libraries(lammps PRIVATE Python::Python)
 endif()

cmake/presets/all_off.cmake

@@ -12,7 +12,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/all_on.cmake

@@ -14,7 +14,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/clang.cmake

@@ -3,6 +3,13 @@
 # prefer flang over gfortran, if available
 find_program(CLANG_FORTRAN NAMES flang gfortran f95)
 set(ENV{OMPI_FC} ${CLANG_FORTRAN})
+get_filename_component(_tmp_fc ${CLANG_FORTRAN} NAME)
+if (_tmp_fc STREQUAL "flang")
+  set(FC_STD_VERSION "-std=f2018")
+  set(BUILD_MPI OFF)
+else()
+  set(FC_STD_VERSION "-std=f2003")
+endif()
 
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
@@ -10,9 +17,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} 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 -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g ${FC_STD_VERSION}" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG ${FC_STD_VERSION}" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG ${FC_STD_VERSION}" 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)

cmake/presets/mingw-cross.cmake

@@ -8,7 +8,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/most.cmake

@@ -10,7 +10,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/windows.cmake

@@ -6,7 +6,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

doc/Makefile

@@ -242,7 +242,6 @@ $(MATHJAX):
 $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
-		(cd utils/converters;\
+		pip $(PIP_OPTIONS) install -e utils/converters;\
-		python setup.py develop);\
 		deactivate;\
 	)

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "23 June 2022" "2022-6-23"
+.TH LAMMPS "1" "15 September 2022" "2022-9-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 23 June 2022
+\- Molecular Dynamics Simulator.  Version 15 September 2022
 
 .SH SYNOPSIS
 .B lmp
@@ -161,7 +161,7 @@ list references for specific cite-able features used during a
 run.
 .TP
 \fB\-pk <style> [options]\fR or \fB\-package <style> [options]\fR
-Invoke the \fBpackage\R command with <style> and optional arguments.
+Invoke the \fBpackage\fR command with <style> and optional arguments.
 The syntax is the same as if the command appeared in an input script.
 For example "-pk gpu 2" is the same as "package gpu 2" in the input
 script. The possible styles and options are discussed in the

doc/src/Bibliography.rst

@@ -314,7 +314,7 @@ Bibliography
    Espanol, Revenga, Physical Review E, 67, 026705 (2003).
 
 **(Espanol1997)**
-   Espanol, Europhys Lett, 40(6): 631-636 (1997).  DOI: 10.1209/epl/i1997-00515-8
+   Espanol, Europhys Lett, 40(6): 631-636 (1997).  DOI:10.1209/epl/i1997-00515-8
 
 **(Evans and Morriss)**
    Evans and Morriss, Phys Rev A, 30, 1528 (1984).
@@ -368,7 +368,7 @@ Bibliography
    Frenkel and Smit, Understanding Molecular Simulation, Academic Press, London, 2002.
 
 **(GLE4MD)**
-   `http://gle4md.org/ <http://gle4md.org/>`_
+   `https://gle4md.org/ <https://gle4md.org/>`_
 
 **(Gao)**
    Gao and Weber, Nuclear Instruments and Methods in Physics Research B 191 (2012) 504.
@@ -401,13 +401,13 @@ Bibliography
    Hayre, and Farago, Comp Phys Comm, 185, 524 (2014)
 
 **(Groot)**
-   Groot and Warren, J Chem Phys, 107: 4423-4435 (1997).  DOI: 10.1063/1.474784
+   Groot and Warren, J Chem Phys, 107: 4423-4435 (1997).  DOI:10.1063/1.474784
 
 **(Guenole)**
    Guenole, Noehring, Vaid, Houlle, Xie, Prakash, Bitzek, Comput Mater Sci, 175, 109584 (2020).
 
 **(Gullet)**
-   Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003).
+   Gullet, Wagner, Slepoy, SANDIA Report 2003-8782 (2003). DOI:10.2172/918395
 
 **(Guo)**
    Guo and Thirumalai, Journal of Molecular Biology, 263, 323-43 (1996).
@@ -461,7 +461,7 @@ Bibliography
    Hunt, Mol Simul, 42, 347 (2016).
 
 **(IPI)**
-   `http://epfl-cosmo.github.io/gle4md/index.html?page=ipi <http://epfl-cosmo.github.io/gle4md/index.html?page=ipi>`_
+   `https://ipi-code.org/ <https://ipi-code.org/>`
 
 **(IPI-CPC)**
    Ceriotti, More and Manolopoulos, Comp Phys Comm, 185, 1019-1026 (2014).
@@ -605,16 +605,16 @@ Bibliography
    I.\  Leven et al, J. Chem.Theory Comput. 12, 2896-905 (2016).
 
 **(Li2013_POF)**
-   Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI: 10.1063/1.4812366.
+   Li, Hu, Wang, Ma, Zhou, Phys Fluids, 25: 072103 (2013). DOI:10.1063/1.4812366.
 
 **(Li2014_JCP)**
-   Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014).  DOI: 10.1016/j.jcp.2014.02.003.
+   Li, Tang, Lei, Caswell, Karniadakis, J Comput Phys, 265: 113-127 (2014).  DOI:10.1016/j.jcp.2014.02.003.
 
 **(Li2015_CC)**
-   Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015).  DOI: 10.1039/C5CC01684C.
+   Li, Tang, Li, Karniadakis, Chem Commun, 51: 11038-11040 (2015).  DOI:10.1039/C5CC01684C.
 
 **(Li2015_JCP)**
-   Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015).  DOI: 10.1063/1.4923254.
+   Li, Yazdani, Tartakovsky, Karniadakis, J Chem Phys, 143: 014101 (2015).  DOI:10.1063/1.4923254.
 
 **(Lisal)**
    M.\  Lisal, J.K. Brennan, J. Bonet Avalos, "Dissipative particle dynamics at isothermal, isobaric, isoenergetic, and isoenthalpic conditions using Shardlow-like splitting algorithms.",
@@ -733,8 +733,8 @@ Bibliography
 **(Mishin)**
    Mishin, Mehl, and Papaconstantopoulos, Acta Mater, 53, 4029 (2005).
 
-**(Mitchell and Finchham)**
+**(Mitchell and Fincham)**
-   Mitchell, Finchham, J Phys Condensed Matter, 5, 1031-1038 (1993).
+   Mitchell, Fincham, J Phys Condensed Matter, 5, 1031-1038 (1993).
 
 **(Mitchell2011)**
    Mitchell. A non-local, ordinary-state-based viscoelasticity model for peridynamics. Sandia National Lab Report, 8064:1-28 (2011).
@@ -875,7 +875,7 @@ Bibliography
    G.A. Tribello, M. Bonomi, D. Branduardi, C. Camilloni and G. Bussi, Comp. Phys. Comm 185, 604 (2014)
 
 **(Paquay)**
-   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+   Paquay and Kusters, Biophys. J., 110, 6, (2016). preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.
 
 **(Park)**
    Park, Schulten, J. Chem. Phys. 120 (13), 5946 (2004)
@@ -1373,7 +1373,7 @@ Bibliography
    Zhu, Tajkhorshid, and Schulten, Biophys. J. 83, 154 (2002).
 
 **(Ziegler)**
-   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter," Volume 1, Pergamon, 1985.
+   J.F. Ziegler, J. P. Biersack and U. Littmark, "The Stopping and Range of Ions in Matter", Volume 1, Pergamon, 1985.
 
 **(Zimmerman2004)**
    Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004),12:S319.

doc/src/Build_development.rst

@@ -140,7 +140,7 @@ of the LAMMPS project on GitHub.
 The unit testing facility is integrated into the CMake build process
 of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <http://pyyaml.org/>`_ library and development
+It requires the `YAML <https://pyyaml.org/>`_ library and development
 headers (if those are not found locally a recent version will be
 downloaded and compiled along with LAMMPS and the test program) to
 compile and will download and compile a specific recent version of the

doc/src/Build_extras.rst

@@ -123,6 +123,7 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
+   -D HIP_PATH                  # path to HIP installation. Must be set if GPU_API=HIP
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
@@ -179,10 +180,17 @@ set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
+Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
+code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
+set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
+yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
+should only use this option in preparations to run on Aurora system at ANL.
+
 .. code:: bash
 
    # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
+   export HIP_PATH=/path/to/HIP/install
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
@@ -191,6 +199,7 @@ and the linker to work correctly.
 
    # AMDGPU target (ROCm >= 4.1)
    export HIP_PLATFORM=amd
+   export HIP_PATH=/path/to/HIP/install
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
@@ -199,10 +208,20 @@ and the linker to work correctly.
    # CUDA target (not recommended, use GPU_ARCH=cuda)
    # !!! DO NOT set CMAKE_CXX_COMPILER !!!
    export HIP_PLATFORM=nvcc
+   export HIP_PATH=/path/to/HIP/install
    export CUDA_PATH=/usr/local/cuda
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
    make -j 4
 
+.. code:: bash
+
+   # SPIR-V target (Intel GPUs)
+   export HIP_PLATFORM=spirv
+   export HIP_PATH=/path/to/HIP/install
+   export CMAKE_CXX_COMPILER=<hipcc/clang++>
+   cmake -D PKG_GPU=on -D GPU_API=HIP ..
+   make -j 4
+
 Traditional make
 ^^^^^^^^^^^^^^^^
 
@@ -295,7 +314,7 @@ detailed information is available at:
 
 In addition to installing the KIM API, it is also necessary to install the
 library of KIM models (interatomic potentials).
-See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
 learn how to install a pre-build binary of the OpenKIM Repository of Models.
 See the list of all KIM models here: https://openkim.org/browse/models
 
@@ -413,7 +432,7 @@ Enabling the extra unit tests have some requirements,
   ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
   ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
   ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
-  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+  See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
   to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
   `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@@ -788,8 +807,10 @@ library.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
+         -D DOWNLOAD_LATTE=value      # download LATTE for build, value = no (default) or yes
-         -D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location)
+         -D LATTE_LIBRARY=path        # LATTE library file (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
 
       If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
       and built inside the CMake build directory.  If the LATTE library
@@ -797,6 +818,13 @@ library.
       ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
       file, not the directory the library file is in.
 
+      The LATTE library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the LATTE build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
    .. tab:: Traditional make
 
       You can download and build the LATTE library manually if you
@@ -1025,7 +1053,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
+`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
 binary package provided by your operating system.
 
 .. tabs::
@@ -1913,14 +1941,25 @@ within CMake will download the non-commercial use version.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_QUIP=value   # download OpenKIM API v2 for build, value = no (default) or yes
+         -D DOWNLOAD_QUIP=value       # download QUIP library for build, value = no (default) or yes
-         -D QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
+         -D QUIP_LIBRARY=path         # path to libquip.a (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
 
-      CMake will try to download and build the QUIP library from GitHub, if it is not
+      CMake will try to download and build the QUIP library from GitHub,
-      found on the local machine. This requires to have git installed. It will use the same compilers
+      if it is not found on the local machine. This requires to have git
-      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU and the
+      installed. It will use the same compilers and flags as used for
-      Intel compilers. Set the ``QUIP_LIBRARY`` variable if you want to use a previously compiled
+      compiling LAMMPS.  Currently this is only supported for the GNU
-      and installed QUIP library and CMake cannot find it.
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
 
    .. tab:: Traditional make
 

doc/src/Build_manual.rst

@@ -48,18 +48,15 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<sphinx_>`_ document generator tool.  It also incorporates programmer
+<https://sphinx-doc.org>`_ document generator tool.  It also
-documentation extracted from the LAMMPS C++ sources through the `Doxygen
+incorporates programmer documentation extracted from the LAMMPS C++
-<https://doxygen.nl>`_ program.  Currently the translation to HTML, PDF
+sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
-(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
+the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
-readers) are supported.  For that to work a Python 3 interpreter, the
+and MOBI (for Amazon Kindle readers) are supported.  For that to work a
-``doxygen`` tools and internet access to download additional files and
+Python 3 interpreter, the ``doxygen`` tools and internet access to
-tools are required.  This download is usually only required once or
+download additional files and tools are required.  This download is
-after the documentation folder is returned to a pristine state with
+usually only required once or after the documentation folder is returned
-``make clean-all``.
+to a pristine state with ``make clean-all``.
-
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-.. _sphinx: https://www.sphinx-doc.org
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -179,7 +176,7 @@ math expressions transparently into embedded images.
 For converting the generated ePUB file to a MOBI format file (for e-book
 readers, like Kindle, that cannot read ePUB), you also need to have the
 ``ebook-convert`` tool from the "calibre" software
-installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
 Typing ``make mobi`` will first create the ePUB file and then convert
 it.  On the Kindle readers in particular, you also have support for PDF
 files, so you could download and view the PDF version as an alternative.
@@ -252,6 +249,5 @@ manual with ``make spelling``.  This requires `a library called enchant
 positives* (e.g. keywords, names, abbreviations) those can be added to
 the file ``lammps/doc/utils/sphinx-config/false_positives.txt``.
 
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-
 .. _lws: https://www.lammps.org
+.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html

doc/src/Build_settings.rst

@@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
-The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
-distribution.  It is portable across all platforms.  Depending on the size
+included in the LAMMPS distribution.  It is portable across all
-of the FFTs and the number of processors used, the other libraries listed
+platforms.  Depending on the size of the FFTs and the number of
-here can be faster.
+processors used, the other libraries listed here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
-per-timestep CPU cost, FFTs are only a portion of long-range
+per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
-Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+and 1d FFTs are only a portion of the FFT cost (parallel communication
-communication can be costly).  A breakdown of these timings is printed
+can be costly).  A breakdown of these timings is printed to the screen
-to the screen at the end of a run when using the
+at the end of a run when using the :doc:`kspace_style pppm
-:doc:`kspace_style pppm <kspace_style>` command. The
+<kspace_style>` command. The :doc:`Screen and logfile output
-:doc:`Screen and logfile output <Run_output>`
+<Run_output>` page gives more details.  A more detailed (and time
-page gives more details.  A more detailed (and time consuming)
+consuming) report of the FFT performance is generated with the
-report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
-platform and can be faster than the KISS FFT library.  You can
+platform and can be faster than the KISS FFT library.  You can download
-download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
-version 3.X; the legacy version 2.1.X is no longer supported.
+3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges

doc/src/Commands.rst

@@ -21,6 +21,7 @@ commands in it are used to define a LAMMPS simulation.
    Commands_pair
    Commands_bond
    Commands_kspace
+   Commands_dump
 
 .. toctree::
    :maxdepth: 1

doc/src/Commands_all.rst

@@ -10,11 +10,14 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.
+An alphabetic list of general LAMMPS commands.  Note that style
+commands with many variants, can be more easily accessed via the small
+table above.
 
 .. table_from_list::
    :columns: 5
@@ -60,6 +63,7 @@ An alphabetic list of general LAMMPS commands.
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
+   * :doc:`labelmap <labelmap>`
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`

doc/src/Commands_bond.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 .. _bond:
 
@@ -43,6 +44,7 @@ OPT.
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
    * :doc:`nonlinear (o) <bond_nonlinear>`
@@ -91,9 +93,10 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`spica (o) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:

doc/src/Commands_compute.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Compute commands
 ================
@@ -138,6 +139,8 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`smd/vol <compute_smd_vol>`
    * :doc:`snap <compute_sna_atom>`
    * :doc:`sna/atom <compute_sna_atom>`
+   * :doc:`sna/grid <compute_sna_atom>`
+   * :doc:`sna/grid/local <compute_sna_atom>`
    * :doc:`snad/atom <compute_sna_atom>`
    * :doc:`snav/atom <compute_sna_atom>`
    * :doc:`sph/e/atom <compute_sph_e_atom>`

doc/src/Commands_dump.rst

@@ -0,0 +1,56 @@
+.. table_from_list::
+   :columns: 3
+
+   * :doc:`General commands <Commands_all>`
+   * :doc:`Fix styles <Commands_fix>`
+   * :doc:`Compute styles <Commands_compute>`
+   * :doc:`Pair styles <Commands_pair>`
+   * :ref:`Bond styles <bond>`
+   * :ref:`Angle styles <angle>`
+   * :ref:`Dihedral styles <dihedral>`
+   * :ref:`Improper styles <improper>`
+   * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
+
+Dump commands
+=============
+
+An alphabetic list of all LAMMPS :doc:`dump <dump>` commands.
+
+.. table_from_list::
+   :columns: 5
+
+   * :doc:`atom <dump>`
+   * :doc:`atom/adios <dump_adios>`
+   * :doc:`atom/gz <dump>`
+   * :doc:`atom/mpiio <dump>`
+   * :doc:`atom/zstd <dump>`
+   * :doc:`cfg <dump>`
+   * :doc:`cfg/gz <dump>`
+   * :doc:`cfg/mpiio <dump>`
+   * :doc:`cfg/uef <dump_cfg_uef>`
+   * :doc:`cfg/zstd <dump>`
+   * :doc:`custom <dump>`
+   * :doc:`custom/adios <dump_adios>`
+   * :doc:`custom/gz <dump>`
+   * :doc:`custom/mpiio <dump>`
+   * :doc:`custom/zstd <dump>`
+   * :doc:`dcd <dump>`
+   * :doc:`deprecated <dump>`
+   * :doc:`h5md <dump_h5md>`
+   * :doc:`image <dump_image>`
+   * :doc:`local <dump>`
+   * :doc:`local/gz <dump>`
+   * :doc:`local/zstd <dump>`
+   * :doc:`molfile <dump_molfile>`
+   * :doc:`movie <dump_image>`
+   * :doc:`netcdf <dump_netcdf>`
+   * :doc:`netcdf/mpiio <dump>`
+   * :doc:`vtk <dump_vtk>`
+   * :doc:`xtc <dump>`
+   * :doc:`xyz <dump>`
+   * :doc:`xyz/gz <dump>`
+   * :doc:`xyz/mpiio <dump>`
+   * :doc:`xyz/zstd <dump>`
+   * :doc:`yaml <dump>`
+

doc/src/Commands_fix.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Fix commands
 ============
@@ -105,7 +106,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`mdi/aimd <fix_mdi_aimd>`
+   * :doc:`mdi/qm <fix_mdi_qm>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
@@ -164,6 +165,7 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Commands_kspace.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 KSpace solvers
 ==============

doc/src/Commands_pair.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Pair_style potentials
 ======================
@@ -181,9 +182,9 @@ OPT.
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
-   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/spica (gko) <pair_spica>`
-   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/spica/coul/long (go) <pair_spica>`
-   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/spica/coul/msm (o) <pair_spica>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@@ -196,10 +197,11 @@ OPT.
    * :doc:`lubricateU/poly <pair_lubricateU>`
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
-   * :doc:`meam <pair_meam>`
+   * :doc:`meam (k) <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mesocnt/viscous <pair_mesocnt>`
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
@@ -270,6 +272,7 @@ OPT.
    * :doc:`spin/magelec <pair_spin_magelec>`
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
+   * :doc:`srp/react <pair_srp>`
    * :doc:`sw (giko) <pair_sw>`
    * :doc:`sw/angle/table <pair_sw_angle_table>`
    * :doc:`sw/mod (o) <pair_sw>`

doc/src/Commands_parse.rst

@@ -123,14 +123,15 @@ LAMMPS:
 .. _six:
 
 6. If you want text with spaces to be treated as a single argument, it
-   can be enclosed in either single or double or triple quotes.  A long
+   can be enclosed in either single (') or double (") or triple (""")
-   single argument enclosed in single or double quotes can span multiple
+   quotes.  A long single argument enclosed in single or double quotes
-   lines if the "&" character is used, as described above.  When the
+   can span multiple lines if the "&" character is used, as described
-   lines are concatenated together (and the "&" characters and line
+   in :ref:`1 <one>` above.  When the lines are concatenated together
-   breaks removed), the text will become a single line.  If you want
+   by LAMMPS (and the "&" characters and line breaks removed), the
-   multiple lines of an argument to retain their line breaks, the text
+   combined text will become a single line.  If you want multiple lines
-   can be enclosed in triple quotes, in which case "&" characters are
+   of an argument to retain their line breaks, the text can be enclosed
-   not needed.  For example:
+   in triple quotes, in which case "&" characters are not needed and do
+   not function as line continuation character.  For example:
 
    .. code-block:: LAMMPS
 
@@ -144,8 +145,9 @@ LAMMPS:
       System temperature = $t
       """
 
-   In each case, the single, double, or triple quotes are removed when
+   In each of these cases, the single, double, or triple quotes are
-   the single argument they enclose is stored internally.
+   removed and the enclosed text stored internally as a single
+   argument.
 
    See the :doc:`dump modify format <dump_modify>`, :doc:`print
    <print>`, :doc:`if <if>`, and :doc:`python <python>` commands for

doc/src/Developer.rst

@@ -17,6 +17,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_updating
    Developer_plugins
    Developer_unittest
    Classes

doc/src/Developer_updating.rst

@@ -0,0 +1,425 @@
+Notes for updating code written for older LAMMPS versions
+---------------------------------------------------------
+
+This section documents how C++ source files that are available *outside
+of the LAMMPS source distribution* (e.g. in external USER packages or as
+source files provided as a supplement to a publication) that are written
+for an older version of LAMMPS and thus need to be updated to be
+compatible with the current version of LAMMPS.  Due to the active
+development of LAMMPS it is likely to always be incomplete.  Please
+contact developer@lammps.org in case you run across an issue that is not
+(yet) listed here.  Please also review the latest information about the
+LAMMPS :doc:`programming style conventions <Modify_style>`, especially
+if you are considering to submit the updated version for inclusion into
+the LAMMPS distribution.
+
+Available topics in mostly chronological order are:
+
+- `Setting flags in the constructor`_
+- `Rename of pack/unpack_comm() to pack/unpack_forward_comm()`_
+- `Use ev_init() to initialize variables derived from eflag and vflag`_
+- `Use utils::numeric() functions instead of force->numeric()`_
+- `Use utils::open_potential() function to open potential files`_
+- `Simplify customized error messages`_
+- `Use of "override" instead of "virtual"`_
+- `Simplified and more compact neighbor list requests`_
+- `Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM`_
+- `Use Output::get_dump_by_id() instead of Output::find_dump()`_
+
+----
+
+Setting flags in the constructor
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+As LAMMPS gains additional functionality, new flags may need to be set
+in the constructor or a class to signal compatibility with such features.
+Most of the time the defaults are chosen conservatively, but sometimes
+the conservative choice is the uncommon choice, and then those settings
+need to be made when updating code.
+
+Pair styles:
+
+  - ``manybody_flag``: set to 1 if your pair style is not pair-wise additive
+  - ``restartinfo``: set to 0 if your pair style does not store data in restart files
+
+
+Rename of pack/unpack_comm() to pack/unpack_forward_comm()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 8Aug2014
+
+In this change set the functions to pack data into communication buffers
+and to unpack data from communication buffers for :doc:`forward
+communications <Developer_comm_ops>` were renamed from ``pack_comm()``
+and ``unpack_comm()`` to ``pack_forward_comm()`` and
+``unpack_forward_comm()``, respectively.  Also the meaning of the return
+value of these functions was changed: rather than returning the number
+of items per atom stored in the buffer, now the total number of items
+added (or unpacked) needs to be returned.  Here is an example from the
+`PairEAM` class.  Of course the member function declaration in corresponding
+header file needs to be updated accordingly.
+
+Old:
+
+.. code-block:: C++
+
+   int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+   {
+     int m = 0;
+     for (int i = 0; i < n; i++) {
+       int j = list[i];
+       buf[m++] = fp[j];
+     }
+     return 1;
+   }
+
+New:
+
+.. code-block:: C++
+
+   int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
+   {
+     int m = 0;
+     for (int i = 0; i < n; i++) {
+       int j = list[i];
+       buf[m++] = fp[j];
+     }
+     return m;
+   }
+
+.. note::
+
+   Because the various "pack" and "unpack" functions are defined in the
+   respective base classes as dummy functions doing nothing, and because
+   of the the name mismatch the custom versions in the derived class
+   will no longer be called, there will be no compilation error when
+   this change is not applied.  Only calculations will suddenly produce
+   incorrect results because the required forward communication calls
+   will cease to function correctly.
+
+Use ev_init() to initialize variables derived from eflag and vflag
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 29Mar2019
+
+There are several variables that need to be initialized based on
+the values of the "eflag" and "vflag" variables and since sometimes
+there are new bits added and new variables need to be set to 1 or 0.
+To make this consistent, across all styles, there is now an inline
+function ``ev_init(eflag, vflag)`` that makes those settings
+consistently and calls either ``ev_setup()`` or ``ev_unset()``.
+Example from a pair style:
+
+Old:
+
+.. code-block:: C++
+
+   if (eflag || vflag) ev_setup(eflag, vflag);
+   else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
+
+New:
+
+.. code-block:: C++
+
+   ev_init(eflag, vflag);
+
+Not applying this change will not cause a compilation error, but
+can lead to inconsistent behavior and incorrect tallying of
+energy or virial.
+
+Use utils::numeric() functions instead of force->numeric()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+The "numeric()" conversion functions (including "inumeric()",
+"bnumeric()", and "tnumeric()") have been moved from the Force class to
+the utils namespace.  Also they take an additional argument that selects
+whether the ``Error::all()`` or ``Error::one()`` function should be
+called in case of an error.  The former should be used when *all* MPI
+processes call the conversion function and the latter *must* be used
+when they are called from only one or a subset of the MPI processes.
+
+Old:
+
+.. code-block:: C++
+
+    val = force->numeric(FLERR, arg[1]);
+    num = force->inumeric(FLERR, arg[2]);
+
+New:
+
+.. code-block:: C++
+
+    val = utils::numeric(FLERR, true, arg[1], lmp);
+    num = utils::inumeric(FLERR, false, arg[2], lmp);
+
+.. seealso::
+
+   :cpp:func:`utils::numeric() <LAMMPS_NS::utils::numeric>`,
+   :cpp:func:`utils::inumeric() <LAMMPS_NS::utils::inumeric>`,
+   :cpp:func:`utils::bnumeric() <LAMMPS_NS::utils::bnumeric>`,
+   :cpp:func:`utils::tnumeric() <LAMMPS_NS::utils::tnumeric>`
+
+Use utils::open_potential() function to open potential files
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 18Sep2020
+
+The :cpp:func:`utils::open_potential()
+<LAMMPS_NS::utils::open_potential>` function must be used to replace
+calls to ``force->open_potential()`` and should be used to replace
+``fopen()`` for opening potential files for reading.  The custom
+function does three additional steps compared to ``fopen()``: 1) it will
+try to parse the ``UNITS:`` and ``DATE:`` metadata will stop with an
+error on a units mismatch and will print the date info, if present, in
+the log file; 2) for pair styles that support it, it will set up
+possible automatic unit conversions based on the embedded unit
+information and LAMMPS' current units setting; 3) it will not only try
+to open a potential file at the given path, but will also search in the
+folders listed in the ``LAMMPS_POTENTIALS`` environment variable.  This
+allows to keep potential files in a common location instead of having to
+copy them around for simulations.
+
+Old:
+
+.. code-block:: C++
+
+   fp = force->open_potential(filename);
+   fp = fopen(filename, "r");
+
+New:
+
+.. code-block:: C++
+
+   fp = utils::open_potential(filename, lmp);
+
+Simplify customized error messages
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 14May2021
+
+Aided by features of the bundled {fmt} library, error messages now
+can have a variable number of arguments and the string will be interpreted
+as a {fmt} style format string so that custom error messages can be
+easily customized without having to use temporary buffers and ``sprintf()``.
+Example:
+
+Old:
+
+.. code-block:: C++
+
+   if (fptr == NULL) {
+     char str[128];
+     sprintf(str,"Cannot open AEAM potential file %s",filename);
+     error->one(FLERR,str);
+   }
+
+New:
+
+.. code-block:: C++
+
+   if (fptr == nullptr)
+     error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
+
+Use of "override" instead of "virtual"
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 17Feb2022
+
+Since LAMMPS requires C++11 we switched to use the "override" keyword
+instead of "virtual" to indicate polymorphism in derived classes.  This
+allows the C++ compiler to better detect inconsistencies when an
+override is intended or not.  Please note that "override" has to be
+added to **all** polymorph functions in derived classes and "virtual"
+*only* to the function in the base class (or the destructor).  Here is
+an example from the ``FixWallReflect`` class:
+
+Old:
+
+.. code-block:: C++
+
+   FixWallReflect(class LAMMPS *, int, char **);
+   virtual ~FixWallReflect();
+   int setmask();
+   void init();
+   void post_integrate();
+
+New:
+
+.. code-block:: C++
+
+   FixWallReflect(class LAMMPS *, int, char **);
+   ~FixWallReflect() override;
+   int setmask() override;
+   void init() override;
+   void post_integrate() override;
+
+This change set will neither cause a compilation failure, nor will it
+change functionality, but if you plan to submit the updated code for
+inclusion into the LAMMPS distribution, it will be requested for achieve
+a consistent :doc:`programming style <Modify_style>`.
+
+Simplified function names for forward and reverse communication
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 24Mar2022
+
+Rather then using the function name to distinguish between the different
+forward and reverse communication functions for styles, LAMMPS now uses
+the type of the "this" pointer argument.
+
+Old:
+
+.. code-block:: C++
+
+   comm->forward_comm_pair(this);
+   comm->forward_comm_fix(this);
+   comm->forward_comm_compute(this);
+   comm->forward_comm_dump(this);
+   comm->reverse_comm_pair(this);
+   comm->reverse_comm_fix(this);
+   comm->reverse_comm_compute(this);
+   comm->reverse_comm_dump(this);
+
+New:
+
+.. code-block:: C++
+
+   comm->forward_comm(this);
+   comm->reverse_comm(this);
+
+This change is **required** or else the code will not compile.
+
+Simplified and more compact neighbor list requests
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 24Mar2022
+
+This change set reduces the amount of code required to request a
+neighbor list.  It enforces consistency and no longer requires to change
+internal data of the request.  More information on neighbor list
+requests can be :doc:`found here <Developer_notes>`. Example from the
+``ComputeRDF`` class:
+
+Old:
+
+.. code-block:: C++
+
+   int irequest = neighbor->request(this,instance_me);
+   neighbor->requests[irequest]->pair = 0;
+   neighbor->requests[irequest]->compute = 1;
+   neighbor->requests[irequest]->occasional = 1;
+   if (cutflag) {
+     neighbor->requests[irequest]->cut = 1;
+     neighbor->requests[irequest]->cutoff = mycutneigh;
+   }
+
+New:
+
+.. code-block:: C++
+
+   auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
+   if (cutflag) req->set_cutoff(mycutneigh);
+
+Public access to the ``NeighRequest`` class data members has been
+removed so this update is **required** to avoid compilation failure.
+
+Split of fix STORE into fix STORE/GLOBAL and fix STORE/PERATOM
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 15Sep2022
+
+This change splits the GLOBAL and PERATOM modes of fix STORE into two
+separate fixes STORE/GLOBAL and STORE/PERATOM.  There was very little
+shared code between the two fix STORE modes and the two different code
+paths had to be prefixed with if statements.  Furthermore, some flags
+were used differently in the two modes leading to confusion.  Splitting
+the code into two fix styles, makes it more easily maintainable.  Since
+these are internal fixes, there is no user visible change.
+
+Old:
+
+.. code-block:: C++
+
+   #include "fix_store.h"
+
+   FixStore *fix = dynamic_cast<FixStore *>(
+      modify->add_fix(fmt::format("{} {} STORE peratom 1 13",id_pole,group->names[0]));
+
+   FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_pole));
+
+New:
+
+.. code-block:: C++
+
+   #include "fix_store_peratom.h"
+
+   FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(
+      modify->add_fix(fmt::format("{} {} STORE/PERATOM 1 13",id_pole,group->names[0]));
+
+   FixStorePeratom *fix = dynamic_cast<FixStorePeratom *>(modify->get_fix_by_id(id_pole));
+
+Old:
+
+.. code-block:: C++
+
+   #include "fix_store.h"
+
+   FixStore *fix = dynamic_cast<FixStore *>(
+      modify->add_fix(fmt::format("{} {} STORE global 1 1",id_fix,group->names[igroup]));
+
+   FixStore *fix = dynamic_cast<FixStore *>(modify->get_fix_by_id(id_fix));
+
+New:
+
+.. code-block:: C++
+
+   #include "fix_store_global.h"
+
+   FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(
+      modify->add_fix(fmt::format("{} {} STORE/GLOBAL 1 1",id_fix,group->names[igroup]));
+
+   FixStoreGlobal *fix = dynamic_cast<FixStoreGlobal *>(modify->get_fix_by_id(id_fix));
+
+This change is **required** or else the code will not compile.
+
+Use Output::get_dump_by_id() instead of Output::find_dump()
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionchanged:: 15Sep2022
+
+The accessor function to individual dump style instances has been changed
+from ``Output::find_dump()`` returning the index of the dump instance in
+the list of dumps to ``Output::get_dump_by_id()`` returning a pointer to
+the dump directly.  Example:
+
+Old:
+
+.. code-block:: C++
+
+   int idump = output->find_dump(arg[iarg+1]);
+   if (idump < 0)
+     error->all(FLERR,"Dump ID in hyper command does not exist");
+   memory->grow(dumplist,ndump+1,"hyper:dumplist");
+   dumplist[ndump++] = idump;
+
+   [...]
+
+   if (dumpflag)
+     for (int idump = 0; idump < ndump; idump++)
+       output->dump[dumplist[idump]]->write();
+
+New:
+
+.. code-block:: C++
+
+   auto idump = output->get_dump_by_id(arg[iarg+1]);
+   if (!idump) error->all(FLERR,"Dump ID {} in hyper command does not exist", arg[iarg+1]);
+   dumplist.emplace_back(idump);
+
+   [...]
+
+   if (dumpflag) for (auto idump : dumplist) idump->write();
+
+This change is **required** or else the code will not compile.

doc/src/Developer_utils.rst

@@ -154,6 +154,9 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_and_count_words
    :project: progguide
 
+.. doxygenfunction:: join_words
+   :project: progguide
+
 .. doxygenfunction:: split_words
    :project: progguide
 
@@ -172,6 +175,12 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
+.. doxygenfunction:: is_id
+   :project: progguide
+
+.. doxygenfunction:: is_type
+   :project: progguide
+
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -202,10 +211,13 @@ Argument processing
 .. doxygenfunction:: expand_args
    :project: progguide
 
+.. doxygenfunction:: expand_type
+   :project: progguide
+
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &format, Args&&... args)
    :project: progguide
 
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)

doc/src/Errors_debug.rst

@@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
 There are two options to use the GDB debugger for identifying the origin
 of the segmentation fault or similar crash. The GDB debugger has many
 more features and options, as can be seen for example its `online
-documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Errors_messages.rst

@@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Bonds defined but no bond types*
    The data file header lists bonds but no bond types.
 
-*Bond/react: Cannot use fix bond/react with non-molecular systems*
-   Only systems with bonds that can be changed can be used. Atom_style
-   template does not qualify.
-
-*Bond/react: Invalid template atom ID in map file*
-   Atom IDs in molecule templates range from 1 to the number of atoms in the template.
-
-*Bond/react: Rmax cutoff is longer than pairwise cutoff*
-   This is not allowed because bond creation is done using the pairwise
-   neighbor list.
-
-*Bond/react: Molecule template ID for fix bond/react does not exist*
-   A valid molecule template must have been created with the molecule
-   command.
-
-*Bond/react: Reaction templates must contain the same number of atoms*
-   There should be a one-to-one correspondence between atoms in the
-   pre-reacted and post-reacted templates, as specified by the map file.
-
-*Bond/react: Unknown section in map file*
-   Please ensure reaction map files are properly formatted.
-
-*Bond/react: Atom/Bond type affected by reaction too close to template edge*
-   This means an atom which changes type or connectivity during the
-   reaction is too close to an 'edge' atom defined in the map
-   file.  This could cause incorrect assignment of bonds, angle, etc.
-   Generally, this means you must include more atoms in your templates,
-   such that there are at least two atoms between each atom involved in
-   the reaction and an edge atom.
-
-*Bond/react: Fix bond/react needs ghost atoms from farther away*
-   This is because a processor needs to map the entire unreacted
-   molecule template onto simulation atoms it knows about. The
-   comm_modify cutoff command can be used to extend the communication
-   range.
-
-*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
-   Self-explanatory.
-
-*Bond/react: First neighbors of chiral atoms must be of mutually different types*
-   Self-explanatory.
-
-*Bond/react: Chiral atoms must have exactly four first neighbors*
-   Self-explanatory.
-
-*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
-   The coordinates of atoms in the pre-reacted template are used to determine
-   chirality.
-
-*Bond/react special bond generation overflow*
-   The number of special bonds per-atom created by a reaction exceeds the
-   system setting. See the read_data or create_box command for how to
-   specify this value.
-
-*Bond/react topology/atom exceed system topology/atom*
-   The number of bonds, angles etc per-atom created by a reaction exceeds
-   the system setting. See the read_data or create_box command for how to
-   specify this value.
-
 *Both restart files must use % or neither*
    Self-explanatory.
 
@@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Cannot use chosen neighbor list style with lj/gromacs/kk*
    Self-explanatory.
 
-*Cannot use chosen neighbor list style with lj/sdk/kk*
+*Cannot use chosen neighbor list style with lj/spica/kk*
    That style is not supported by Kokkos.
 
 *Cannot use chosen neighbor list style with pair eam/kk*
@@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Cannot use newton pair with lj/gromacs/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
+*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/sdk/gpu pair style*
+*Cannot use newton pair with lj/spica/gpu pair style*
    Self-explanatory.
 
 *Cannot use newton pair with lj96/cut/gpu pair style*
@@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    acquire needed info, The comm_modify cutoff command can be used to
    extend the communication range.
 
+*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
+   Only systems with bonds that can be changed can be used. Atom_style
+   template does not qualify.
+
+*Fix bond/react: Invalid template atom ID in map file*
+   Atom IDs in molecule templates range from 1 to the number of atoms in the template.
+
+*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
+   This is not allowed because bond creation is done using the pairwise
+   neighbor list.
+
+*Fix bond/react: Molecule template ID for fix bond/react does not exist*
+   A valid molecule template must have been created with the molecule
+   command.
+
+*Fix bond/react: Reaction templates must contain the same number of atoms*
+   There should be a one-to-one correspondence between atoms in the
+   pre-reacted and post-reacted templates, as specified by the map file.
+
+*Fix bond/react: Unknown section in map file*
+   Please ensure reaction map files are properly formatted.
+
+*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the map
+   file.  This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
+*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
+   This is because a processor needs to map the entire unreacted
+   molecule template onto simulation atoms it knows about. The
+   comm_modify cutoff command can be used to extend the communication
+   range.
+
+*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
+   Self-explanatory.
+
+*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
+   Self-explanatory.
+
+*Fix bond/react: Chiral atoms must have exactly four first neighbors*
+   Self-explanatory.
+
+*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
+   The coordinates of atoms in the pre-reacted template are used to determine
+   chirality.
+
+*Fix bond/react special bond generation overflow*
+   The number of special bonds per-atom created by a reaction exceeds the
+   system setting. See the read_data or create_box command for how to
+   specify this value.
+
+*Fix bond/react topology/atom exceed system topology/atom*
+   The number of bonds, angles etc per-atom created by a reaction exceeds
+   the system setting. See the read_data or create_box command for how to
+   specify this value.
+
 *Fix bond/swap cannot use dihedral or improper styles*
    These styles cannot be defined when using this fix.
 
@@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Mass command must set a type from 1-N where N is the number of atom
    types.
 
+*Invalid label2type() function syntax in variable formula*
+   The first argument must be a label map kind (atom, bond, angle,
+   dihedral, or improper) and the second argument must be a valid type
+   label that has been assigned to a numeric type.
+
 *Invalid use of library file() function*
    This function is called through the library interface.  This
    error should not occur.  Contact the developers if it does.
@@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *LJ6 off not supported in pair_style buck/long/coul/long*
    Self-explanatory.
 
+*Label map is incomplete: all types must be assigned a unique type label*
+   For a given type-kind (atom types, bond types, etc.) to be written to
+   the data file, all associated types must be assigned a type label, and
+   each type label can be assigned to only one numeric type.
+
 *Label wasn't found in input script*
    Self-explanatory.
 
+*Labelmap command before simulation box is defined*
+   The labelmap command cannot be used before a read_data,
+   read_restart, or create_box command.
+
 *Lattice orient vectors are not orthogonal*
    The three specified lattice orientation vectors must be mutually
    orthogonal.
@@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Must not have multiple fixes change box parameter ...*
    Self-explanatory.
 
+*Must read Angle Type Labels before Angles*
+   An Angle Type Labels section of a data file must come before the Angles section.
+
+*Must read Atom Type Labels before Atoms*
+   An Atom Type Labels section of a data file must come before the Atoms section.
+
 *Must read Atoms before Angles*
    The Atoms section of a data file must come before an Angles section.
 
@@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    The Atoms section of a data file must come before a Velocities
    section.
 
+*Must read Bond Type Labels before Bonds*
+   A Bond Type Labels section of a data file must come before the Bonds section.
+
+*Must read Dihedral Type Labels before Dihedrals*
+   An Dihedral Type Labels section of a data file must come before the Dihedrals section.
+
+*Must read Improper Type Labels before Impropers*
+   An Improper Type Labels section of a data file must come before the Impropers section.
+
 *Must re-specify non-restarted pair style (xxx) after read_restart*
    For pair styles, that do not store their settings in a restart file,
    it must be defined with a new 'pair_style' command after read_restart.
@@ -6782,7 +6811,7 @@ keyword to allow for additional bonds to be formed
    This is because the computation of constraint forces within a water
    molecule adds forces to atoms owned by other processors.
 
-*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
+*Pair style lj/spica/coul/long/gpu requires atom attribute q*
    The atom style defined does not have this attribute.
 
 *Pair style nb3b/harmonic requires atom IDs*
@@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
    Number of local atoms times number of columns must fit in a 32-bit
    integer for dump.
 
+*Topology type exceeds system topology type*
+   The number of bond, angle, etc types exceeds the system setting. See
+   the create_box or read_data command for how to specify these values.
+
 *Tree structure in joint connections*
    Fix poems cannot (yet) work with coupled bodies whose joints connect
    the bodies in a tree structure.
@@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
 *Two groups cannot be the same in fix spring couple*
    Self-explanatory.
 
+*The %s type label %s is already in use for type %s*
+   For a given type-kind (atom types, bond types, etc.), a given type
+   label can be assigned to only one numeric type.
+
+*Type label string %s for %s type %s is invalid*
+   See the labelmap command documentation for valid type labels.
+
 *Unable to initialize accelerator for use*
    There was a problem initializing an accelerator for the gpu package
 

doc/src/Errors_warnings.rst

@@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    length, multiplying by the number of bonds in the interaction (e.g. 3
    for a dihedral) and adding a small amount of stretch.
 
-*Bond/react: Atom affected by reaction too close to template edge*
-   This means an atom which changes type or connectivity during the
-   reaction is too close to an 'edge' atom defined in the superimpose
-   file. This could cause incorrect assignment of bonds, angle, etc.
-   Generally, this means you must include more atoms in your templates,
-   such that there are at least two atoms between each atom involved in
-   the reaction and an edge atom.
-
 *Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
    Self-explanatory.
 
@@ -206,12 +198,20 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Fix SRD walls overlap but fix srd overlap not set*
    You likely want to set this in your input script.
 
-* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
+*Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
    When using fix bond/create multiple times or in combination with
    fix bond/break, the individual fix instances do not share information
    about changes they made at the same time step and thus it may result
    in unexpected behavior.
 
+*Fix bond/react: Atom affected by reaction too close to template edge*
+   This means an atom which changes type or connectivity during the
+   reaction is too close to an 'edge' atom defined in the superimpose
+   file. This could cause incorrect assignment of bonds, angle, etc.
+   Generally, this means you must include more atoms in your templates,
+   such that there are at least two atoms between each atom involved in
+   the reaction and an edge atom.
+
 *Fix bond/swap will ignore defined angles*
    See the page for fix bond/swap for more info on this
    restriction.
@@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
 *More than one compute sna/atom*
    Self-explanatory.
 
+*More than one compute sna/grid*
+   Self-explanatory.
+
+*More than one compute sna/grid/local*
+   Self-explanatory.
+
 *More than one compute snad/atom*
    Self-explanatory.
 
@@ -804,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
 
 *Using pair tail corrections with pair_modify compute no*
    The tail corrections will thus not be computed.
-

doc/src/Fortran.rst

@@ -3,7 +3,9 @@ The ``LIBLAMMPS`` Fortran Module
 
 The ``LIBLAMMPS`` module provides an interface to call LAMMPS from a
 Fortran code.  It is based on the LAMMPS C-library interface and
-requires a Fortran 2003 compatible compiler to be compiled.
+requires a Fortran 2003 compatible compiler to be compiled.  It is
+designed to be self-contained and not require any support functions
+written in C, C++, or Fortran.
 
 While C libraries have a defined binary interface (ABI) and can thus be
 used from multiple compiler versions from different vendors for as long
@@ -19,12 +21,20 @@ for a simple program using the Fortran interface would be:
    mpifort -o testlib.x  lammps.f90 testlib.f90 -L. -llammps
 
 Please note, that the MPI compiler wrapper is only required when the
-calling the library from an MPI parallel code.  Please also note the
+calling the library from an MPI parallel code.  Otherwise, using the
-order of the source files: the ``lammps.f90`` file needs to be compiled
+fortran compiler (gfortran, ifort, flang, etc.) will suffice.  It may be
-first, since it provides the ``LIBLAMMPS`` module that is imported by
+necessary to link to additional libraries depending on how LAMMPS was
-the Fortran code using the interface.  A working example code can be
+configured and whether the LAMMPS library :doc:`was compiled as a static
-found together with equivalent examples in C and C++ in the
+or shared library <Build_link>`.
-``examples/COUPLE/simple`` folder of the LAMMPS distribution.
+
+If the LAMMPS library itself has been compiled with MPI support, the
+resulting executable will still be able to run LAMMPS in parallel with
+``mpirun`` or equivalent.  Please also note that the order of the source
+files matters: the ``lammps.f90`` file needs to be compiled first, since
+it provides the ``LIBLAMMPS`` module that is imported by the Fortran
+code using the interface.  A working example code can be found together
+with equivalent examples in C and C++ in the ``examples/COUPLE/simple``
+folder of the LAMMPS distribution.
 
 .. versionadded:: 9Oct2020
 
@@ -38,35 +48,37 @@ found together with equivalent examples in C and C++ in the
 
 .. note::
 
-   A contributed (and complete!) Fortran interface that more
+   A contributed (and more complete!) Fortran interface that more
-   closely resembles the C-library interface is available
+   closely resembles the C-library interface is available in the
-   in the ``examples/COUPLE/fortran2`` folder.  Please see the
+   ``examples/COUPLE/fortran2`` folder.  Please see the ``README`` file
-   ``README`` file in that folder for more information about it
+   in that folder for more information about it and how to contact its
-   and how to contact its author and maintainer.
+   author and maintainer.
 
 ----------
 
 Creating or deleting a LAMMPS object
 ************************************
 
-With the Fortran interface the creation of a :cpp:class:`LAMMPS
+With the Fortran interface, the creation of a :cpp:class:`LAMMPS
 <LAMMPS_NS::LAMMPS>` instance is included in the constructor for
 creating the :f:func:`lammps` derived type.  To import the definition of
-that type and its type bound procedures you need to add a ``USE
+that type and its type bound procedures, you need to add a ``USE
 LIBLAMMPS`` statement.  Internally it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
 optional and :cpp:func:`lammps_mpi_init` will be called automatically,
-if it is needed.  Similarly, a possible call to :cpp:func:`lammps_finalize`
+if it is needed.  Similarly, a possible call to
-is integrated into the :f:func:`close` function and triggered with
+:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
-the optional logical argument set to ``.true.``. Here is a simple example:
+function and triggered with the optional logical argument set to
+``.true.``. Here is a simple example:
 
 .. code-block:: fortran
 
    PROGRAM testlib
      USE LIBLAMMPS                 ! include the LAMMPS library interface
+     IMPLICIT NONE
      TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
-     CHARACTER(len=*), DIMENSION(*), PARAMETER :: args = &
+     CHARACTER(len=*), PARAMETER :: args(3) = &
          [ CHARACTER(len=12) :: 'liblammps', '-log', 'none' ]
 
      ! create a LAMMPS instance (and initialize MPI)
@@ -78,16 +90,51 @@ the optional logical argument set to ``.true.``. Here is a simple example:
 
    END PROGRAM testlib
 
+It is also possible to pass command line flags from Fortran to C/C++ and
+thus make the resulting executable behave similarly to the standalone
+executable (it will ignore the `-in/-i` flag, though).  This allows
+using the command line to configure accelerator and suffix settings,
+configure screen and logfile output, or to set index style variables
+from the command line and more.  Here is a correspondingly adapted
+version of the previous example:
+
+.. code-block:: fortran
+
+   PROGRAM testlib2
+     USE LIBLAMMPS                 ! include the LAMMPS library interface
+     IMPLICIT NONE
+     TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
+     CHARACTER(len=128), ALLOCATABLE :: command_args(:)
+     INTEGER :: i, argc
+
+     ! copy command line flags to `command_args()`
+     argc = COMMAND_ARGUMENT_COUNT()
+     ALLOCATE(command_args(0:argc))
+     DO i=0, argc
+       CALL GET_COMMAND_ARGUMENT(i, command_args(i))
+     END DO
+
+     ! create a LAMMPS instance (and initialize MPI)
+     lmp = lammps(command_args)
+     ! get and print numerical version code
+     PRINT*, 'Program name:   ', command_args(0)
+     PRINT*, 'LAMMPS Version: ', lmp%version()
+     ! delete LAMMPS instance (and shuts down MPI)
+     CALL lmp%close(.TRUE.)
+     DEALLOCATE(command_args)
+
+   END PROGRAM testlib2
+
 --------------------
 
 Executing LAMMPS commands
-=========================
+*************************
 
 Once a LAMMPS instance is created, it is possible to "drive" the LAMMPS
-simulation by telling LAMMPS to read commands from a file, or pass
+simulation by telling LAMMPS to read commands from a file or to pass
 individual or multiple commands from strings or lists of strings.  This
-is done similar to how it is implemented in the `C-library
+is done similarly to how it is implemented in the :doc:`C-library
-<pg_lib_execute>` interface. Before handing off the calls to the
+interface <Library_execute>`. Before handing off the calls to the
 C-library interface, the corresponding Fortran versions of the calls
 (:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and
 :f:func:`commands_string`) have to make a copy of the strings passed as
@@ -102,7 +149,7 @@ Below is a small demonstration of the uses of the different functions:
      USE LIBLAMMPS
      TYPE(lammps)     :: lmp
      CHARACTER(len=512) :: cmds
-     CHARACTER(len=40),ALLOCATABLE :: cmdlist(:)
+     CHARACTER(len=40), ALLOCATABLE :: cmdlist(:)
      CHARACTER(len=10) :: trimmed
      INTEGER :: i
 
@@ -111,10 +158,10 @@ Below is a small demonstration of the uses of the different functions:
      CALL lmp%command('variable zpos index 1.0')
      ! define 10 groups of 10 atoms each
      ALLOCATE(cmdlist(10))
-     DO i=1,10
+     DO i=1, 10
          WRITE(trimmed,'(I10)') 10*i
          WRITE(cmdlist(i),'(A,I1,A,I10,A,A)')       &
-             'group g',i-1,' id ',10*(i-1)+1,':',ADJUSTL(trimmed)
+             'group g', i-1, ' id ', 10*(i-1)+1, ':', ADJUSTL(trimmed)
      END DO
      CALL lmp%commands_list(cmdlist)
      ! run multiple commands from multi-line string
@@ -123,12 +170,63 @@ Below is a small demonstration of the uses of the different functions:
          'create_box 1 box' // NEW_LINE('A') //               &
          'create_atoms 1 single 1.0 1.0 ${zpos}'
      CALL lmp%commands_string(cmds)
-     CALL lmp%close()
+     CALL lmp%close(.TRUE.)
 
    END PROGRAM testcmd
 
 ---------------
 
+Accessing system properties
+***************************
+
+The C-library interface allows the :doc:`extraction of different kinds
+of information <Library_properties>` about the active simulation
+instance and also - in some cases - to apply modifications to it.  In
+some cases, the C-library interface makes pointers to internal data
+structures accessible, thus when accessing them from Fortran, special
+care is needed to avoid data corruption and crashes.  Thus please see
+the documentation of the individual type bound procedures for details.
+
+Below is an example demonstrating some of the possible uses.
+
+.. code-block:: fortran
+
+  PROGRAM testprop
+    USE LIBLAMMPS
+    USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t
+    TYPE(lammps)     :: lmp
+    INTEGER(kind=8)  :: natoms
+    REAL(c_double), POINTER :: dt
+    INTEGER(c_int64_t), POINTER :: ntimestep
+    REAL(kind=8) :: pe, ke
+
+    lmp = lammps()
+    CALL lmp%file('in.sysinit')
+    natoms = INT(lmp%get_natoms(),8)
+    WRITE(6,'(A,I8,A)') 'Running a simulation with', natoms, ' atoms'
+    WRITE(6,'(I8,A,I8,A,I3,A)') lmp%extract_setting('nlocal'), ' local and', &
+        lmp%extract_setting('nghost'), ' ghost atom. ',                      &
+        lmp%extract_setting('ntypes'), ' atom types'
+
+    CALL lmp%command('run 2 post no')
+    dt = lmp%extract_global('dt')
+    ntimestep = lmp%extract_global('ntimestep')
+    WRITE(6,'(A,I4,A,F4.1,A)') 'At step:', ntimestep, '  Changing timestep from', dt, ' to 0.5'
+    dt = 0.5
+    CALL lmp%command('run 2 post no')
+
+    WRITE(6,'(A,I4)') 'At step:', ntimestep
+    pe = lmp%get_thermo('pe')
+    ke = lmp%get_thermo('ke')
+    PRINT*, 'PE = ', pe
+    PRINT*, 'KE = ', ke
+
+    CALL lmp%close(.TRUE.)
+
+  END PROGRAM testprop
+
+---------------
+
 The ``LIBLAMMPS`` module API
 ****************************
 
@@ -137,19 +235,29 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
 
 .. f:type:: lammps
 
-   Derived type that is the general class of the Fortran interface.
+   Derived type that is the general class of the Fortran interface.  It
-   It holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
+   holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>`
-   that any of the included calls are forwarded to.
+   class instance that any of the included calls are forwarded to.
 
    :f c_ptr handle: reference to the LAMMPS class
-   :f close: :f:func:`close`
+   :f subroutine close: :f:func:`close`
-   :f version: :f:func:`version`
+   :f subroutine error: :f:func:`error`
-   :f file: :f:func:`file`
+   :f function version: :f:func:`version`
-   :f command: :f:func:`command`
+   :f subroutine file: :f:func:`file`
-   :f commands_list: :f:func:`commands_list`
+   :f subroutine command: :f:func:`command`
-   :f commands_string: :f:func:`commands_string`
+   :f subroutine commands_list: :f:func:`commands_list`
+   :f subroutine commands_string: :f:func:`commands_string`
+   :f function get_natoms: :f:func:`get_natoms`
+   :f function get_thermo: :f:func:`get_thermo`
+   :f subroutine extract_box: :f:func:`extract_box`
+   :f subroutine reset_box: :f:func:`reset_box`
+   :f subroutine memory_usage: :f:func:`memory_usage`
+   :f function extract_setting: :f:func:`extract_setting`
+   :f function extract_global: :f:func:`extract_global`
 
-.. f:function:: lammps(args[,comm])
+--------
+
+.. f:function:: lammps([args][,comm])
 
    This is the constructor for the Fortran class and will forward
    the arguments to a call to either :cpp:func:`lammps_open_fortran`
@@ -162,10 +270,31 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For
    more details please see the documentation of :cpp:func:`lammps_open`.
 
-   :p character(len=*) args(*) [optional]: arguments as list of strings
+   :o character(len=\*) args(\*) [optional]: arguments as list of strings
    :o integer comm [optional]: MPI communicator
    :r lammps: an instance of the :f:type:`lammps` derived type
 
+   .. note::
+
+      The ``MPI_F08`` module, which defines Fortran 2008 bindings for MPI,
+      is not directly supported by this interface due to the complexities of
+      supporting both the ``MPI_F08`` and ``MPI`` modules at the same time.
+      However, you should be able to use the ``MPI_VAL`` member of the
+      ``MPI_comm`` derived type to access the integer value of the
+      communicator, such as in
+
+      .. code-block:: Fortran
+
+         PROGRAM testmpi
+            USE LIBLAMMPS
+            USE MPI_F08
+            TYPE(lammps) :: lmp
+            lmp = lammps(MPI_COMM_SELF%MPI_VAL)
+         END PROGRAM testmpi
+
+Procedures Bound to the lammps Derived Type
+===========================================
+
 .. f:subroutine:: close([finalize])
 
    This method will close down the LAMMPS instance through calling
@@ -175,6 +304,20 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
 
    :o logical finalize [optional]: shut down the MPI environment of the LAMMPS library if true.
 
+--------
+
+.. f:subroutine:: error(error_type, error_text)
+
+   This method is a wrapper around the :cpp:func:`lammps_error` function and will dispatch
+   an error through the LAMMPS Error class.
+
+   .. versionadded:: TBD
+
+   :p integer error_type: constant to select which Error class function to call
+   :p character(len=\*) error_text: error message
+
+--------
+
 .. f:function:: version()
 
    This method returns the numeric LAMMPS version like :cpp:func:`lammps_version`
@@ -188,26 +331,243 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    This method will call :cpp:func:`lammps_file` to have LAMMPS read
    and process commands from a file.
 
-   :p character(len=*) filename: name of file with LAMMPS commands
+   :p character(len=\*) filename: name of file with LAMMPS commands
+
+--------
 
 .. f:subroutine:: command(cmd)
 
    This method will call :cpp:func:`lammps_command` to have LAMMPS
    execute a single command.
 
-   :p character(len=*) cmd: single LAMMPS command
+   :p character(len=\*) cmd: single LAMMPS command
+
+--------
 
 .. f:subroutine:: commands_list(cmds)
 
    This method will call :cpp:func:`lammps_commands_list` to have LAMMPS
    execute a list of input lines.
 
-   :p character(len=*) cmd(*): list of LAMMPS input lines
+   :p character(len=\*) cmd(:): list of LAMMPS input lines
+
+--------
 
 .. f:subroutine:: commands_string(str)
 
    This method will call :cpp:func:`lammps_commands_string` to have LAMMPS
    execute a block of commands from a string.
 
-   :p character(len=*) str: LAMMPS input in string
+   :p character(len=\*) str: LAMMPS input in string
 
+--------
+
+.. f:function:: get_natoms()
+
+   This function will call :cpp:func:`lammps_get_natoms` and return the number
+   of atoms in the system.
+
+   :r real(c_double): number of atoms
+
+--------
+
+.. f:function:: get_thermo(name)
+
+   This function will call :cpp:func:`lammps_get_thermo` and return the value
+   of the corresponding thermodynamic keyword.
+
+   .. versionadded:: TBD
+
+   :p character(len=\*) name: string with the name of the thermo keyword
+   :r real(c_double): value of the requested thermo property or `0.0_c_double`
+
+--------
+
+.. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag])
+
+   This subroutine will call :cpp:func:`lammps_extract_box`. All
+   parameters are optional, though obviously at least one should be
+   present. The parameters *pflags* and *boxflag* are stored in LAMMPS
+   as integers, but should be declared as ``LOGICAL`` variables when
+   calling from Fortran.
+
+   .. versionadded:: TBD
+
+   :o real(c_double) boxlo [dimension(3),optional]: vector in which to store
+    lower-bounds of simulation box
+   :o real(c_double) boxhi [dimension(3),optional]: vector in which to store
+    upper-bounds of simulation box
+   :o real(c_double) xy [optional]: variable in which to store *xy* tilt factor
+   :o real(c_double) yz [optional]: variable in which to store *yz* tilt factor
+   :o real(c_double) xz [optional]: variable in which to store *xz* tilt factor
+   :o logical pflags [dimension(3),optional]: vector in which to store
+    periodicity flags (``.TRUE.`` means periodic in that dimension)
+   :o logical boxflag [optional]: variable in which to store boolean denoting
+    whether the box will change during a simulation
+    (``.TRUE.`` means box will change)
+
+.. note::
+
+   Note that a frequent use case of this function is to extract only one or
+   more of the options rather than all seven. For example, assuming "lmp"
+   represents a properly-initialized LAMMPS instance, the following code will
+   extract the periodic box settings into the variable "periodic":
+
+   .. code-block:: Fortran
+
+      ! code to start up
+      logical :: periodic(3)
+      ! code to initialize LAMMPS / run things / etc.
+      call lmp%extract_box(pflags = periodic)
+
+--------
+
+.. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz)
+
+   This subroutine will call :cpp:func:`lammps_reset_box`. All parameters
+   are required.
+
+   .. versionadded:: TBD
+
+   :p real(c_double) boxlo [dimension(3)]: vector of three doubles containing
+    the lower box boundary
+   :p real(c_double) boxhi [dimension(3)]: vector of three doubles containing
+    the upper box boundary
+   :p real(c_double) xy: *x--y* tilt factor
+   :p real(c_double) yz: *y--z* tilt factor
+   :p real(c_double) xz: *x--z* tilt factor
+
+--------
+
+.. f:subroutine:: memory_usage(meminfo)
+
+   This subroutine will call :cpp:func:`lammps_memory_usage` and store the
+   result in the three-element array *meminfo*.
+
+   .. versionadded:: TBD
+
+   :p real(c_double) meminfo [dimension(3)]: vector of three doubles in which
+    to store memory usage data
+
+--------
+
+.. f:function:: get_mpi_comm()
+
+   This function returns a Fortran representation of the LAMMPS "world"
+   communicator.
+
+   .. versionadded:: TBD
+
+   :r integer: Fortran integer equivalent to the MPI communicator LAMMPS is
+    using
+
+   .. note::
+
+       The C library interface currently returns type ``int`` instead of
+       type ``MPI_Fint``, which is the C type corresponding to Fortran
+       ``INTEGER`` types of the default kind.  On most compilers, these
+       are the same anyway, but this interface exchanges values this way
+       to avoid warning messages.
+
+   .. note::
+
+      The `MPI_F08` module, which defines Fortran 2008 bindings for MPI,
+      is not directly supported by this function.  However, you should be
+      able to convert between the two using the `MPI_VAL` member of the
+      communicator.  For example,
+
+      .. code-block:: fortran
+
+         USE MPI_F08
+         USE LIBLAMMPS
+         TYPE (LAMMPS) :: lmp
+         TYPE (MPI_Comm) :: comm
+         ! ... [commands to set up LAMMPS/etc.]
+         comm%MPI_VAL = lmp%get_mpi_comm()
+
+      should assign an `MPI_F08` communicator properly.
+
+--------
+
+.. f:function:: extract_setting(keyword)
+
+   Query LAMMPS about global settings. See the documentation for the
+   :cpp:func:`lammps_extract_setting` function from the C library.
+
+   .. versionadded:: TBD
+
+   :p character(len=\*) keyword: string containing the name of the thermo keyword
+   :r integer(c_int): value of the queried setting or :math:`-1` if unknown
+
+--------
+
+.. f:function:: extract_global(name)
+
+   This function calls :cpp:func:`lammps_extract_global` and returns
+   either a string or a pointer to internal global LAMMPS data,
+   depending on the data requested through *name*.
+
+   .. versionadded:: TBD
+
+   Note that this function actually does not return a value, but rather
+   associates the pointer on the left side of the assignment to point to
+   internal LAMMPS data (with the exception of string data, which are
+   copied and returned as ordinary Fortran strings). Pointers must be of
+   the correct data type to point to said data (typically
+   ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``)
+   and have compatible kind and rank.  The pointer being associated with
+   LAMMPS data is type-, kind-, and rank-checked at run-time via an
+   overloaded assignment operator.  The pointers returned by this
+   function are generally persistent; therefore it is not necessary to
+   call the function again, unless a :doc:`clear` command has been
+   issued, which wipes out and recreates the contents of the
+   :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class.
+
+   For example,
+
+   .. code-block:: fortran
+
+      PROGRAM demo
+       USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
+       USE LIBLAMMPS
+       TYPE(lammps) :: lmp
+       INTEGER(c_int), POINTER :: nlocal
+       INTEGER(c_int64_t), POINTER :: ntimestep
+       CHARACTER(LEN=10) :: units
+       REAL(c_double), POINTER :: dt
+       lmp = lammps()
+       ! other commands
+       nlocal = lmp%extract_global('nlocal')
+       ntimestep = lmp%extract_global('ntimestep')
+       dt = lmp%extract_global('dt')
+       units = lmp%extract_global('units')
+       ! more commands
+       lmp.close(.TRUE.)
+      END PROGRAM demo
+
+   would extract the number of atoms on this processor, the current time step,
+   the size of the current time step, and the units being used into the
+   variables *nlocal*, *ntimestep*, *dt*, and *units*, respectively.
+
+   .. note::
+
+      if this function returns a string, the string must have
+      length greater than or equal to the length of the string (not including the
+      terminal NULL character) that LAMMPS returns. If the variable's length is
+      too short, the string will be truncated. As usual in Fortran, strings
+      are padded with spaces at the end.
+
+   :p character(len=\*) name: string with the name of the extracted property
+   :r polymorphic: pointer to LAMMPS data. The left-hand side of the assignment
+    should be either a string (if expecting string data) or a C-compatible
+    pointer (e.g., ``INTEGER (c_int), POINTER :: nlocal``) to the extracted
+    property. If expecting vector data, the pointer should have dimension ":".
+
+.. warning::
+
+   Modifying the data in the location pointed to by the returned pointer
+   may lead to inconsistent internal data and thus may cause failures or
+   crashes or bogus simulations.  In general it is thus usually better
+   to use a LAMMPS input command that sets or changes these parameters.
+   Those will take care of all side effects and necessary updates of
+   settings derived from such settings.

doc/src/Howto.rst

@@ -34,6 +34,7 @@ Settings howto
    :maxdepth: 1
 
    Howto_2d
+   Howto_type_labels
    Howto_triclinic
    Howto_thermostat
    Howto_barostat
@@ -84,6 +85,7 @@ Packages howto
    Howto_coreshell
    Howto_drude
    Howto_drude2
+   Howto_peri
    Howto_manifold
    Howto_spins
 

doc/src/Howto_amoeba.rst

@@ -2,14 +2,14 @@ AMOEBA and HIPPO force fields
 =============================
 
 The AMOEBA and HIPPO polarizable force fields were developed by Jay
-Ponder's group at the U Washington at St Louis.  Their implementation
+Ponder's group at the U Washington at St Louis.  The LAMMPS
-in LAMMPS was done using F90 code provided by the Ponder group from
+implementation is based on Fortran 90 code provided by the Ponder
-their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_.
+group in their `Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
 
-The current implementaion (May 2022) of AMOEBA in LAMMPS matches the
+The current implementation (July 2022) of AMOEBA in LAMMPS matches the
 version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
 <amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`.  Likewise the current
-implementaion of HIPPO in LAMMPS matches the version discussed in
+implementation of HIPPO in LAMMPS matches the version discussed in
 :ref:`(Rackers) <amoeba-Rackers>`.
 
 These force fields can be used when polarization effects are desired
@@ -140,7 +140,7 @@ amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined.  In the
 example above, the IDs for these two fixes are *pit* and *bit*.
 
 Of course, if the system being modeled does not have one or more of
-the following -- bond, angle, dihedral, improper, pitorision,
+the following -- bond, angle, dihedral, improper, pitorsion,
 bitorsion interactions -- then the corresponding style and fix
 commands above do not need to be used.  See the example scripts in
 examples/amoeba for water systems as examples; they are simpler than
@@ -157,7 +157,7 @@ namely a PRM and KEY file.  The keyfile can be specified as NULL and
 default values for a various settings will be used.  Note that these 2
 files are meant to allow use of native Tinker files as-is.  However
 LAMMPS does not support all the options which can be included
-in a Tinker PRM or KEY file.  See specifis below.
+in a Tinker PRM or KEY file.  See specifics below.
 
 A :doc:`special_bonds <special_bonds>` command with the *one/five*
 option is required, since the AMOEBA/HIPPO force fields define
@@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and
 used by Tinker, and links to programs that convert standard PDB files
 to the extended XYZ format:
 
-* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
+* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
 * `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
 * `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
 
@@ -308,11 +308,11 @@ compatible with the LAMMPS data file format.
 
 .. _howto-Ponder:
 
-**(Ponder)** Ponder, Wu, Ren, Pande, Chodera†, Schnieders, Haque,  Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark,  Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549–2564 (2010).
+**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque,  Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark,  Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
 
 .. _howto-Rackers:
 
-**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056–7084 (2021).
+**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
 
 .. _howto-Ren:
 
@@ -320,5 +320,5 @@ compatible with the LAMMPS data file format.
 
 .. _howto-Shi:
 
-**(Shi)** Shi, Xiz, Znahg, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
+**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
 

doc/src/Howto_bioFF.rst

@@ -3,24 +3,20 @@ CHARMM, AMBER, COMPASS, and DREIDING force fields
 
 A force field has 2 parts: the formulas that define it and the
 coefficients used for a particular system.  Here we only discuss
-formulas implemented in LAMMPS that correspond to formulas commonly
+formulas implemented in LAMMPS that correspond to formulas commonly used
-used in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
+in the CHARMM, AMBER, COMPASS, and DREIDING force fields.  Setting
 coefficients is done either from special sections in an input data file
 via the :doc:`read_data <read_data>` command or in the input script with
-commands like :doc:`pair_coeff <pair_coeff>` or
+commands like :doc:`pair_coeff <pair_coeff>` or :doc:`bond_coeff
-:doc:`bond_coeff <bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc
+<bond_coeff>` and so on.  See the :doc:`Tools <Tools>` doc page for
-page for additional tools that can use CHARMM, AMBER, or Materials
+additional tools that can use CHARMM, AMBER, or Materials Studio
-Studio generated files to assign force field coefficients and convert
+generated files to assign force field coefficients and convert their
-their output into LAMMPS input.
+output into LAMMPS input.
 
-See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM force
+See :ref:`(MacKerell) <howto-MacKerell>` for a description of the CHARMM
-field.  See :ref:`(Cornell) <howto-Cornell>` for a description of the AMBER
+force field.  See :ref:`(Cornell) <howto-Cornell>` for a description of
-force field.  See :ref:`(Sun) <howto-Sun>` for a description of the COMPASS
+the AMBER force field.  See :ref:`(Sun) <howto-Sun>` for a description
-force field.
+of the COMPASS force field.
-
-.. _charmm: http://www.scripps.edu/brooks
-
-.. _amber: http://amber.scripps.edu
 
 The interaction styles listed below compute force field formulas that
 are consistent with common options in CHARMM or AMBER.  See each
@@ -41,9 +37,10 @@ command's documentation for the formula it computes.
 
 .. note::
 
-   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released
+   For CHARMM, newer *charmmfsw* or *charmmfsh* styles were released in
-   in March 2017.  We recommend they be used instead of the older *charmm*
+   March 2017.  We recommend they be used instead of the older *charmm*
-   styles.  See discussion of the differences on the :doc:`pair charmm <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
+   styles.  See discussion of the differences on the :doc:`pair charmm
+   <pair_charmm>` and :doc:`dihedral charmm <dihedral_charmm>` doc
    pages.
 
 COMPASS is a general force field for atomistic simulation of common

doc/src/Howto_bpm.rst

@@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
 such as those created by pouring grains using :doc:`fix pour
 <fix_pour>`, are initialized on that timestep.
 
-As bonds can be broken between neighbor list builds, the
-:doc:`special_bonds <special_bonds>` command works differently for BPM
-bond styles. There are two possible settings which determine how pair
-interactions work between bonded particles.  First, one can turn off
-all pair interactions between bonded particles.  Unlike :doc:`bond
-quartic <bond_quartic>`, this is not done by subtracting pair forces
-during the bond computation but rather by dynamically updating the
-special bond list. This is the default behavior of BPM bond styles and
-is done by updating the 1-2 special bond list as bonds break.  To do
-this, LAMMPS requires :doc:`newton <newton>` bond off such that all
-processors containing an atom know when a bond breaks. Additionally,
-one must do either (A) or (B).
-
-A) Use the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj 0 1 1 coul 1 1 1
-
-   These settings accomplish two goals. First, they turn off 1-3 and 1-4
-   special bond lists, which are not currently supported for BPMs. As
-   BPMs often have dense bond networks, generating 1-3 and 1-4 special
-   bond lists is expensive.  By setting the lj weight for 1-2 bonds to
-   zero, this turns off pairwise interactions.  Even though there are no
-   charges in BPM models, setting a nonzero coul weight for 1-2 bonds
-   ensures all bonded neighbors are still included in the neighbor list
-   in case bonds break between neighbor list builds.
-
-B) Alternatively, one can simply overlay pair interactions such that all
-   bonded particles also feel pair interactions. This can be
-   accomplished by using the *overlay/pair* keyword present in all bpm
-   bond styles and by using the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj/coul 1 1 1
-
-See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
-more information.
-
 ----------
 
 Currently there are two types of bonds included in the BPM
@@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
 <fix_nve_bpm_sphere>` which numerically integrates orientation similar
 to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
-To monitor the fracture of bonds in the system, all BPM bond styles
-have the ability to record instances of bond breakage to output using
-the :doc:`dump local <dump>` command. Additionally, one can use
-:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
-number of bonds per atom.
-
 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
@@ -104,6 +58,73 @@ velocity damping as its sister bond style.
 
 ----------
 
+Bond data can be output using a combination of standard LAMMPS commands.
+A list of IDs for bonded atoms can be generated using the
+:doc:`compute property/local <compute_property_local>` command.
+Various properties of bonds can be computed using the
+:doc:`compute bond/local <compute_bond_local>` command. This
+command allows one to access data saved to the bond's history
+such as the reference length of the bond. More information on
+bond history data can be found on the documentation pages for the specific
+BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
+command. As one may output many columns from the same compute, the
+:doc:`dump modify <dump_modify>` *colname* option may be used to provide
+more helpful column names. An example of this procedure is found in
+/examples/bpm/pour/. External software, such as OVITO, can read these dump
+files to render bond data.
+
+----------
+
+As bonds can be broken between neighbor list builds, the
+:doc:`special_bonds <special_bonds>` command works differently for BPM
+bond styles. There are two possible settings which determine how pair
+interactions work between bonded particles.  First, one can overlay
+pair forces with bond forces such that all bonded particles also
+feel pair interactions. This can be accomplished by using the *overlay/pair*
+keyword present in all bpm bond styles and by using the following special
+bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj/coul 1 1 1
+
+Alternatively, one can turn off all pair interactions between bonded
+particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
+by subtracting pair forces during the bond computation but rather by
+dynamically updating the special bond list. This is the default behavior
+of BPM bond styles and is done by updating the 1-2 special bond list as
+bonds break.  To do this, LAMMPS requires :doc:`newton <newton>` bond off
+such that all processors containing an atom know when a bond breaks.
+Additionally, one must use the following special bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 1 1 1
+
+These settings accomplish two goals. First, they turn off 1-3 and 1-4
+special bond lists, which are not currently supported for BPMs. As
+BPMs often have dense bond networks, generating 1-3 and 1-4 special
+bond lists is expensive.  By setting the lj weight for 1-2 bonds to
+zero, this turns off pairwise interactions.  Even though there are no
+charges in BPM models, setting a nonzero coul weight for 1-2 bonds
+ensures all bonded neighbors are still included in the neighbor list
+in case bonds break between neighbor list builds.
+
+To monitor the fracture of bonds in the system, all BPM bond styles
+have the ability to record instances of bond breakage to output using
+the :doc:`dump local <dump>` command. Since one may frequently output
+a list of broken bonds and the time they broke, the
+:doc:`dump modify <dump_modify>` option *header no* may be useful to
+avoid repeatedly printing the header of the dump file. An example of
+this procedure is found in /examples/bpm/impact/. Additionally,
+one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
+current number of bonds per atom.
+
+See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
+more information.
+
+----------
+
 While LAMMPS has many utilities to create and delete bonds, *only*
 the following are currently compatible with BPM bond styles:
 

doc/src/Howto_github.rst

@@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
 distribution.  It uses the process of updating this very tutorial as an
 example to describe the individual steps and options.  You need to be
 familiar with git and you may want to have a look at the `git book
-<http://git-scm.com/book/>`_ to familiarize yourself with some of the
+<https://git-scm.com/book/>`_ to familiarize yourself with some of the
 more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests

doc/src/Howto_manifold.rst

@@ -47,4 +47,4 @@ to the relevant fixes.
 .. _Paquay1:
 
 **(Paquay)** Paquay and Kusters, Biophys. J., 110, 6, (2016).
-preprint available at `arXiv:1411.3019 <http://arxiv.org/abs/1411.3019/>`_.
+preprint available at `arXiv:1411.3019 <https://arxiv.org/abs/1411.3019/>`_.

doc/src/Howto_mdi.rst

@@ -5,9 +5,9 @@ Client/server coupling of two (or more) codes is where one code is the
 "client" and sends request messages (data) to one (or more) "server"
 code(s).  A server responds to each request with a reply message
 (data).  This enables two (or more) codes to work in tandem to perform
-a simulation.  LAMMPS can act as either a client or server code; it
+a simulation.  In this context, LAMMPS can act as either a client or
-does this by using the `MolSSI Driver Interface (MDI) library
+server code.  It does this by using the `MolSSI Driver Interface (MDI)
-<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
+library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
 developed by the `Molecular Sciences Software Institute (MolSSI)
 <https://molssi.org>`_, which is supported by the :ref:`MDI <PKG-MDI>`
 package.
@@ -63,22 +63,39 @@ The package also provides a :doc:`mdi plugin <mdi>` command which
 enables LAMMPS to operate as an MDI driver and load an MDI engine as a
 plugin library.
 
-The package also has a `fix mdi/aimd <fix_mdi_aimd>` command in which
+The package also has a `fix mdi/qm <fix_mdi_qm>` command in which
-LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
+LAMMPS operates as an MDI driver in conjunction with a quantum
-in conjunction with a quantum mechanics code.  Its post_force() method
+mechanics code as an MDI engine.  The post_force() method of the
-illustrates how a driver issues MDI commands to another code.  This
+fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
-command can be used to couple to an MDI engine which is either a
+code.  This command can be used to couple to an MDI engine which is
-stand-alone code or a plugin library.
+either a stand-alone code or a plugin library.
+
+As explained on the `fix mdi/qm <fix_mdi_qm>` command doc page, it can
+be used to perform *ab initio* MD simulations or energy minimizations,
+or to evaluate the quantum energy and forces for a series of
+independent systems.  The examples/mdi directory has example input
+scripts for all of these use cases.
 
 ----------
 
 The examples/mdi directory contains Python scripts and LAMMPS input
 script which use LAMMPS as either an MDI driver or engine or both.
-Three example use cases are provided:
+Currently, 5 example use cases are provided:
 
-* Run ab initio MD (AIMD) using 2 instances of LAMMPS, one as driver
+* Run ab initio MD (AIMD) using 2 instances of LAMMPS.  As a driver
-  and one as an engine.  As an engine, LAMMPS is a surrogate for a
+  LAMMPS performs the timestepping in either NVE or NPT mode.  As an
-  quantum code.
+  engine, LAMMPS computes forces and is a surrogate for a quantum
+  code.
+
+* As a driver, LAMMPS runs an MD simulation.  Every N steps it passes
+  the current snapshot to an MDI engine to evaluate the energy,
+  virial, and peratom forces.  As the engine LAMMPS is a surrogate for
+  a quantum code.
+
+* As a driver, LAMMPS loops over a series of data files and passes the
+  configuration to an MDI engine to evaluate the energy, virial, and
+  peratom forces.  As the engine LAMMPS is a surrogate for a quantum
+  code.
 
 * A Python script driver invokes a sequence of unrelated LAMMPS
   calculations.  Calculations can be single-point energy/force
@@ -91,20 +108,22 @@ Three example use cases are provided:
 
 Note that in any of these example where LAMMPS is used as an engine,
 an actual QM code (which supports MDI) could be used in its place,
-without modifying other code or scripts, except to specify the name of
+without modifying the input scripts or launch commands, except to
-the QM code.
+specify the name of the QM code.
 
-The examples/mdi/README file explains how to launch both driver and
+The examples/mdi/Run.sh file illustrates how to launch both driver and
 engine codes so that they communicate using the MDI library via either
-MPI or sockets.
+MPI or sockets.  Or using the engine as a stand-alone code or plugin
+library.
 
 -------------
 
-Currently there are two quantum DFT codes which have direct MDI
+Currently there are at least two quantum DFT codes which have direct
-support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
+MDI support, `Quantum ESPRESSO (QE)
-and `INQ <https://qsg.llnl.gov/node/101.html>`_.  There are also
+<https://www.quantum-espresso.org/>`_ and `INQ
-several QM codes which have indirect support through QCEngine or i-PI.
+<https://qsg.llnl.gov/node/101.html>`_.  There are also several QM
-The former means they require a wrapper program (QCEngine) with MDI
+codes which have indirect support through QCEngine or i-PI.  The
+former means they require a wrapper program (QCEngine) with MDI
 support which writes/read files to pass data to the quantum code
 itself.  The list of QCEngine-supported and i-PI-supported quantum
 codes is on the `MDI webpage

doc/src/Howto_spc.rst

@@ -38,7 +38,7 @@ the partial charge assignments change:
 See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_spins.rst

@@ -30,9 +30,11 @@ can be coupled to another Langevin thermostat applied to the atoms
 using :doc:`fix langevin <fix_langevin>` in order to simulate
 thermostatted spin-lattice systems.
 
-The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin <fix_langevin_spin>`. It allows to either dissipate
+The magnetic damping can also be applied
-the thermal energy of the Langevin thermostat, or to perform a
+using :doc:`fix langevin/spin <fix_langevin_spin>`.
-relaxation of the magnetic configuration toward an equilibrium state.
+It allows to either dissipate the thermal energy of the Langevin
+thermostat, or to perform a relaxation of the magnetic configuration
+toward an equilibrium state.
 
 The command :doc:`fix setforce/spin <fix_setforce>` allows to set the
 components of the magnetic precession vectors (while erasing and
@@ -52,9 +54,11 @@ All the computed magnetic properties can be output by two main
 commands. The first one is :doc:`compute spin <compute_spin>`, that
 enables to evaluate magnetic averaged quantities, such as the total
 magnetization of the system along x, y, or z, the spin temperature, or
-the magnetic energy. The second command is :doc:`compute property/atom <compute_property_atom>`. It enables to output all the
+the magnetic energy. The second command
-per atom magnetic quantities. Typically, the orientation of a given
+is :doc:`compute property/atom <compute_property_atom>`.
-magnetic spin, or the magnetic force acting on this spin.
+It enables to output all the per atom magnetic quantities. Typically,
+the orientation of a given magnetic spin, or the magnetic force
+acting on this spin.
 
 ----------
 

doc/src/Howto_tip3p.rst

@@ -49,7 +49,7 @@ details:
 | :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
 |
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_tip4p.rst

@@ -97,7 +97,7 @@ This leads to slightly larger cost for the long-range calculation, so
 you can test the trade-off for your model.  The OM distance and the LJ
 and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
 
-Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_type_labels.rst

@@ -0,0 +1,126 @@
+Type labels
+===========
+
+.. versionadded:: 15Sep2022
+
+Each atom in LAMMPS has an associated numeric atom type. Similarly,
+each bond, angle, dihedral, and improper is assigned a bond type,
+angle type, and so on.  The primary use of these types is to map
+potential (force field) parameters to the interactions of the atom,
+bond, angle, dihedral, and improper.
+
+By default, type values are entered as integers from 1 to Ntypes
+wherever they appear in LAMMPS input or output files.  The total number
+Ntypes for each interaction is "locked in" when the simulation box
+is created.
+
+A recent addition to LAMMPS is the option to use strings - referred
+to as type labels - as an alternative.  Using type labels instead of
+numeric types can be advantageous in various scenarios.  For example,
+type labels can make inputs more readable and generic (i.e. usable through
+the :doc:`include command <include>` for different systems with different
+numerical values assigned to types.  This generality also applies to
+other inputs like data files read by :doc:`read_data <read_data>` or
+molecule template files read by the :doc:`molecule <molecule>`
+command.  See below for a list of other commands that can use
+type labels in different ways.
+
+LAMMPS will *internally* continue to use numeric types, which means
+that many previous restrictions still apply.  For example, the total
+number of types is locked in when creating the simulation box, and
+potential parameters for each type must be provided even if not used
+by any interactions.
+
+A collection of type labels for all type-kinds (atom types, bond types,
+etc.) is stored as a "label map" which is simply a list of numeric types
+and their associated type labels.  Within a type-kind, each type label
+must be unique.  It can be assigned to only one numeric type.  To read
+and write type labels to data files for a given type-kind, *all*
+associated numeric types need have a type label assigned.  Partial
+maps can be saved with the :doc:`labelmap write <labelmap>` command
+and read back with the :doc:`include <include>` command.
+
+Valid type labels can contain most ASCII characters, but cannot start
+with a number, a '#', or a '*'.  Also, labels must not contain whitespace
+characters.  When using the :doc:`labelmap command <labelmap>` in the
+LAMMPS input, if certain characters appear in the type label, such as
+the single (') or double (") quote or the '#' character, the label
+must be put in either double, single, or triple (""") quotes.  Triple
+quotes allow for the most generic type label strings, but they require
+to have a leading and trailing blank space.  When defining type labels
+the blanks will be ignored. Example:
+
+.. code-block:: LAMMPS
+
+   labelmap angle 1 """ C1'-C2"-C3# """
+
+This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
+
+There are two ways to define label maps.  One is via the :doc:`labelmap
+<labelmap>` command.  The other is via the :doc:`read_data <read_data>`
+command.  A data file can have sections such as *Atom Type Labels*, *Bond
+Type Labels*, etc., which assign type labels to numeric types.  The
+label map can be written out to data files by the :doc:`write_data
+<write_data>` command.  This map is also written to and read from
+restart files, by the :doc:`write_restart <write_restart>` and
+:doc:`read_restart <read_restart>` commands.
+
+----------
+
+Use of type labels in LAMMPS input or output
+""""""""""""""""""""""""""""""""""""""""""""
+
+Many LAMMPS input script commands that take a numeric type as an
+argument can use the associated type label instead.  If a type label
+is not defined for a particular numeric type, only its numeric type
+can be used.
+
+This example assigns labels to the atom types, and then uses the type
+labels to redefine the pair coefficients.
+
+.. code-block:: LAMMPS
+
+   pair_coeff 1 2 1.0 1.0              # numeric types
+   labelmap atom 1 C 2 H
+   pair_coeff C H 1.0 1.0              # type labels
+
+Adding support for type labels to various commands is an ongoing
+project.  If an input script command (or a section in a file read by a
+command) allows substituting a type label for a numeric type argument,
+it will be explicitly mentioned in that command's documentation page.
+
+As a temporary measure, input script commands can take advantage of
+variables and how they can be expanded during processing of the input.
+The variables can use functions that will translate type label strings
+to their respective number as defined in the current label map.  See the
+:doc:`variable <variable>` command for details.
+
+For example, here is how the pair_coeff command could be used with
+type labels if it did not yet support them, either with an explicit
+variable command or an implicit variable used in the pair_coeff
+command.
+
+.. code-block:: LAMMPS
+
+   labelmap atom 1 C 2 H
+   variable atom1 equal label2type(atom,C)
+   variable atom2 equal label2type(atom,H)
+   pair_coeff ${atom1} ${atom2} 1.0 1.0
+
+.. code-block:: LAMMPS
+
+   labelmap atom 1 C 2 H
+   pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
+
+----------
+
+Commands that can use label types
+"""""""""""""""""""""""""""""""""
+
+Any workflow that involves reading multiple data files, molecule
+templates or a combination of the two can be streamlined by using type
+labels instead of numeric types, because types are automatically synced
+between the files.  The creation of simulation-ready reaction templates
+for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
+type labels, and results in templates that can be used without
+modification in multiple simulations or different systems.

doc/src/Howto_viscosity.rst

@@ -68,7 +68,8 @@ liquid Ar via the GK formalism:
    # Sample LAMMPS input script for viscosity of liquid Ar
 
    units       real
-   variable    T equal 86.4956
+   variable    T equal 200.0       # run temperature
+   variable    Tinit equal 250.0   # equilibration temperature
    variable    V equal vol
    variable    dt equal 4.0
    variable    p equal 400     # correlation length
@@ -99,12 +100,14 @@ liquid Ar via the GK formalism:
 
    # equilibration and thermalization
 
-   velocity     all create $T 102486 mom yes rot yes dist gaussian
+   velocity     all create ${Tinit} 102486 mom yes rot yes dist gaussian
-   fix          NVT all nvt temp $T $T 10 drag 0.2
+   fix          NVT all nvt temp ${Tinit} ${Tinit} 10 drag 0.2
    run          8000
 
    # viscosity calculation, switch to NVE if desired
 
+   velocity     all create $T 102486 mom yes rot yes dist gaussian
+   fix          NVT all nvt temp $T $T 10 drag 0.2
    #unfix       NVT
    #fix         NVE all nve
 
@@ -122,7 +125,7 @@ liquid Ar via the GK formalism:
    run          100000
    variable     v equal (v_v11+v_v22+v_v33)/3.0
    variable     ndens equal count(all)/vol
-   print        "average viscosity: $v [Pa.s] @ $T K, ${ndens} /A^3"
+   print        "average viscosity: $v [Pa.s] @ $T K, ${ndens} atoms/A^3"
 
 The fifth method is related to the above Green-Kubo method,
 but uses the Einstein formulation, analogous to the Einstein
@@ -131,9 +134,9 @@ time-integrated momentum fluxes play the role of Cartesian
 coordinates, whose mean-square displacement increases linearly
 with time at sufficiently long times.
 
-The sixth is periodic perturbation method. It is also a non-equilibrium MD method.
+The sixth is the periodic perturbation method, which is also a non-equilibrium MD method.
-However, instead of measure the momentum flux in response of applied velocity gradient,
+However, instead of measuring the momentum flux in response to an applied velocity gradient,
-it measures the velocity profile in response of applied stress.
+it measures the velocity profile in response to applied stress.
 A cosine-shaped periodic acceleration is added to the system via the
 :doc:`fix accelerate/cos <fix_accelerate_cos>` command,
 and the :doc:`compute viscosity/cos<compute_viscosity_cos>` command is used to monitor the

doc/src/Howto_viz.rst

@@ -17,9 +17,10 @@ formats.  See the :doc:`Tools <Tools>` page for details.
 
 A Python-based toolkit distributed by our group can read native LAMMPS
 dump files, including custom dump files with additional columns of
-user-specified atom information, and convert them to various formats
+user-specified atom information, and convert them to various formats or
-or pipe them into visualization software directly.  See the `Pizza.py WWW site <pizza_>`_ for details.  Specifically, Pizza.py can convert
+pipe them into visualization software directly.  See the `Pizza.py WWW
-LAMMPS dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
+site <pizza_>`_ for details.  Specifically, Pizza.py can convert LAMMPS
+dump files into PDB, XYZ, `EnSight <ensight_>`_, and VTK formats.
 Pizza.py can pipe LAMMPS dump files directly into the Raster3d and
 RasMol visualization programs.  Pizza.py has tools that do interactive
 3d OpenGL visualization and one that creates SVG images of dump file

doc/src/Install.rst

@@ -3,10 +3,20 @@ Install LAMMPS
 
 You can download LAMMPS as an executable or as source code.
 
-With source code, you also have to :doc:`build LAMMPS <Build>`.  But you
+When downloading the LAMMPS source code, you also have to :doc:`build
-have more flexibility as to what features to include or exclude in the
+LAMMPS <Build>`.  But you have more flexibility as to what features to
-build.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
+include or exclude in the build.  When you download and install
-need the source code.
+pre-compiled LAMMPS executables, you are limited to install which
+version of LAMMPS is available and which features are included of these
+builds.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then
+you **must** build LAMMPS from the source code.
+
+.. note::
+
+   If you have questions about the pre-compiled LAMMPS executables, you
+   need to contact the people preparing those executables.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.
 
 .. toctree::
    :maxdepth: 1

doc/src/Install_conda.rst

@@ -5,7 +5,7 @@ Binaries are available for MacOS or Linux via `Conda <conda_>`_.
 
 First, one must setup the Conda package manager on your system.  Follow the
 instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
-environment (named `my-lammps-env` or whatever you prefer) for your lammps
+environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
 install:
 
 .. code-block:: bash
@@ -13,7 +13,7 @@ install:
    % conda config --add channels conda-forge
    % conda create -n my-lammps-env
 
-Then, you can install lammps on your system with the following command:
+Then, you can install LAMMPS on your system with the following command:
 
 .. code-block:: bash
 
@@ -38,3 +38,10 @@ up the Conda capability.
 .. _openkim: https://openkim.org
 .. _conda: https://docs.conda.io/en/latest/index.html
 .. _mini_conda_install: https://docs.conda.io/en/latest/miniconda.html
+
+.. note::
+
+   If you have questions about these pre-compiled LAMMPS executables,
+   you need to contact the people preparing those packages.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.

doc/src/Install_linux.rst

@@ -3,13 +3,19 @@ Download an executable for Linux
 
 Binaries are available for different versions of Linux:
 
-| :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
+- :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
-| :ref:`Pre-built Fedora Linux executables <fedora>`
+- :ref:`Pre-built Fedora Linux executables <fedora>`
-| :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
+- :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
-| :ref:`Pre-built OpenSuse Linux executables <opensuse>`
+- :ref:`Pre-built OpenSuse Linux executables <opensuse>`
-| :ref:`Gentoo Linux executable <gentoo>`
+- :ref:`Gentoo Linux executable <gentoo>`
-| :ref:`Arch Linux build-script <arch>`
+- :ref:`Arch Linux build-script <arch>`
-|
+
+.. note::
+
+   If you have questions about these pre-compiled LAMMPS executables,
+   you need to contact the people preparing those packages.  The LAMMPS
+   developers have no control over their choices of how they configure
+   and build their packages and when they update them.
 
 ----------
 
@@ -18,41 +24,28 @@ Binaries are available for different versions of Linux:
 Pre-built Ubuntu Linux executables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-A pre-built LAMMPS executable suitable for running on the latest
+A pre-built LAMMPS executable suitable for running on the latest Ubuntu
-Ubuntu Linux versions, can be downloaded as a Debian package.  This
+Linux versions, can be downloaded as a Debian package.  This allows you
-allows you to install LAMMPS with a single command, and stay
+to install LAMMPS with a single command, and stay (mostly) up-to-date
-up-to-date with the current stable version of LAMMPS by simply updating
+with the current stable version of LAMMPS by simply updating your
-your operating system.  Please note, that the repository below offers
+operating system.
-two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``.  The
-LAMMPS developers recommend to use the ``lammps-stable`` package for
-any production simulations.  The ``lammps-daily`` package is built
-from the LAMMPS development sources, and those versions may have known
-issues and bugs when new features are added and the software has not
-undergone full release testing.
-
-To install the appropriate personal-package archives (PPAs), do the
-following once:
-
-.. code-block:: bash
-
-   $ sudo add-apt-repository ppa:gladky-anton/lammps
-   $ sudo add-apt-repository ppa:openkim/latest
-   $ sudo apt-get update
 
 To install LAMMPS do the following once:
 
 .. code-block:: bash
 
-   $ sudo apt-get install lammps-stable
+   $ sudo apt-get install lammps
 
-This downloads an executable named ``lmp_stable`` to your box, which
+This downloads an executable named ``lmp`` to your box and multiple
-can then be used in the usual way to run input scripts:
+packages with supporting data, examples and libraries as well as any
+missing dependencies.  This executable can then be used in the usual way
+to run input scripts:
 
 .. code-block:: bash
 
-   $ lmp_stable -in in.lj
+   $ lmp -in in.lj
 
-To update LAMMPS to the most current stable version, do the following:
+To update LAMMPS to the latest packaged version, do the following:
 
 .. code-block:: bash
 
@@ -60,44 +53,24 @@ To update LAMMPS to the most current stable version, do the following:
 
 which will also update other packages on your system.
 
-To get a copy of the current documentation and examples:
+The ``lmp`` binary is built with the :ref:`KIM package <kim>` included,
-
+which results in the above command also installing the ``kim-api``
-.. code-block:: bash
+binaries when LAMMPS is installed.  In order to use potentials from
-
+`openkim.org <openkim_>`_, you can also install the ``openkim-models``
-   $ sudo apt-get install lammps-stable-doc
+package
-
-which will download the doc files in
-``/usr/share/doc/lammps-stable-doc/doc`` and example problems in
-``/usr/share/doc/lammps-doc/examples``.
-
-To get a copy of the current potentials files:
-
-.. code-block:: bash
-
-   $ sudo apt-get install lammps-stable-data
-
-which will download the potentials files to
-``/usr/share/lammps-stable/potentials``.  The ``lmp_stable`` binary is
-hard-coded to look for potential files in this directory (it does not
-use the ``LAMMPS_POTENTIALS`` environment variable, as described
-in :doc:`pair_coeff <pair_coeff>` command).
-
-The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which
-results in the above command also installing the ``kim-api`` binaries when LAMMPS
-is installed.  In order to use potentials from `openkim.org <openkim_>`_, you
-can install the ``openkim-models`` package
 
 .. code-block:: bash
 
    $ sudo apt-get install openkim-models
 
+Or use the KIM-API commands to download and install individual models.
 To un-install LAMMPS, do the following:
 
 .. code-block:: bash
 
-   $ sudo apt-get remove lammps-stable
+   $ sudo apt-get remove lammps
 
-Please use ``lmp_stable -help`` to see which compilation options, packages,
+Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
 
 Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this
@@ -110,21 +83,21 @@ Ubuntu package capability.
 Pre-built Fedora Linux executables
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Pre-built LAMMPS packages for stable releases are available
+Pre-built LAMMPS packages for stable releases are available in the
-in the Fedora Linux distribution as of version 28. The packages
+Fedora Linux distribution as of Fedora version 28. The packages can be
-can be installed via the dnf package manager. There are 3 basic
+installed via the dnf package manager. There are 3 basic varieties
-varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
+(lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi =
-lammps-openmpi = OpenMPI MPI library) and for each support for
+OpenMPI MPI library) and for each support for linking to the C library
-linking to the C library interface (lammps-devel, lammps-mpich-devel,
+interface (lammps-devel, lammps-mpich-devel, lammps-openmpi-devel), the
-lammps-openmpi-devel), the header for compiling programs using
+header for compiling programs using the C library interface
-the C library interface (lammps-headers), and the LAMMPS python
+(lammps-headers), and the LAMMPS python module for Python 3. All
-module for Python 3. All packages can be installed at the same
+packages can be installed at the same time and the name of the LAMMPS
-time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
+executable is ``lmp`` and ``lmp_openmpi`` or ``lmp_mpich`` respectively.
-or ``lmp_mpich`` respectively.  By default, ``lmp`` will refer to the
+By default, ``lmp`` will refer to the serial executable, unless one of
-serial executable, unless one of the MPI environment modules is loaded
+the MPI environment modules is loaded (``module load mpi/mpich-x86_64``
-(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
+or ``module load mpi/openmpi-x86_64``).  Then the corresponding parallel
-Then the corresponding parallel LAMMPS executable can be used.
+LAMMPS executable can be used.  The same mechanism applies when loading
-The same mechanism applies when loading the LAMMPS python module.
+the LAMMPS python module.
 
 To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
 
@@ -273,3 +246,10 @@ Alternatively, you may use an AUR helper to install these packages.
 
 Note that the AUR provides build-scripts that download the source and
 the build the package on your machine.
+
+.. note::
+
+   It looks like the Arch Linux AUR repository build scripts for LAMMPS
+   have not been updated since the 29 October 2020 version.  You may want
+   to consider installing a more current version of LAMMPS from source
+   directly.

doc/src/Install_windows.rst

@@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
 
 .. parsed-literal::
 
-  `http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
+  `https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for

doc/src/Intro_authors.rst

@@ -4,13 +4,13 @@ Authors of LAMMPS
 The primary LAMMPS developers are at Sandia National Labs and Temple
 University:
 
-* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
+* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
 * Aidan Thompson, athomps at sandia.gov
 * Stan Moore, stamoor at sandia.gov
 * Axel Kohlmeyer, akohlmey at gmail.com
 * Richard Berger, richard.berger at outlook.com
 
-.. _sjp: http://www.cs.sandia.gov/~sjplimp
+.. _sjp: https://sjplimp.github.io
 .. _lws: https://www.lammps.org
 
 Past developers include Paul Crozier and Mark Stevens, both at Sandia,

doc/src/Intro_citing.rst

@@ -27,15 +27,15 @@ namely https://www.lammps.org.
 The original publication describing the parallel algorithms used in the
 initial versions of LAMMPS is:
 
-  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
+  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
 
 
 DOI for the LAMMPS source code
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
+The LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
-to create digital object identifies (DOI) for stable releases of the
+to create digital object identifiers (DOI) for stable releases of the
-LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
+LAMMPS source code.  There are two types of DOIs for the LAMMPS source code.
 
 The canonical DOI for **all** versions of LAMMPS, which will always
 point to the **latest** stable release version is:

doc/src/Intro_features.rst

@@ -95,7 +95,7 @@ commands)
 * metal-organic framework potentials (QuickFF, MO-FF)
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim command <kim_commands>`
+* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :doc:`kim command <kim_commands>`
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
 
@@ -205,7 +205,7 @@ Pre- and post-processing
 
 .. _pizza: https://lammps.github.io/pizza
 
-.. _python: http://www.python.org
+.. _python: https://www.python.org
 
 .. _special:
 

doc/src/Intro_nonfeatures.rst

@@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
   linear bead-spring polymer chains.  The moltemplate program is a true
   molecular builder that will generate complex molecular models.  See
   the :doc:`Tools <Tools>` page for details on tools packaged with
-  LAMMPS.  The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
+  LAMMPS.  The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
   describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
   topology information, as well as provide the option to insert molecule
@@ -80,5 +80,5 @@ Here are suggestions on how to perform these tasks:
   `Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
   setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
   simulations.  It thus provides some functionality for several of the
-  above bullets.  Pizza.py is written in `Python <http://www.python.org>`_
+  above bullets.  Pizza.py is written in `Python <https://www.python.org>`_
-  and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
+  and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

doc/src/Intro_opensource.rst

@@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
 
-.. _gnuorg: http://www.gnu.org
+.. _gnuorg: https://www.gnu.org
 
-.. _opensource: http://www.opensource.org
+.. _opensource: https://www.opensource.org
 
 Here is a more specific summary of what the GPL means for LAMMPS users:
 

doc/src/Library_create.rst

@@ -11,6 +11,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_mpi_finalize`
 - :cpp:func:`lammps_kokkos_finalize`
 - :cpp:func:`lammps_python_finalize`
+- :cpp:func:`lammps_error`
 
 --------------------
 
@@ -115,3 +116,8 @@ calling program.
 
 .. doxygenfunction:: lammps_python_finalize
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_error
+   :project: progguide

doc/src/Library_properties.rst

@@ -15,21 +15,21 @@ This section documents the following functions:
 
 --------------------
 
-The library interface allows extraction of different kinds of
+The library interface allows the extraction of different kinds of
-information about the active simulation instance and also
+information about the active simulation instance and also - in some
-modifications to it.  This enables combining of a LAMMPS simulation
+cases - to apply modifications to it.  This enables combining of a
-with other processing and simulation methods computed by the calling
+LAMMPS simulation with other processing and simulation methods computed
-code, or by another code that is coupled to LAMMPS via the library
+by the calling code, or by another code that is coupled to LAMMPS via
-interface.  In some cases the data returned is direct reference to the
+the library interface.  In some cases the data returned is direct
-original data inside LAMMPS, cast to a void pointer.  In that case the
+reference to the original data inside LAMMPS, cast to a void pointer.
-data needs to be cast to a suitable pointer for the calling program to
+In that case the data needs to be cast to a suitable pointer for the
-access it, and you may need to know the correct dimensions and
+calling program to access it, and you may need to know the correct
-lengths.  This also means you can directly change those value(s) from
+dimensions and lengths.  This also means you can directly change those
-the calling program, e.g. to modify atom positions.  Of course, this
+value(s) from the calling program, e.g. to modify atom positions.  Of
-should be done with care.  When accessing per-atom data, please note
+course, this should be done with care.  When accessing per-atom data,
-that this data is the per-processor **local** data and is indexed
+please note that this data is the per-processor **local** data and is
-accordingly. Per-atom data can change sizes and ordering at every
+indexed accordingly. Per-atom data can change sizes and ordering at
-neighbor list rebuild or atom sort event as atoms migrate between
+every neighbor list rebuild or atom sort event as atoms migrate between
 sub-domains and processors.
 
 .. code-block:: C

doc/src/Library_utility.rst

@@ -19,6 +19,7 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_force_timeout`
 - :cpp:func:`lammps_has_error`
 - :cpp:func:`lammps_get_last_error_message`
+- :cpp:func:`lammps_python_api_version`
 
 The :cpp:func:`lammps_free` function is a clean-up function to free
 memory that the library had allocated previously via other function
@@ -100,3 +101,9 @@ where such memory buffers were allocated that require the use of
 
 .. doxygenfunction:: lammps_get_last_error_message
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_python_api_version
+   :project: progguide
+

doc/src/Manual.rst

@@ -49,12 +49,12 @@ descriptions of all commands included in the LAMMPS code.
 
 ----------
 
+.. _user_documentation:
 
 ************
 User Guide
 ************
 
-.. _user_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3
@@ -75,11 +75,12 @@ User Guide
    Errors
 
 
+.. _programmer_documentation:
+
 ******************
 Programmer Guide
 ******************
 
-.. _programmer_documentation:
 .. toctree::
    :maxdepth: 2
    :numbered: 3
@@ -110,6 +111,7 @@ Command Reference
    angles
    dihedrals
    impropers
+   dumps
    fix_modify_atc_commands
    Bibliography
 

doc/src/Modify_fix.rst

@@ -23,6 +23,8 @@ derived class.  See fix.h for details.
 +---------------------------+--------------------------------------------------------------------------------------------+
 | init                      | initialization before a run (optional)                                                     |
 +---------------------------+--------------------------------------------------------------------------------------------+
+| init_list                 | store pointer to neighbor list; called by neighbor list code (optional)                    |
++---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_exchange        | called before atom exchange in setup (optional)                                            |
 +---------------------------+--------------------------------------------------------------------------------------------+
 | setup_pre_force           | called before force computation in setup (optional)                                        |

doc/src/Modify_style.rst

@@ -100,13 +100,14 @@ Documentation (strict)
 
 Contributions that add new styles or commands or augment existing ones
 must include the corresponding new or modified documentation in
-`ReStructuredText format <rst>`_ (.rst files in the ``doc/src/`` folder). The
+`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
-documentation shall be written in American English and the .rst file
+folder). The documentation shall be written in American English and the
-must use only ASCII characters so it can be cleanly translated to PDF
+.rst file must use only ASCII characters so it can be cleanly translated
-files (via `sphinx <sphinx>`_ and PDFLaTeX).  Special characters may be included via
+to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
-embedded math expression typeset in a LaTeX subset.
+Special characters may be included via embedded math expression typeset
+in a LaTeX subset.
 
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
+.. _rst: https://www.sphinx-doc.org/en/master/usage/restructuredtext/index.html
 
 When adding new commands, they need to be integrated into the sphinx
 documentation system, and the corresponding command tables and lists
@@ -133,7 +134,7 @@ error free completion of the HTML and PDF build will be performed and
 also a spell check, a check for correct anchors and labels, and a check
 for completeness of references all styles in their corresponding tables
 and lists is run.  In case the spell check reports false positives they
-can be added to the file doc/utils/sphinx-config/false_positives.txt
+can be added to the file ``doc/utils/sphinx-config/false_positives.txt``
 
 Contributions that add or modify the library interface or "public" APIs
 from the C++ code or the Fortran module must include suitable doxygen

doc/src/Packages_details.rst

@@ -36,7 +36,7 @@ page gives those details.
    * :ref:`BPM <PKG-BPM>`
    * :ref:`BROWNIAN <PKG-BROWNIAN>`
    * :ref:`CG-DNA <PKG-CG-DNA>`
-   * :ref:`CG-SDK <PKG-CG-SDK>`
+   * :ref:`CG-SPICA <PKG-CG-SPICA>`
    * :ref:`CLASS2 <PKG-CLASS2>`
    * :ref:`COLLOID <PKG-COLLOID>`
    * :ref:`COLVARS <PKG-COLVARS>`
@@ -134,6 +134,8 @@ commands to write and read data using the ADIOS library.
 
 **Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
 
+.. versionadded:: 28Feb2019
+
 **Install:**
 
 This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
@@ -157,14 +159,28 @@ AMOEBA package
 
 **Contents:**
 
-TODO
+Implementation of the AMOEBA and HIPPO polarized force fields
+originally developed by Jay Ponder's group at the U Washington at St
+Louis.  The LAMMPS implementation is based on Fortran 90 code
+provided by the Ponder group in their
+`Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
+
+**Authors:** Josh Rackers and Steve Plimpton (Sandia), Trung Nguyen (U
+ Chicago)
 
 **Supporting info:**
 
 * src/AMOEBA: filenames -> commands
 * :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
+* :doc:`pair_style amoeba <pair_amoeba>`
+* :doc:`pair_style hippo <pair_amoeba>`
+* :doc:`atom_style amoeba <atom_style>`
+* :doc:`angle_style amoeba <angle_amoeba>`
+* :doc:`improper_style amoeba <improper_amoeba>`
+* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
+* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
+* tools/tinker/tinker2lmp.py
 * examples/amoeba
-* TODO
 
 ----------
 
@@ -200,9 +216,10 @@ ATC package
 
 **Contents:**
 
-ATC stands for atoms-to-continuum.  This package implements a :doc:`fix atc <fix_atc>` command to either couple molecular dynamics with
+ATC stands for atoms-to-continuum.  This package implements a
-continuum finite element equations or perform on-the-fly conversion of
+:doc:`fix atc <fix_atc>` command to either couple molecular dynamics
-atomic information to continuum fields.
+with continuum finite element equations or perform on-the-fly
+conversion of atomic information to continuum fields.
 
 **Authors:** Reese Jones, Jeremy Templeton, Jon Zimmerman (Sandia).
 
@@ -261,7 +278,7 @@ the barostat as outlined in:
 
 N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
 accurately describe the structure, pressure, and compressibility of
-molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+molecular liquids", J. Chem. Phys. 143, 243148 (2015).
 
 **Authors:** Nicholas J. H. Dunn and Michael R. DeLyser (The
 Pennsylvania State University)
@@ -317,6 +334,8 @@ models for mesoscale simulations of solids and fracture.  See the
 
 **Authors:** Joel T. Clemmer (Sandia National Labs)
 
+.. versionadded:: 4May2022
+
 **Supporting info:**
 
 * src/BPM filenames -> commands
@@ -347,6 +366,8 @@ and also support self-propelled particles.
 **Authors:** Sam Cameron (University of Bristol),
 Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
 
+.. versionadded:: 14May2021
+
 Example inputs are in the examples/PACKAGES/brownian folder.
 
 ----------
@@ -384,28 +405,30 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
 
 ----------
 
-.. _PKG-CG-SDK:
+.. _PKG-CG-SPICA:
 
-CG-SDK package
+CG-SPICA package
 ------------------
 
 **Contents:**
 
 Several pair styles and an angle style which implement the
-coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
+coarse-grained SPICA (formerly called SDK) model which enables
-simulation of ionic liquids, electrolytes, lipids and charged amino
+simulation of biological or soft material systems.
-acids.
 
-**Author:** Axel Kohlmeyer (Temple U).
+**Original Author:** Axel Kohlmeyer (Temple U).
+
+**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
 
 **Supporting info:**
 
-* src/CG-SDK: filenames -> commands
+* src/CG-SPICA: filenames -> commands
-* src/CG-SDK/README
+* src/CG-SPICA/README
-* :doc:`pair_style lj/sdk/\* <pair_sdk>`
+* :doc:`pair_style lj/spica/\* <pair_spica>`
-* :doc:`angle_style sdk <angle_sdk>`
+* :doc:`angle_style spica <angle_spica>`
-* examples/PACKAGES/cgsdk
+* examples/PACKAGES/cgspica
 * https://www.lammps.org/pictures.html#cg
+* https://www.spica-ff.org/
 
 ----------
 
@@ -573,6 +596,8 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
 
 **Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
 
+.. versionadded:: 2Jul2021
+
 **Supporting info:**
 
 * src/DIELECTRIC: filenames -> commands
@@ -633,7 +658,7 @@ short-range or long-range interactions.
 * :doc:`pair_style lj/cut/dipole/cut <pair_dipole>`
 * :doc:`pair_style lj/cut/dipole/long <pair_dipole>`
 * :doc:`pair_style lj/long/dipole/long <pair_dipole>`
-* :doc: `angle_style dipole <angle_dipole>`
+* :doc:`angle_style dipole <angle_dipole>`
 * examples/dipole
 
 ----------
@@ -843,6 +868,8 @@ groups of atoms that interact with the remaining atoms as electrolyte.
 Ahrens-Iwers (TUHH, Hamburg, Germany), Shern Tee (UQ, Brisbane, Australia) and
 Robert Meissner (TUHH, Hamburg, Germany).
 
+.. versionadded:: 4May2022
+
 **Install:**
 
 This package has :ref:`specific installation instructions <electrode>` on the
@@ -911,6 +938,10 @@ EXTRA-MOLECULE package
 
 Additional bond, angle, dihedral, and improper styles that are less commonly used.
 
+**Install:**
+
+To use this package, also the :ref:`MOLECULE <PKG-MOLECULE>` package needs to be installed.
+
 **Supporting info:**
 
 * src/EXTRA-MOLECULE: filenames -> commands
@@ -1046,7 +1077,7 @@ H5MD is a format for molecular simulations, built on top of HDF5.
 This package implements a :doc:`dump h5md <dump_h5md>` command to output
 LAMMPS snapshots in this format.
 
-.. _HDF5: http://www.hdfgroup.org/HDF5
+.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
 
 To use this package you must have the HDF5 library available on your
 system.
@@ -1383,7 +1414,7 @@ This package has :ref:`specific installation instructions <machdyn>` on the :doc
 
 * src/MACHDYN: filenames -> commands
 * src/MACHDYN/README
-* doc/PDF/MACHDYN_LAMMPS_userguide.pdf
+* `doc/PDF/MACHDYN_LAMMPS_userguide.pdf <PDF/MACHDYN_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/machdyn
 * https://www.lammps.org/movies.html#smd
 
@@ -1487,6 +1518,8 @@ workflows via the `MolSSI Driver Interface
 
 **Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
 
+.. versionadded:: 14May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <mdi>` on
@@ -1498,7 +1531,7 @@ the :doc:`Build extras <Build_extras>` page.
 * lib/mdi/README
 * :doc:`Howto MDI <Howto_mdi>`
 * :doc:`mdi <mdi>`
-* :doc:`fix mdi/aimd <fix_mdi_aimd>`
+* :doc:`fix mdi/qm <fix_mdi_qm>`
 * examples/PACKAGES/mdi
 
 ----------
@@ -1535,33 +1568,44 @@ MESONT package
 
 **Contents:**
 
-MESONT is a LAMMPS package for simulation of nanomechanics of
+MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
-nanotubes (NTs). The model is based on a coarse-grained representation
+(NTs). The model is based on a coarse-grained representation of NTs as
-of NTs as "flexible cylinders" consisting of a variable number of
+"flexible cylinders" consisting of a variable number of
 segments. Internal interactions within a NT and the van der Waals
 interaction between the tubes are described by a mesoscopic force field
 designed and parameterized based on the results of atomic-level
 molecular dynamics simulations. The description of the force field is
-provided in the papers listed below. This package contains two
+provided in the papers listed below.
-independent implementations of this model: :doc:`pair_style mesocnt
+
-<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
+This package contains two independent implementations of this model:
-mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
+:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
-implementation based on a Fortran library in the ``lib/mesont`` folder.
+implementation of the model based on a Fortran library in the
+``lib/mesont`` folder. The second implementation is provided by the
+mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`,
+:doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt
+<pair_mesocnt>`).  The mesocnt implementation has the same features as
+the original implementation with the addition of friction, but is
+directly implemented in C++, interfaces more cleanly with general LAMMPS
+functionality, and is typically faster. It also does not require its own
+atom style and can be installed without any external libraries.
 
 **Download of potential files:**
 
-The potential files for these pair styles are *very* large and thus
+The potential files for these pair styles are *very* large and thus are
-are not included in the regular downloaded packages of LAMMPS or the
+not included in the regular downloaded packages of LAMMPS or the git
-git repositories.  Instead, they will be automatically downloaded
+repositories.  Instead, they will be automatically downloaded from a web
-from a web server when the package is installed for the first time.
+server when the package is installed for the first time.
 
 **Authors of the *mesont* styles:**
 
-Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University of Alabama), Leonid V. Zhigilei (University of Virginia)
+Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
+of Alabama), Leonid V. Zhigilei (University of Virginia)
 
-**Author of the *mesocnt* pair style:**
+**Author of the *mesocnt* styles:**
 Philipp Kloza (U Cambridge)
 
+.. versionadded:: 15Jun2020
+
 **Supporting info:**
 
 * src/MESONT: filenames -> commands
@@ -1569,6 +1613,8 @@ Philipp Kloza (U Cambridge)
 * :doc:`atom_style mesont <atom_style>`
 * :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
 * :doc:`compute mesont <compute_mesont>`
+* :doc:`bond_style mesocnt <bond_mesocnt>`
+* :doc:`angle_style mesocnt <angle_mesocnt>`
 * :doc:`pair_style mesocnt <pair_mesocnt>`
 * examples/PACKAGES/mesont
 * tools/mesont
@@ -1652,6 +1698,8 @@ compiled on your system.
 
 **Author:** Andreas Singraber
 
+.. versionadded:: 27May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@@ -1686,6 +1734,10 @@ must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
+.. versionadded:: 30Jun2020
+
+   .. versionadded:: 30Jun2020
+
 **Supporting info:**
 
 * src/ML-IAP: filenames -> commands
@@ -1730,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
 
  ^4: University of British Columbia, Vancouver, BC, Canada
 
+.. versionadded:: 14May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-pace>` on the
@@ -1793,6 +1847,8 @@ of a neural network.
 This package was written by Christopher Barrett
 with contributions by Doyl Dickel, Mississippi State University.
 
+.. versionadded:: 27May2021
+
 **Supporting info:**
 
 * src/ML-RANN: filenames -> commands
@@ -1820,6 +1876,8 @@ computes which analyze attributes of the potential.
 * src/ML-SNAP: filenames -> commands
 * :doc:`pair_style snap <pair_snap>`
 * :doc:`compute sna/atom <compute_sna_atom>`
+* :doc:`compute sna/grid <compute_sna_atom>`
+* :doc:`compute sna/grid/local <compute_sna_atom>`
 * :doc:`compute snad/atom <compute_sna_atom>`
 * :doc:`compute snav/atom <compute_sna_atom>`
 * examples/snap
@@ -1916,7 +1974,7 @@ support for new file formats can be added to LAMMPS (or VMD or other
 programs that use them) without having to re-compile the application
 itself.  More information about the VMD molfile plugins can be found
 at
-`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
+`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
 
 **Author:** Axel Kohlmeyer (Temple U).
 
@@ -2007,7 +2065,7 @@ NETCDF package
 Dump styles for writing NetCDF formatted dump files.  NetCDF is a
 portable, binary, self-describing file format developed on top of
 HDF5. The file contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
+(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
 
 To use this package you must have the NetCDF library available on your
 system.
@@ -2018,7 +2076,7 @@ tools:
 * `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
 * `VMD <vmd-home_>`_
 
-.. _ovito: http://www.ovito.org
+.. _ovito: https://www.ovito.org
 
 .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
 
@@ -2162,6 +2220,7 @@ Foster (UTSA).
 **Supporting info:**
 
 * src/PERI: filenames -> commands
+* :doc:`Peridynamics Howto <Howto_peri>`
 * `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
 * `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
 * `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_
@@ -2226,6 +2285,8 @@ try to load the contained plugins automatically at start-up.
 
 **Authors:** Axel Kohlmeyer (Temple U)
 
+.. versionadded:: 8Apr2021
+
 **Supporting info:**
 
 * src/PLUGIN: filenames -> commands
@@ -2379,7 +2440,7 @@ A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
 the MM code in a QM/MM simulation.  This is currently only available
 in combination with the `Quantum ESPRESSO <espresso_>`_ package.
 
-.. _espresso: http://www.quantum-espresso.org
+.. _espresso: https://www.quantum-espresso.org
 
 To use this package you must have Quantum ESPRESSO (QE) available on
 your system and include its coupling library in the compilation and
@@ -2669,7 +2730,7 @@ Dynamics, Ernst Mach Institute, Germany).
 
 * src/SPH: filenames -> commands
 * src/SPH/README
-* doc/PDF/SPH_LAMMPS_userguide.pdf
+* `doc/PDF/SPH_LAMMPS_userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_
 * examples/PACKAGES/sph
 * https://www.lammps.org/movies.html#sph
 
@@ -2791,7 +2852,7 @@ collection of atoms by wrapping the `Voro++ library <voro-home_>`_.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-.. _voro-home: http://math.lbl.gov/voro++
+.. _voro-home: https://math.lbl.gov/voro++
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -2825,9 +2886,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
 `VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
 other visualization packages.
 
-.. _vtk: http://www.vtk.org
+.. _vtk: https://www.vtk.org
 
-.. _paraview: http://www.paraview.org
+.. _paraview: https://www.paraview.org
 
 To use this package you must have VTK library available on your
 system.
@@ -2864,11 +2925,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 
 .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
-.. _quickff: http://molmod.github.io/QuickFF
+.. _quickff: https://molmod.github.io/QuickFF
 .. _yaff: https://github.com/molmod/yaff
 
 **Author:** Steven Vandenbrande.
 
+.. versionadded:: 1Feb2019
+
 **Supporting info:**
 
 * src/YAFF/README

doc/src/Packages_list.rst

@@ -78,10 +78,10 @@ whether an extra library is needed to build and use the package:
      - src/CG-DNA/README
      - PACKAGES/cgdna
      - no
-   * - :ref:`CG-SDK <PKG-CG-SDK>`
+   * - :ref:`CG-SPICA <PKG-CG-SPICA>`
-     - SDK coarse-graining model
+     - SPICA (SDK) coarse-graining model
-     - :doc:`pair_style lj/sdk <pair_sdk>`
+     - :doc:`pair_style lj/spica <pair_spica>`
-     - PACKAGES/cgsdk
+     - PACKAGES/cgspica
      - no
    * - :ref:`CLASS2 <PKG-CLASS2>`
      - class 2 force fields

doc/src/Python_examples.rst

@@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the
 scripts that specifies the path and name of the executable.  See the
 AtomEye web pages for more details:
 
-* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_
+* `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
-* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
+* `http://li.mit.edu/Archive/Graphics/A3/A3.html <http://li.mit.edu/Archive/Graphics/A3/A3.html>`_
 
-.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
+The latter link is to AtomEye 3 which has the scripting capability
-
+needed by these Python scripts.
-.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html
-
-The latter link is to AtomEye 3 which has the scripting
-capability needed by these Python scripts.
 
 Note that for PyMol, you need to have built and installed the
 open-source version of PyMol in your Python, so that you can import it
 from a Python script.  See the PyMol web pages for more details:
 
- * `https://www.pymol.org <pymolhome_>`_
+ * `https://www.pymol.org <https://www.pymol.org>`_
- * `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
+ * `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
-
-.. _pymolhome: https://www.pymol.org
-
-.. _pymolopen: https://github.com/schrodinger/pymol-open-source
 
 The latter link is to the open-source version.
 

doc/src/Python_head.rst

@@ -18,17 +18,17 @@ together.
    Python_error
    Python_trouble
 
-If you are not familiar with `Python <http://www.python.org>`_, it is a
+If you are not familiar with `Python <https://www.python.org>`_, it is a
 powerful scripting and programming language which can do almost
 everything that compiled languages like C, C++, or Fortran can do in
 fewer lines of code. It also comes with a large collection of add-on
 modules for many purposes (either bundled or easily installed from
 Python code repositories).  The major drawback is slower execution speed
 of the script code compared to compiled programming languages.  But when
-the script code is interfaced to optimized compiled code, performance can
+the script code is interfaced to optimized compiled code, performance
-be on par with a standalone executable, for as long as the scripting is
+can be on par with a standalone executable, for as long as the scripting
-restricted to high-level operations.  Thus Python is also convenient to
+is restricted to high-level operations.  Thus Python is also convenient
-use as a "glue" language to "drive" a program through its library
+to use as a "glue" language to "drive" a program through its library
 interface, or to hook multiple pieces of software together, such as a
 simulation code and a visualization tool, or to run a coupled
 multi-scale or multi-physics model.

doc/src/Run_options.rst

@@ -14,6 +14,7 @@ letter abbreviation can be used:
 * :ref:`-m or -mpicolor <mpicolor>`
 * :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
+* :ref:`-nb or -nonbuf <nonbuf>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
 * :ref:`-pl or -plog <plog>`
@@ -257,6 +258,24 @@ Disable generating a citation reminder (see above) at all.
 
 ----------
 
+.. _nonbuf:
+
+**-nonbuf**
+
+Turn off buffering for screen and logfile output.  For performance
+reasons, output to the screen and logfile is usually buffered, i.e.
+output is only written to a file if its buffer - typically 4096 bytes -
+has been filled.  When LAMMPS crashes for some reason, however, that can
+mean that there is important output missing.  With this flag the
+buffering can be turned off (only for screen and logfile output) and any
+output will be committed immediately.  Note that when running in
+parallel with MPI, the screen output may still be buffered by the MPI
+library and this cannot be changed by LAMMPS.  This flag should only be
+used for debugging and not for production simulations as the performance
+impact can be significant, especially for large parallel runs.
+
+----------
+
 .. _package:
 
 **-package style args ....**
@@ -476,7 +495,7 @@ run:
    write_dump group-ID dumpstyle dumpfile arg1 arg2 ...
 
 Note that the specified restartfile and dumpfile names may contain
-wild-card characters ("\*","%") as explained on the
+wild-card characters ("\*" or "%") as explained on the
 :doc:`read_restart <read_restart>` and :doc:`write_dump <write_dump>` doc
 pages.  The use of "%" means that a parallel restart file and/or
 parallel dump file can be read and/or written.  Note that a filename

doc/src/Run_windows.rst

@@ -25,8 +25,8 @@ in parallel, follow these steps.
 
 Download and install a compatible MPI library binary package:
 
-* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
+* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
-* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
+* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the

doc/src/Speed_gpu.rst

@@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
 and unsupported on Windows):
 
 * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
-* Go to http://www.nvidia.com/object/cuda_get.html
+* Go to https://developer.nvidia.com/cuda-downloads
 * Install a driver and toolkit appropriate for your system (SDK is not necessary)
 * Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
   list supported devices and properties

doc/src/Speed_intel.rst

@@ -536,6 +536,6 @@ supported.
 References
 """"""""""
 
-* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS," in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
+* Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
-* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
+* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <https://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
 * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

doc/src/Speed_omp.rst

@@ -97,7 +97,7 @@ sub-section.
 
 A description of the multi-threading strategy used in the OPENMP
 package and some performance examples are
-`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_.
+`presented here <https://drive.google.com/file/d/1d1gLK6Ru6aPYB50Ld2tO10Li8zgPVNB8/view?usp=sharing>`_.
 
 Guidelines for best performance
 """""""""""""""""""""""""""""""

doc/src/Tools.rst

@@ -205,6 +205,7 @@ scripts are available:
    whitespace.py    # detects TAB characters and trailing whitespace
    homepage.py      # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
    errordocs.py     # detects deprecated error docs in header files
+   versiontags.py   # detects .. versionadded:: or .. versionchanged:: with pending version date
 
 The tools need to be given the main folder of the LAMMPS distribution
 or individual file names as argument and will by default check them
@@ -397,7 +398,7 @@ ipp tool
 ------------------
 
 The tools/ipp directory contains a Perl script ipp which can be used
-to facilitate the creation of a complicated file (say, a lammps input
+to facilitate the creation of a complicated file (say, a LAMMPS input
 script or tools/createatoms input file) using a template file.
 
 ipp was created and is maintained by Reese Jones (Sandia), rjones at
@@ -512,8 +513,8 @@ with an ``.inputrc`` file in the home directory.  For application
 specific customization, the LAMMPS shell uses the name "lammps-shell".
 For more information about using and customizing an application using
 readline, please see the available documentation at:
-`http://www.gnu.org/s/readline/#Documentation
+https://www.gnu.org/software/readline/
-<http://www.gnu.org/s/readline/#Documentation>`_
+
 
 Additional commands
 ^^^^^^^^^^^^^^^^^^^
@@ -715,7 +716,7 @@ See the README.pdf file for more information.
 These scripts were written by Arun Subramaniyan at Purdue Univ
 (asubrama at purdue.edu).
 
-.. _matlabhome: http://www.mathworks.com
+.. _matlabhome: https://www.mathworks.com
 
 ----------
 
@@ -1046,7 +1047,7 @@ the binary file.  This usually is a so-called little endian hardware
 SWIG interface
 --------------
 
-The `SWIG tool <http://swig.org>`_ offers a mostly automated way to
+The `SWIG tool <https://swig.org>`_ offers a mostly automated way to
 incorporate compiled code modules into scripting languages.  It
 processes the function prototypes in C and generates wrappers for a wide
 variety of scripting languages from it.  Thus it can also be applied to
@@ -1126,7 +1127,7 @@ data passed or returned as pointers are included in the ``lammps.i``
 file.  So most of the functionality of the library interface should be
 accessible.  What works and what does not depends a bit on the
 individual language for which the wrappers are built and how well SWIG
-supports those.  The `SWIG documentation <http://swig.org/doc.html>`_
+supports those.  The `SWIG documentation <https://swig.org/doc.html>`_
 has very detailed instructions and recommendations.
 
 Usage examples

doc/src/accel_styles.rst

@@ -6,7 +6,7 @@ page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
 These accelerated styles are part of the GPU, INTEL, KOKKOS,
-OPENMP and OPT packages, respectively.  They are only enabled if
+OPENMP, and OPT packages, respectively.  They are only enabled if
 LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
 You can specify the accelerated styles explicitly in your input script

doc/src/angle_amoeba.rst

@@ -41,8 +41,8 @@ length.
 
 These formulas match how the Tinker MD code performs its angle
 calculations for the AMOEBA and HIPPO force fields.  See the
-:doc:`Howto amoeba <howto_ameoba>` doc page for more information about
+:doc:`Howto amoeba <Howto_amoeba>` page for more information about
-the implemention of AMOEBA and HIPPO in LAMMPS.
+the implementation of AMOEBA and HIPPO in LAMMPS.
 
 Note that the :math:`E_a` and :math:`E_{ba}` formulas are identical to
 those used for the :doc:`angle_style class2/p6 <angle_class2>`
@@ -75,7 +75,7 @@ restart files read by the :doc:`read_data <read_data>` or
 These are the 8 coefficients for the :math:`E_a` formula:
 
 * pflag = 0 or 1
-* ublag = 0 or 1
+* ubflag = 0 or 1
 * :math:`\theta_0` (degrees)
 * :math:`K_2` (energy)
 * :math:`K_3` (energy)
@@ -87,7 +87,7 @@ A pflag value of 0 vs 1 selects between the "in-plane" and
 "out-of-plane" options described above.  Ubflag is 1 if there is a
 Urey-Bradley term associated with this angle type, else it is 0.
 :math:`\theta_0` is specified in degrees, but LAMMPS converts it to
-radians internally; hence the various :math:`K` vaues are effectively
+radians internally; hence the various :math:`K` values are effectively
 energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or
 radian\^6.
 

doc/src/angle_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    angle_coeff N args
 
-* N = angle type (see asterisk form below)
+* N = numeric angle type (see asterisk form below), or type label
 * args = coefficients for one or more angle types
 
 Examples
@@ -22,6 +22,9 @@ Examples
    angle_coeff * 5.0
    angle_coeff 2*10 5.0
 
+   labelmap angle 1 hydroxyl
+   angle_coeff hydroxyl 300.0 107.0
+
 Description
 """""""""""
 
@@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
 Angle coefficients can also be set in the data file read by the
 :doc:`read_data <read_data>` command or in a restart file.
 
-N can be specified in one of two ways.  An explicit numeric value can
+:math:`N` can be specified in one of two ways.  An explicit numeric
-be used, as in the first example above.  Or a wild-card asterisk can be
+value can be used, as in the first example above.  Or :math:`N` can be a
-used to set the coefficients for multiple angle types.  This takes the
+type label, which is an alphanumeric string defined by the
-form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
+:doc:`labelmap <labelmap>` command or in a section of a data file read
-then an asterisk with no numeric values means all types from 1 to N.  A
+by the :doc:`read_data <read_data>` command.
-leading asterisk means all types from 1 to n (inclusive).  A trailing
-asterisk means all types from n to N (inclusive).  A middle asterisk
-means all types from m to n (inclusive).
 
-Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting
+For numeric values only, a wild-card asterisk can be used to set the
-for the same angle type.  For example, these commands set the coeffs
+coefficients for multiple angle types.  This takes the form "\*" or
-for all angle types, then overwrite the coeffs for just angle type 2:
+"\*n" or "n\*" or "m\*n".  If :math:`N` is the number of angle types,
+then an asterisk with no numeric values means all types from 1 to
+:math:`N`.  A leading asterisk means all types from 1 to n (inclusive).
+A trailing asterisk means all types from n to :math:`N` (inclusive).  A
+middle asterisk means all types from m to n (inclusive).
+
+Note that using an :doc:`angle_coeff <angle_coeff>` command can
+override a previous setting for the same angle type.  For example,
+these commands set the coeffs for all angle types, then overwrite the
+coeffs for just angle type 2:
 
 .. code-block:: LAMMPS
 
@@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
    angle_coeff 2 50.0 107.0
 
 A line in a data file that specifies angle coefficients uses the exact
-same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input
+same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
-script, except that wild-card asterisks should not be used since
+command in an input script, except that wild-card asterisks should not
-coefficients for all N types must be listed in the file.  For example,
+be used since coefficients for all :math:`N` types must be listed in the
-under the "Angle Coeffs" section of a data file, the line that
+file.  For example, under the "Angle Coeffs" section of a data file, the
-corresponds to the first example above would be listed as
+line that corresponds to the first example above would be listed as
 
 .. parsed-literal::
 
@@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
 
 The :doc:`angle_style class2 <angle_class2>` is an exception to this
 rule, in that an additional argument is used in the input script to
-allow specification of the cross-term coefficients.   See its
+allow specification of the cross-term coefficients.  See its doc page
-doc page for details.
+for details.
 
 ----------
 
 The list of all angle styles defined in LAMMPS is given on the
 :doc:`angle_style <angle_style>` doc page.  They are also listed in more
-compact form on the :ref:`Commands angle <angle>` doc
+compact form on the :ref:`Commands angle <angle>` doc page.
-page.
 
 On either of those pages, click on the style to display the formula it
 computes and its coefficients as specified by the associated

doc/src/angle_mesocnt.rst

@@ -0,0 +1,146 @@
+.. index:: angle_style mesocnt
+
+angle_style mesocnt command
+===========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+   angle_coeff 1 buckling C 10 10 20.0
+   angle_coeff 4 harmonic C 8 4 10.0
+   angle_coeff 2 buckling custom 400.0 50.0 5.0
+   angle_coeff 1 harmonic custom 300.0
+
+Description
+"""""""""""
+
+.. versionadded:: 15Sep2022
+
+The *mesocnt* angle style uses the potential
+
+.. math::
+
+   E = K_\text{H} \Delta \theta^2, \qquad |\Delta \theta| < \Delta
+   \theta_\text{B} \\
+   E = K_\text{H} \Delta \theta_\text{B}^2 +
+   K_\text{B} (\Delta \theta - \Delta \theta_\text{B}), \qquad |\Delta
+   \theta| \geq \Delta \theta_\text{B}
+
+where :math:`\Delta \theta = \theta - \pi` is the bending angle of the
+nanotube, :math:`K_\text{H}` and :math:`K_\text{B}` are prefactors for
+the harmonic and linear regime respectively and :math:`\Delta
+\theta_\text{B}` is the buckling angle. Note that the usual 1/2 factor
+for the harmonic potential is included in :math:`K_\text{H}`.
+
+The style implements parameterization presets of :math:`K_\text{H}`,
+:math:`K_\text{B}` and :math:`\Delta \theta_\text{B}` for mesoscopic
+simulations of carbon nanotubes based on the atomistic simulations of
+:ref:`(Srivastava) <Srivastava_2>` and buckling considerations of
+:ref:`(Zhigilei) <Zhigilei1_1>`.
+
+The following coefficients must be defined for each angle type via the
+:doc:`angle_coeff <angle_coeff>` command as in the examples above, or
+in the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* mode = *buckling* or *harmonic*
+* preset = *C* or *custom*
+* additional parameters depending on preset
+
+If mode *harmonic* is chosen, the potential is simply harmonic and
+does not switch to the linear term when the buckling angle is
+reached. In *buckling* mode, the full piecewise potential is used.
+
+Preset *C* is for carbon nanotubes, and the additional parameters are:
+
+* chiral index :math:`n` (unitless)
+* chiral index :math:`m` (unitless)
+* :math:`r_0` (distance)
+
+Here, :math:`r_0` is the equilibrium distance of the bonds included in
+the angle, see :doc:`bond_style mesocnt <bond_mesocnt>`.
+
+In harmonic mode with preset *custom*, the additional parameter is:
+
+* :math:`K_\text{H}` (energy)
+
+Hence, this setting is simply a wrapper for :doc:`bond_style harmonic
+<bond_harmonic>` with an equilibrium angle of 180 degrees.
+
+In harmonic mode with preset *custom*, the additional parameters are:
+
+* :math:`K_\text{H}` (energy)
+* :math:`K_\text{B}` (energy)
+* :math:`\Delta \theta_\text{B}` (degrees)
+
+:math:`\Delta \theta_\text{B}` is specified in degrees, but LAMMPS
+converts it to radians internally; hence :math:`K_\text{H}` is
+effectively energy per radian\^2 and :math:`K_\text{B}` is energy per
+radian.
+
+----------
+
+In *buckling* mode, this angle style adds the *buckled* property to
+all atoms in the simulation, which is an integer flag indicating
+whether the bending angle at a given atom has exceeded :math:`\Delta
+\theta_\text{B}`. It can be accessed as an atomic variable, e.g. for
+custom dump commands, as *i_buckled*.
+
+.. note::
+
+   If the initial state of the simulation contains buckled nanotubes
+   and :doc:`pair_style mesocnt <pair_mesocnt>` is used, the
+   *i_buckled* atomic variable needs to be initialized before the
+   pair_style is defined by doing a *run 0* command straight after the
+   angle_style command. See below for an example.
+
+If CNTs are already buckled at the start of the simulation, this
+script will correctly initialize *i_buckled*:
+
+.. code-block:: LAMMPS
+
+   angle_style mesocnt
+   angle_coeff 1 buckling C 10 10 20.0
+
+   run 0
+
+   pair_style mesocnt 60.0
+   pair_coeff * * C_10_10.mesocnt 1
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the
+MOLECULE and MESONT packages.  See the :doc:`Build package
+<Build_package>` doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Srivastava_2:
+
+**(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417
+(2005).
+
+.. _Zhigilei1_1:
+
+**(Zhigilei)** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

doc/src/angle_spica.rst

@@ -1,32 +1,32 @@
-.. index:: angle_style sdk
+.. index:: angle_style spica
-.. index:: angle_style sdk/omp
+.. index:: angle_style spica/omp
 
-angle_style sdk command
+angle_style spica command
-=======================
+=========================
 
-Accelerator Variants: *sdk/omp*
+Accelerator Variants: *spica/omp*
 
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   angle_style sdk
+   angle_style spica
 
-   angle_style sdk/omp
+   angle_style spica/omp
 
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
-   angle_style sdk
+   angle_style spica
    angle_coeff 1 300.0 107.0
 
 Description
 """""""""""
 
-The *sdk* angle style is a combination of the harmonic angle potential,
+The *spica* angle style is a combination of the harmonic angle potential,
 
 .. math::
 
@@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
 
 where :math:`\theta_0` is the equilibrium value of the angle and
 :math:`K` a prefactor, with the *repulsive* part of the non-bonded
-*lj/sdk* pair style between the atoms 1 and 3.  This angle potential is
+*lj/spica* pair style between the atoms 1 and 3.  This angle potential is
-intended for coarse grained MD simulations with the CMM parameterization
+intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
-using the :doc:`pair_style lj/sdk <pair_sdk>`.  Relative to the
+using the :doc:`pair_style lj/spica <pair_spica>`.  Relative to the
-pair_style *lj/sdk*, however, the energy is shifted by
+pair_style *lj/spica*, however, the energy is shifted by
 :math:`\epsilon`, to avoid sudden jumps.  Note that the usual 1/2 factor
 is included in :math:`K`.
 
@@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
 radians internally; hence :math:`K` is effectively energy per
 radian\^2.
 
-The required *lj/sdk* parameters are extracted automatically from the
+The required *lj/spica* parameters are extracted automatically from the
 pair_style.
 
+Style *sdk*, the original implementation of style *spica*, is available
+for backward compatibility.
+
 ----------
 
 .. include:: accel_styles.rst
@@ -64,14 +67,14 @@ Restrictions
 """"""""""""
 
 This angle style can only be used if LAMMPS was built with the
-CG-SDK package.  See the :doc:`Build package <Build_package>` doc
+CG-SPICA package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
+:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
-:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
+:doc:`pair_style lj/spica/coul/long <pair_spica>`
 
 Default
 """""""

doc/src/angle_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    angle_style style
 
-* style = *none* or *hybrid* or *charmm* or *class2* or *cosine* or         *cosine/squared* or *harmonic*
+* style = *none* or *zero* or *hybrid* or *amoeba* or *charmm* or *class2* or *class2/p6* or *cosine* or *cosine/buck6d* or *cosine/delta* or *cosine/periodic* or *cosine/shift* or *cosine/shift/exp* or *cosine/squared* or *cross* or *dipole* or *fourier* or *fourier/simple* or *gaussian* or *harmonic* or *mm3* or *quartic* or *spica* or *table*
 
 Examples
 """"""""
@@ -90,9 +90,10 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
 * :doc:`gaussian <angle_gaussian>` - multi-centered Gaussian-based angle potential
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
+* :doc:`mesocnt <angle_mesocnt>` - piecewise harmonic and linear angle for bending-buckling of nanotubes
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
-* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
+* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
 * :doc:`table <angle_table>` - tabulated by angle
 
 ----------