Merge pull request #3446 from akohlmey/next-patch-release

Update versions strings for the next patch release

.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/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/codeql-analysis.yml

@@ -5,12 +5,19 @@ on:
   push:
     branches: [develop]
 
+  workflow_dispatch:
+
 jobs:
   analyze:
     name: Analyze
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: ubuntu-latest
 
+    permissions:
+      security-events: write
+      actions: read
+      contents: read
+
     strategy:
       fail-fast: false
       matrix:
@@ -18,17 +25,17 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Setup Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
 
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v1
+      uses: github/codeql-action/init@v2
       with:
         languages: ${{ matrix.language }}
         config-file: ./.github/codeql/${{ matrix.language }}.yml
@@ -46,4 +53,4 @@ jobs:
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v1
+      uses: github/codeql-action/analyze@v2

.github/workflows/compile-msvc.yml

@@ -3,7 +3,13 @@ name: "Native Windows Compilation and Unit Tests"
 
 on:
   push:
-    branches: [develop]
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+  workflow_dispatch:
 
 jobs:
   build:
@@ -13,12 +19,12 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
     - name: Select Python version
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.10'
 

.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 +3,13 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches: [develop]
+    branches:
+      - develop
+  pull_request:
+    branches:
+      - develop
+
+  workflow_dispatch:
 
 jobs:
   build:
@@ -15,7 +21,7 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         fetch-depth: 2
 
@@ -26,7 +32,7 @@ jobs:
       run: mkdir build
 
     - name: Set up ccache
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{ env.CCACHE_DIR }}
         key: macos-ccache-${{ github.sha }}
@@ -37,6 +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"

cmake/CMakeLists.jpeg

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

cmake/CMakeLists.png

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

cmake/CMakeLists.txt

@@ -107,7 +107,7 @@ endif()
 
 # silence excessive warnings for new Intel Compilers
 if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
-  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare")
+  set(CMAKE_TUNE_DEFAULT "-Wno-tautological-constant-compare -Wno-unused-command-line-argument")
 endif()
 
 # silence excessive warnings for PGI/NVHPC compilers
@@ -116,7 +116,7 @@ if((CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "
 endif()
 
 # silence nvcc warnings
-if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA))
+if((PKG_KOKKOS) AND (Kokkos_ENABLE_CUDA) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "Clang"))
   set(CMAKE_TUNE_DEFAULT "${CMAKE_TUNE_DEFAULT} -Xcudafe --diag_suppress=unrecognized_pragma")
 endif()
 
@@ -135,9 +135,12 @@ 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)
-  add_compile_options(/Zc:__cplusplus)
-  add_compile_options(/wd4244)
-  add_compile_options(/wd4267)
+  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)
+    add_compile_options(/EHsc)
+  endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
@@ -149,6 +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)
@@ -161,10 +177,12 @@ option(CMAKE_POSITION_INDEPENDENT_CODE "Create object compatible with shared lib
 option(BUILD_TOOLS "Build and install LAMMPS tools (msi2lmp, binary2txt, chain)" OFF)
 option(BUILD_LAMMPS_SHELL "Build and install the LAMMPS shell" OFF)
 
-# allow enabling clang-tidy for C++ files
+# Support using clang-tidy for C++ files with selected options
 set(ENABLE_CLANG_TIDY OFF CACHE BOOL "Include clang-tidy processing when compiling")
 if(ENABLE_CLANG_TIDY)
-  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=*-header-filter=.*" CACHE STRING "")
+  set(CMAKE_CXX_CLANG_TIDY "clang-tidy;-checks=-*,performance-trivially-destructible,performance-unnecessary-copy-initialization,performance-unnecessary-value-param,readability-redundant-control-flow,readability-redundant-declaration,readability-redundant-function-ptr-dereference,readability-redundant-member-init,readability-redundant-string-cstr,readability-redundant-string-init,readability-simplify-boolean-expr,readability-static-accessed-through-instance,readability-static-definition-in-anonymous-namespace,modernize-use-override,modernize-use-bool-literals,modernize-use-emplace,modernize-return-braced-init-list,modernize-use-equals-default,modernize-use-equals-delete,modernize-replace-random-shuffle,modernize-deprecated-headers,modernize-use-nullptr,modernize-use-noexcept,modernize-redundant-void-arg;-fix;-header-filter=.*,header-filter=library.h,header-filter=fmt/*.h" CACHE STRING "clang-tidy settings")
+else()
+  unset(CMAKE_CXX_CLANG_TIDY CACHE)
 endif()
 
 include(GNUInstallDirs)
@@ -187,6 +205,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES
   ADIOS
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -195,7 +214,7 @@ set(STANDARD_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -328,7 +347,9 @@ string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
 target_compile_definitions(lammps PUBLIC -DLAMMPS_${LAMMPS_SIZES})
 
 # posix_memalign is not available on Windows
-if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+# with INTEL package and Intel compilers we use TBB's aligned malloc
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows")
+   AND NOT (PKG_INTEL AND ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))))
   set(LAMMPS_MEMALIGN "0" CACHE STRING "posix_memalign() is not available on Windows" FORCE)
 else()
   set(LAMMPS_MEMALIGN "64" CACHE STRING "enables the use of the posix_memalign() call instead of malloc() when large chunks or memory are allocated by LAMMPS. Set to 0 to disable")
@@ -349,11 +370,13 @@ pkg_depends(MPIIO MPI)
 pkg_depends(ATC MANYBODY)
 pkg_depends(LATBOLTZ MPI)
 pkg_depends(SCAFACOS MPI)
+pkg_depends(AMOEBA KSPACE)
 pkg_depends(DIELECTRIC KSPACE)
 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)
@@ -393,9 +416,11 @@ 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)
-  find_package(BLAS)
-  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+  if (NOT USE_INTERNAL_LINALG)
+    find_package(LAPACK)
+    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")
@@ -624,7 +649,7 @@ 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()
@@ -771,20 +796,26 @@ 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)
-    set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/$<CONFIG>/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(MY_BUILD_DIR ${CMAKE_BINARY_DIR}/$<CONFIG>)
   else()
-    set(LIBLAMMPS_SHARED_BINARY ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
+    set(MY_BUILD_DIR ${CMAKE_BINARY_DIR})
   endif()
+  set(LIBLAMMPS_SHARED_BINARY ${MY_BUILD_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX})
   if(Python_EXECUTABLE)
     add_custom_target(
       install-python ${CMAKE_COMMAND} -E remove_directory build
-      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps -l ${LIBLAMMPS_SHARED_BINARY}
+      COMMAND ${Python_EXECUTABLE} ${LAMMPS_PYTHON_DIR}/install.py -p ${LAMMPS_PYTHON_DIR}/lammps
+              -l ${LIBLAMMPS_SHARED_BINARY} -w ${MY_BUILD_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()
     add_custom_target(
@@ -804,11 +835,17 @@ 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)
@@ -947,6 +984,12 @@ if(PKG_KSPACE)
       else()
         message(STATUS "Kokkos FFT: cuFFT")
       endif()
+    elseif(Kokkos_ENABLE_HIP)
+      if(FFT STREQUAL "KISS")
+        message(STATUS "Kokkos FFT: KISS")
+      else()
+        message(STATUS "Kokkos FFT: hipFFT")
+      endif()
     else()
       message(STATUS "Kokkos FFT: ${FFT}")
     endif()

cmake/CMakeLists.zlib

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

cmake/CMakeSettings.json

@@ -8,7 +8,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "msvc_x64_x64" ],
       "variables": [
         {
@@ -26,11 +26,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -46,7 +41,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "msvc_x64_x64" ],
       "variables": [
         {
@@ -64,11 +59,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -102,11 +92,6 @@
           "value": "True",
           "type": "BOOL"
         },
-        {
-          "name": "PKG_PYTHON",
-          "value": "True",
-          "type": "BOOL"
-        },
         {
           "name": "ENABLE_TESTING",
           "value": "True",
@@ -122,7 +107,7 @@
       "installRoot": "${workspaceRoot}\\install\\${name}",
       "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
       "buildCommandArgs": "",
-      "ctestCommandArgs": "",
+      "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "clang_cl_x64" ],
       "variables": [
         {
@@ -141,7 +126,40 @@
           "type": "BOOL"
         },
         {
-          "name": "PKG_PYTHON",
+          "name": "ENABLE_TESTING",
+          "value": "True",
+          "type": "BOOL"
+        }
+      ]
+    },
+    {
+      "name": "x64-Debug-IntelLLVM",
+      "generator": "Ninja",
+      "configurationType": "Debug",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
           "value": "True",
           "type": "BOOL"
         },
@@ -149,8 +167,142 @@
           "name": "ENABLE_TESTING",
           "value": "True",
           "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Release-IntelLLVM",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-llvm.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Debug-Intel-Classic",
+      "generator": "Ninja",
+      "configurationType": "Debug",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
+        }
+      ]
+    },
+    {
+      "name": "x64-Release-Intel-Classic",
+      "generator": "Ninja",
+      "configurationType": "Release",
+      "buildRoot": "${workspaceRoot}\\build\\${name}",
+      "installRoot": "${workspaceRoot}\\install\\${name}",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows-intel-classic.cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
+      "buildCommandArgs": "",
+      "ctestCommandArgs": "-V",
+      "inheritEnvironments": [],
+      "variables": [
+        {
+          "name": "PKG_ELECTRODE",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_SHARED_LIBS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "BUILD_TOOLS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "LAMMPS_EXCEPTIONS",
+          "value": "True",
+          "type": "BOOL"
+        },
+        {
+          "name": "ENABLE_TESTING",
+          "value": "False",
+          "type": "BOOL"
+        },
+        {
+          "name": "FFT",
+          "value": "MKL",
+          "type": "STRING"
         }
       ]
     }
   ]
-}
+}

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -0,0 +1,208 @@
+# CMake script code to define LAMMPS settings required for building LAMMPS plugins
+
+# enforce out-of-source build
+if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+  message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
+    "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)
+  message(FATAL_ERROR "Must set LAMMPS_SOURCE_DIR")
+endif()
+
+# by default, install into $HOME/.local (not /usr/local),
+# so that no root access (and sudo) is needed
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# 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")
+    add_compile_options(/Zc:__cplusplus)
+    add_compile_options(/wd4244)
+    add_compile_options(/wd4267)
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
+  endif()
+  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
+endif()
+
+# C++11 is required
+set(CMAKE_CXX_STANDARD 11)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+# Need -restrict with Intel compilers
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+endif()
+set(CMAKE_POSITION_INDEPENDENT_CODE TRUE)
+
+#######
+# helper functions from LAMMPSUtils.cmake
+function(validate_option name values)
+  string(TOLOWER ${${name}} needle_lower)
+  string(TOUPPER ${${name}} needle_upper)
+  list(FIND ${values} ${needle_lower} IDX_LOWER)
+  list(FIND ${values} ${needle_upper} IDX_UPPER)
+  if(${IDX_LOWER} LESS 0 AND ${IDX_UPPER} LESS 0)
+    list_to_bulletpoints(POSSIBLE_VALUE_LIST ${${values}})
+    message(FATAL_ERROR "\n########################################################################\n"
+      "Invalid value '${${name}}' for option ${name}\n"
+      "\n"
+      "Possible values are:\n"
+      "${POSSIBLE_VALUE_LIST}"
+      "########################################################################")
+  endif()
+endfunction(validate_option)
+
+# helper function for getting the most recently modified file or folder from a glob pattern
+function(get_newest_file path variable)
+  file(GLOB _dirs ${path})
+  set(_besttime 2000-01-01T00:00:00)
+  set(_bestfile "<unknown>")
+  foreach(_dir ${_dirs})
+    file(TIMESTAMP ${_dir} _newtime)
+    if(_newtime IS_NEWER_THAN _besttime)
+      set(_bestfile ${_dir})
+      set(_besttime ${_newtime})
+    endif()
+  endforeach()
+  if(_bestfile STREQUAL "<unknown>")
+    message(FATAL_ERROR "Could not find valid path at: ${path}")
+  endif()
+  set(${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)
+target_include_directories(lammps INTERFACE ${LAMMPS_SOURCE_DIR})
+if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+  target_link_libraries(lammps INTERFACE ${CMAKE_BINARY_DIR}/../liblammps.dll.a)
+endif()
+
+################################################################################
+# MPI configuration
+if(NOT CMAKE_CROSSCOMPILING)
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  find_package(MPI QUIET)
+  option(BUILD_MPI "Build MPI version" ${MPI_FOUND})
+else()
+  option(BUILD_MPI "Build MPI version" OFF)
+endif()
+
+if(BUILD_MPI)
+  # do not include the (obsolete) MPI C++ bindings which makes
+  # for leaner object files and avoids namespace conflicts
+  set(MPI_CXX_SKIP_MPICXX TRUE)
+  # We use a non-standard procedure to cross-compile with MPI on Windows
+  if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
+    # Download and configure custom MPICH files for Windows
+    message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
+    set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
+    set(MPICH2_WIN32_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win32-devel.tar.gz" CACHE STRING "URL for MPICH2 (win32) tarball")
+    set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
+    set(MPICH2_WIN32_DEVEL_MD5 "a61d153500dce44e21b755ee7257e031" CACHE STRING "MD5 checksum of MPICH2 (win32) tarball")
+    mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
+    mark_as_advanced(MPICH2_WIN32_DEVEL_URL)
+    mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+    mark_as_advanced(MPICH2_WIN32_DEVEL_MD5)
+
+    include(ExternalProject)
+    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN64_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+    else()
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN32_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN32_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
+    endif()
+
+    ExternalProject_get_property(mpi4win_build SOURCE_DIR)
+    file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
+    add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
+    set_target_properties(MPI::MPI_CXX PROPERTIES
+      IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmpi.a"
+      INTERFACE_INCLUDE_DIRECTORIES "${SOURCE_DIR}/include"
+      INTERFACE_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    add_dependencies(MPI::MPI_CXX mpi4win_build)
+
+    # set variables for status reporting at the end of CMake run
+    set(MPI_CXX_INCLUDE_PATH "${SOURCE_DIR}/include")
+    set(MPI_CXX_COMPILE_DEFINITIONS "MPICH_SKIP_MPICXX")
+    set(MPI_CXX_LIBRARIES "${SOURCE_DIR}/lib/libmpi.a")
+  else()
+    find_package(MPI REQUIRED)
+    option(LAMMPS_LONGLONG_TO_LONG "Workaround if your system or MPI version does not recognize 'long long' data types" OFF)
+    if(LAMMPS_LONGLONG_TO_LONG)
+      target_compile_definitions(lammps INTERFACE -DLAMMPS_LONGLONG_TO_LONG)
+    endif()
+  endif()
+  target_link_libraries(lammps INTERFACE MPI::MPI_CXX)
+else()
+  add_library(mpi_stubs INTERFACE)
+  target_include_directories(mpi_stubs INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
+  target_link_libraries(lammps INTERFACE mpi_stubs)
+endif()
+
+################################################################################
+# detect if we may enable OpenMP support by default
+set(BUILD_OMP_DEFAULT OFF)
+find_package(OpenMP QUIET)
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(HAVE_OMP_H_INCLUDE)
+    set(BUILD_OMP_DEFAULT ON)
+  endif()
+endif()
+
+option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
+
+if(BUILD_OMP)
+  find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  if(NOT HAVE_OMP_H_INCLUDE)
+    message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
+  endif()
+
+  if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
+      ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
+    # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
+    # Intel 18.0 was tested to support both, so we switch to OpenMP 4+ from 19.x onward to be safe.
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=4)
+  else()
+    target_compile_definitions(lammps INTERFACE -DLAMMPS_OMP_COMPAT=3)
+  endif()
+  target_link_libraries(lammps INTERFACE OpenMP::OpenMP_CXX)
+endif()
+
+################
+# integer size selection
+set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
+set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
+set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
+validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
+string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
+target_compile_definitions(lammps INTERFACE -DLAMMPS_${LAMMPS_SIZES})

cmake/Modules/LAMMPSUtils.cmake

@@ -24,6 +24,24 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+# helper function for getting the most recently modified file or folder from a glob pattern
+function(get_newest_file path variable)
+  file(GLOB _dirs ${path})
+  set(_besttime 2000-01-01T00:00:00)
+  set(_bestfile "<unknown>")
+  foreach(_dir ${_dirs})
+    file(TIMESTAMP ${_dir} _newtime)
+    if(_newtime IS_NEWER_THAN _besttime)
+      set(_bestfile ${_dir})
+      set(_besttime ${_newtime})
+    endif()
+  endforeach()
+  if(_bestfile STREQUAL "<unknown>")
+    message(FATAL_ERROR "Could not find valid path at: ${path}")
+  endif()
+  set(${variable} ${_bestfile} PARENT_SCOPE)
+endfunction()
+
 function(get_lammps_version version_header variable)
     file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
@@ -92,14 +110,16 @@ function(FetchPotentials pkgfolder potfolder)
       math(EXPR plusone "${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 ${LAMMPS_POTENTIALS_URL}")
-        file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}"
+        message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
+        string(MD5 TMP_EXT "${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

@@ -233,7 +233,8 @@ 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()
@@ -261,6 +262,8 @@ 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)")
@@ -340,7 +343,14 @@ 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/INTEL.cmake

@@ -38,7 +38,7 @@ if(INTEL_LRT_MODE STREQUAL "C++11")
   endif()
 endif()
 
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
   if(CMAKE_CXX_COMPILER_VERSION VERSION_LESS 16)
     message(FATAL_ERROR "INTEL needs at least a 2016 Intel compiler, found ${CMAKE_CXX_COMPILER_VERSION}")
   endif()
@@ -46,12 +46,12 @@ else()
   message(WARNING "INTEL gives best performance with Intel compilers")
 endif()
 
-find_package(TBB_MALLOC QUIET)
+find_package(TBB_MALLOC)
 if(TBB_MALLOC_FOUND)
   target_link_libraries(lammps PRIVATE TBB::TBB_MALLOC)
 else()
   target_compile_definitions(lammps PRIVATE -DLMP_INTEL_NO_TBB)
-  if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
     message(WARNING "INTEL with Intel compilers should use TBB malloc libraries")
   endif()
 endif()

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/3.5.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "079323d973ae0e1c38c0a54a150c674e" CACHE STRING "MD5 checksum of 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 "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 3.5.00 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()
@@ -130,6 +130,11 @@ if(PKG_KSPACE)
       target_compile_definitions(lammps PRIVATE -DFFT_CUFFT)
       target_link_libraries(lammps PRIVATE cufft)
     endif()
+  elseif(Kokkos_ENABLE_HIP)
+    if(NOT (FFT STREQUAL "KISS"))
+      target_compile_definitions(lammps PRIVATE -DFFT_HIPFFT)
+      target_link_libraries(lammps PRIVATE hipfft)
+    endif()
   endif()
 endif()
 

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))
-    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1) AND NOT USE_INTERNAL_LINALG)
+    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation. "
+                        "Try to configure LAMMPS with '-D USE_INTERNAL_LINALG=on' added as a workaround.")
   endif()
 
   include(ExternalProject)

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_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" 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()
@@ -44,15 +57,17 @@ 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=${CMAKE_BUILD_TYPE}
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+    -DCMAKE_POSITION_INDEPENDENT_CODE=ON
     -Dlanguage=C
     -Dlibtype=STATIC
     -Dmpi=${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-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
@@ -13,8 +13,12 @@ execute_process(
   COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
+get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
+# enforce building libyaml-cpp as static library and turn off optional features
+set(YAML_BUILD_SHARED_LIBS OFF)
+set(YAML_CPP_BUILD_CONTRIB OFF)
+set(YAML_CPP_BUILD_TOOLS OFF)
 add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
 set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
 
@@ -28,5 +32,6 @@ target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_
 
 
 target_link_libraries(pace PRIVATE yaml-cpp-pace)
-
-target_link_libraries(lammps PRIVATE pace)
+if(CMAKE_PROJECT_NAME STREQUAL "lammps")
+  target_link_libraries(lammps PRIVATE pace)
+endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -43,6 +43,7 @@ if(DOWNLOAD_QUIP)
   file(WRITE ${CMAKE_BINARY_DIR}/quip.config "${temp}")
 
   message(STATUS "QUIP download via git requested - we will build our own")
+  set(CMAKE_EP_GIT_REMOTE_UPDATE_STRATEGY CHECKOUT)
   # QUIP has no releases (except for a tag marking the end of Python 2 support). We use the current "public" branch
   # The LAMMPS interface wrapper has a compatibility constant that is being checked at runtime.
   include(ExternalProject)

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/Modules/Tools.cmake

@@ -3,6 +3,9 @@ if(BUILD_TOOLS)
   target_compile_definitions(binary2txt PRIVATE -DLAMMPS_${LAMMPS_SIZES})
   install(TARGETS binary2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
 
+  add_executable(stl_bin2txt ${LAMMPS_TOOLS_DIR}/stl_bin2txt.cpp)
+  install(TARGETS stl_bin2txt DESTINATION ${CMAKE_INSTALL_BINDIR})
+
   include(CheckGeneratorSupport)
   if(CMAKE_GENERATOR_SUPPORT_FORTRAN)
     include(CheckLanguage)

cmake/Modules/generate_lmpgitversion.cmake

@@ -31,5 +31,7 @@ set(temp "${temp}const char *LAMMPS_NS::LAMMPS::git_descriptor() { return \"${te
 set(temp "${temp}#endif\n\n")
 
 message(STATUS "Generating lmpgitversion.h...")
-file(WRITE "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${temp}" )
-execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h.tmp" "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
+
+string(REPLACE "\\ " " " LAMMPS_GIT_HEADER "${LAMMPS_STYLE_HEADERS_DIR}/lmpgitversion.h")
+file(WRITE "${LAMMPS_GIT_HEADER}.tmp" "${temp}" )
+execute_process(COMMAND ${CMAKE_COMMAND} -E copy_if_different "${LAMMPS_GIT_HEADER}.tmp" "${LAMMPS_GIT_HEADER}")

cmake/presets/all_off.cmake

@@ -3,6 +3,7 @@
 
 set(ALL_PACKAGES
   ADIOS
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -11,7 +12,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/all_on.cmake

@@ -5,6 +5,7 @@
 
 set(ALL_PACKAGES
   ADIOS
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -13,7 +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_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -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 ${FC_STD_VERSION}" 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/kokkos-cuda.cmake

@@ -3,7 +3,9 @@
 # that is compatible with all higher CC, but not the default CC 3.5
 set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
-set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_PASCAL60 ON CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-hip.cmake

@@ -0,0 +1,20 @@
+# preset that enables KOKKOS and selects HIP compilation with OpenMP
+# enabled as well. Also sets some performance related compiler flags.
+set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_SERIAL ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_OPENMP ON CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_HIP    ON CACHE BOOL "" FORCE)
+set(Kokkos_ARCH_VEGA90A on CACHE BOOL "" FORCE)
+set(Kokkos_ENABLE_HIP_MULTIPLE_KERNEL_INSTANTIATIONS ON CACHE BOOL "" FORCE)
+set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+set(CMAKE_CXX_COMPILER hipcc CACHE STRING "" FORCE)
+set(CMAKE_TUNE_FLAGS "-munsafe-fp-atomics" CACHE STRING "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+
+# these flags are needed to build with Cray MPICH on OLCF Crusher
+#-D CMAKE_CXX_FLAGS="-I/${MPICH_DIR}/include"
+#-D MPI_CXX_LIBRARIES="-L${MPICH_DIR}/lib -lmpi -L${CRAY_MPICH_ROOTDIR}/gtl/lib -lmpi_gtl_hsa"

cmake/presets/kokkos-openmp.cmake

@@ -4,3 +4,6 @@ set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_OPENMP ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-serial.cmake

@@ -3,3 +3,6 @@ set(PKG_KOKKOS ON CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_SERIAL ON  CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_OPENMP OFF CACHE BOOL "" FORCE)
 set(Kokkos_ENABLE_CUDA   OFF CACHE BOOL "" FORCE)
+
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)

cmake/presets/kokkos-sycl.cmake

@@ -8,6 +8,9 @@ set(Kokkos_ENABLE_SYCL   ON CACHE BOOL "" FORCE)
 set(Kokkos_ARCH_MAXWELL50 on CACHE BOOL "" FORCE)
 set(BUILD_OMP ON CACHE BOOL "" FORCE)
 
+# hide deprecation warnings temporarily for stable release
+set(Kokkos_ENABLE_DEPRECATION_WARNINGS OFF CACHE BOOL "" FORCE)
+
 set(CMAKE_CXX_COMPILER clang++ CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 set(CMAKE_CXX_STANDARD 17 CACHE STRING "" FORCE)

cmake/presets/mingw-cross.cmake

@@ -1,4 +1,5 @@
 set(WIN_PACKAGES
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -7,7 +8,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -46,8 +47,8 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
-  ML-SNAP
   ML-RANN
+  ML-SNAP
   MOFFF
   MOLECULE
   MOLFILE
@@ -56,6 +57,7 @@ set(WIN_PACKAGES
   ORIENT
   PERI
   PHONON
+  PLUGIN
   POEMS
   PTM
   QEQ

cmake/presets/most.cmake

@@ -3,13 +3,14 @@
 # are removed. The resulting binary should be able to run most inputs.
 
 set(ALL_PACKAGES
+  AMOEBA
   ASPHERE
   BOCS
   BODY
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/windows-intel-classic.cmake

@@ -0,0 +1,8 @@
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icl" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icl" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifort" CACHE STRING "" FORCE)
+
+unset(HAVE_OMP_H_INCLUDE CACHE)
+

cmake/presets/windows-intel-llvm.cmake

@@ -0,0 +1,8 @@
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icx" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(INTEL_LRT_MODE "C++11" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+set(CMAKE_TUNE_FLAGS -Wno-unused-command-line-argument)

cmake/presets/windows.cmake

@@ -1,11 +1,12 @@
 set(WIN_PACKAGES
+  AMOEBA
   ASPHERE
   BOCS
   BODY
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -43,6 +44,7 @@ set(WIN_PACKAGES
   PERI
   PHONON
   POEMS
+  PLUGIN
   PTM
   QEQ
   QTB

doc/Makefile

@@ -13,6 +13,7 @@ VENV           = $(BUILDDIR)/docenv
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
+MATHJAXTAG     = 3.2.2
 
 PYTHON         = $(word 3,$(shell type python3))
 DOXYGEN        = $(word 3,$(shell type doxygen))
@@ -230,17 +231,17 @@ $(VENV):
 		$(PYTHON) -m venv $(VENV); \
 		. $(VENV)/bin/activate; \
 		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install --upgrade wheel; \
 		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
+	@git clone -b $(MATHJAXTAG) -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
 
 $(ANCHORCHECK): $(VENV)
 	@( \
 		. $(VENV)/bin/activate; \
-		(cd utils/converters;\
-		python setup.py develop);\
+		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "4 May 2022" "2022-5-4"
+.TH LAMMPS "1" "15 September 2022" "2022-9-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 24 March 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

@@ -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_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
 ^^^^^^^^^^^^^^^^
 
@@ -641,14 +660,27 @@ This list was last updated for version 3.5.0 of the Kokkos library.
 
          -D CMAKE_CXX_COMPILER=${HOME}/lammps/lib/kokkos/bin/nvcc_wrapper
 
-      To simplify compilation, four preset files are included in the
+      For AMD or NVIDIA GPUs using HIP, set these variables:
+
+      .. code-block:: bash
+
+         -D Kokkos_ARCH_HOSTARCH=yes   # HOSTARCH = HOST from list above
+         -D Kokkos_ARCH_GPUARCH=yes    # GPUARCH = GPU from list above
+         -D Kokkos_ENABLE_HIP=yes
+         -D Kokkos_ENABLE_OPENMP=yes
+
+      This will enable FFTs on the GPU, either by the internal KISSFFT library
+      or with the hipFFT wrapper library, which will call out to the
+      platform-appropriate vendor library: rocFFT on AMD GPUs or cuFFT on
+      NVIDIA GPUs.
+
+      To simplify compilation, five preset files are included in the
       ``cmake/presets`` folder, ``kokkos-serial.cmake``,
-      ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``, and
-      ``kokkos-sycl.cmake``.  They will enable the KOKKOS package and
-      enable some hardware choice.  So to compile with OpenMP host
-      parallelization, CUDA device parallelization (for GPUs with CC 5.0
-      and up) with some common packages enabled, you can do the
-      following:
+      ``kokkos-openmp.cmake``, ``kokkos-cuda.cmake``,
+      ``kokkos-hip.cmake``, and ``kokkos-sycl.cmake``.  They will enable
+      the KOKKOS package and enable some hardware choice.  So to compile
+      with CUDA device parallelization (for GPUs with CC 5.0 and up)
+      with some common packages enabled, you can do the following:
 
       .. code-block:: bash
 
@@ -707,6 +739,15 @@ This list was last updated for version 3.5.0 of the Kokkos library.
          KOKKOS_ABSOLUTE_PATH = $(shell cd $(KOKKOS_PATH); pwd)
          CC = mpicxx -cxx=$(KOKKOS_ABSOLUTE_PATH)/config/nvcc_wrapper
 
+      For AMD or NVIDIA GPUs using HIP:
+
+      .. code-block:: make
+
+         KOKKOS_DEVICES = HIP
+         KOKKOS_ARCH = HOSTARCH,GPUARCH  # HOSTARCH = HOST from list above that is hosting the GPU
+                                         # GPUARCH = GPU from list above
+         FFT_INC = -DFFT_HIPFFT           # enable use of hipFFT (optional)
+         FFT_LIB = -lhipfft               # link to hipFFT library
 
 Advanced KOKKOS compilation settings
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -766,8 +807,10 @@ library.
 
       .. code-block:: bash
 
-         -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 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 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
@@ -775,6 +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
@@ -1891,14 +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 QUIP_LIBRARY=path     # path to libquip.a (only needed if a custom location)
+         -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 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
-      found on the local machine. This requires to have git installed. It will use the same compilers
-      and flags as used for compiling LAMMPS.  Currently this is only supported for the GNU 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.
+      CMake will try to download and build the QUIP library from GitHub,
+      if it is not found on the local machine. This requires to have git
+      installed. It will use the same compilers and flags as used for
+      compiling LAMMPS.  Currently this is only supported for the GNU
+      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
-documentation extracted from the LAMMPS C++ sources through the `Doxygen
-<https://doxygen.nl>`_ program.  Currently the translation to HTML, PDF
-(via LaTeX), ePUB (for many e-book readers) and MOBI (for Amazon Kindle
-readers) are supported.  For that to work a Python 3 interpreter, the
-``doxygen`` tools and internet access to download additional files and
-tools are required.  This download is usually only required once or
-after the documentation folder is returned to a pristine state with
-``make clean-all``.
-
-.. _rst: https://docutils.readthedocs.io/en/sphinx-docs/user/rst/quickstart.html
-.. _sphinx: https://www.sphinx-doc.org
+<https://sphinx-doc.org>`_ document generator tool.  It also
+incorporates programmer documentation extracted from the LAMMPS C++
+sources through the `Doxygen <https://doxygen.nl>`_ program.  Currently
+the translation to HTML, PDF (via LaTeX), ePUB (for many e-book readers)
+and MOBI (for Amazon Kindle readers) are supported.  For that to work a
+Python 3 interpreter, the ``doxygen`` tools and internet access to
+download additional files and tools are required.  This download is
+usually only required once or after the documentation folder is returned
+to a pristine state with ``make clean-all``.
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -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_package.rst

@@ -150,7 +150,7 @@ other files dependent on that package are also excluded.
 .. _cmake_presets:
 
 CMake presets for installing many packages
-""""""""""""""""""""""""""""""""""""""""""
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 Instead of specifying all the CMake options via the command-line,
 CMake allows initializing its settings cache using script files.
@@ -178,6 +178,11 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers
 
+Presets that have names starting with "windows" are specifically for
+compiling LAMMPS :doc:`natively on Windows <Build_windows>` and
+presets that have names starting with "kokkos" are specifically for
+selecting configurations for compiling LAMMPS with :ref:`KOKKOS <kokkos>`.
+
 .. note::
 
    Running cmake this way manipulates the CMake settings cache in your
@@ -220,7 +225,8 @@ These commands install/un-install sets of packages:
 .. code-block:: bash
 
     make yes-all                        # install all packages
-    make no-all                         # uninstall all packages
+    make no-all                         # check for changes and uninstall all packages
+    make no-installed                   # only check and uninstall installed packages
     make yes-basic                      # install a few commonly used packages'
     make no-basic                       # remove a few commonly used packages'
     make yes-most                       # install most packages w/o libs'

doc/src/Build_settings.rst

@@ -287,8 +287,8 @@ Output of JPG, PNG, and movie files
 
 The :doc:`dump image <dump_image>` command has options to output JPEG or
 PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
-outputs movie files in MPEG format.  Using these options requires the
-following settings:
+outputs movie files in a variety of movie formats.  Using these options
+requires the following settings:
 
 .. tabs::
 
@@ -328,11 +328,12 @@ following settings:
          JPG_LIB = -ljpeg -lpng -lz       # library names
 
       As with CMake, you do not need to set ``JPG_INC`` or ``JPG_PATH``,
-      if make can find the graphics header and library files.  You must
-      specify ``JPG_LIB`` with a list of graphics libraries to include
-      in the link.  You must insure ffmpeg is in a directory where
-      LAMMPS can find it at runtime, that is a directory in your PATH
-      environment variable.
+      if make can find the graphics header and library files in their
+      default system locations.  You must specify ``JPG_LIB`` with a
+      list of graphics libraries to include in the link.  You must make
+      certain that the ffmpeg executable (or ffmpeg.exe on Windows) is
+      in a directory where LAMMPS can find it at runtime; that is
+      usually a directory list in your ``PATH`` environment variable.
 
 Using ``ffmpeg`` to output movie files requires that your machine
 supports the "popen" function in the standard runtime library.

doc/src/Build_windows.rst

@@ -5,6 +5,7 @@ Notes for building LAMMPS on Windows
 * :ref:`Running Linux on Windows <linux>`
 * :ref:`Using GNU GCC ported to Windows <gnu>`
 * :ref:`Using Visual Studio <msvc>`
+* :ref:`Using Intel oneAPI compilers and libraries <oneapi>`
 * :ref:`Using a cross-compiler <cross>`
 
 ----------
@@ -25,8 +26,10 @@ assistance in resolving portability issues.  This is particularly true
 for compiling LAMMPS on Windows, since this platform has significant
 differences in some low-level functionality.  As of LAMMPS version 14
 December 2021, large parts of LAMMPS can be compiled natively with the
-Microsoft Visual C++ Compilers.  This is largely facilitated by using
-the :doc:`Developer_platform` in the ``platform`` namespace.
+Microsoft Visual C++ Compilers.  As of LAMMPS version 31 May 2022, also
+the Intel oneAPI compilers can compile large parts of LAMMPS natively on
+Windows.  This is mostly facilitated by using the
+:doc:`Developer_platform` in the ``platform`` namespace and CMake.
 
 Before trying to build LAMMPS on Windows yourself, please consider the
 `pre-compiled Windows installer packages <https://packages.lammps.org/windows.html>`_
@@ -99,6 +102,10 @@ It is possible to use both the integrated CMake support of the Visual
 Studio IDE or use an external CMake installation (e.g. downloaded from
 cmake.org) to create build files and compile LAMMPS from the command line.
 
+Compilation via command line and unit tests are checked automatically
+for the LAMMPS development branch through
+`GitHub Actions <https://github.com/lammps/lammps/actions/workflows/compile-msvc.yml>`_.
+
 .. note::
 
    Versions of Visual Studio before version 17.1 may scan the entire
@@ -111,6 +118,10 @@ Please note, that for either approach CMake will create a so-called
 the command lines for building and testing LAMMPS must be adjusted
 accordingly.
 
+The LAMMPS cmake folder contains a ``CMakeSettings.json`` file with
+build configurations for MSVC compilers and the MS provided Clang
+compiler package in Debug and Release mode.
+
 To support running in parallel you can compile with OpenMP enabled using
 the OPENMP package or install Microsoft MPI (including the SDK) and compile
 LAMMPS with MPI enabled.
@@ -121,6 +132,53 @@ LAMMPS with MPI enabled.
    via GitHub or the `LAMMPS forum at MatSci <https://matsci.org/c/lammps/lammps-development/>`_,
    if you have questions or LAMMPS specific problems.
 
+.. _oneapi:
+
+Using Intel oneAPI Compilers and Libraries
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. versionadded:: 31May2022
+
+After installing the `Intel oneAPI
+<https://www.intel.com/content/www/us/en/developer/tools/oneapi/toolkits.html>`_
+base toolkit and the HPC toolkit, it is also possible to compile large
+parts of LAMMPS natively on Windows using Intel compilers.  The HPC
+toolkit provides two sets of C/C++ and Fortran compilers: the so-called
+"classic" compilers (``icl.exe`` and ``ifort.exe``) and newer, LLVM
+based compilers (``icx.exe`` and ``ifx.exe``).  In addition to the
+compilers and their dependent modules, also the thread building blocks
+(TBB) and the math kernel library (MKL) need to be installed.  Two
+presets (``cmake/presets/windows-intel-llvm.cmake`` and
+``cmake/presets/windows-intel-classic.cmake``) are provided for
+selecting the LLVM based or classic compilers, respectively. The preset
+``cmake/presets/windows.cmake`` enables compatible packages that are not
+dependent on additional features or libraries.  You **must** use the
+CMake based build procedure and use Ninja as build tool.  For compiling
+from the command prompt, thus both `CMake <https://cmake.org>`_ and
+`Ninja-build <https://ninja-build.org>`_ binaries must be installed.  It
+is also possible to use Visual Studio, if it is started (``devenv.exe``)
+from a command prompt that has the Intel oneAPI compilers enabled.  The
+Visual Studio settings file in the ``cmake`` folder contains
+configurations for both compiler variants in debug and release settings.
+Those will use the CMake and Ninja binaries bundled with Visual Studio,
+thus a separate installation is not required.
+
+.. admonition:: Known Limitations
+   :class: note
+
+   In addition to portability issues with several packages and external
+   libraries, the classic Intel compilers are currently not able to
+   compile the googletest libraries and thus enabling the ``-DENABLE_TESTING``
+   option will result in compilation failure.  The LLVM based compilers
+   are compatible.
+
+.. note::
+
+   This is work in progress and you should contact the LAMMPS developers
+   via GitHub or the `LAMMPS forum at MatSci <https://matsci.org/c/lammps/lammps-development/>`_,
+   if you have questions or LAMMPS specific problems.
+
+
 .. _cross:
 
 Using a cross-compiler
@@ -145,14 +203,3 @@ LAMMPS developers.  We instead rely on the feedback of the users
 of these pre-compiled LAMMPS packages for Windows.  We will try to resolve
 issues to the best of our abilities if we become aware of them. However
 this is subject to time constraints and focus on HPC platforms.
-
-.. _native:
-
-Native Visual C++ support
-^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Support for the Visual C++ compilers is currently not available. The
-CMake build system is capable of creating suitable a Visual Studio
-style build environment, but the LAMMPS source code itself is not
-ported to fully support Visual C++. Volunteers to take on this task
-are welcome.

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 all 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
@@ -47,35 +50,27 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
    * :doc:`dump_modify <dump_modify>`
-   * :doc:`dynamical_matrix (k) <dynamical_matrix>`
    * :doc:`echo <echo>`
    * :doc:`fix <fix>`
    * :doc:`fix_modify <fix_modify>`
    * :doc:`group <group>`
-   * :doc:`group2ndx <group2ndx>`
-   * :doc:`hyper <hyper>`
    * :doc:`if <if>`
    * :doc:`improper_coeff <improper_coeff>`
    * :doc:`improper_style <improper_style>`
    * :doc:`include <include>`
    * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim <kim_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:`mdi <mdi>`
    * :doc:`minimize <minimize>`
    * :doc:`min_modify <min_modify>`
    * :doc:`min_style <min_style>`
-   * :doc:`min_style spin <min_spin>`
    * :doc:`molecule <molecule>`
-   * :doc:`ndx2group <group2ndx>`
-   * :doc:`neb <neb>`
-   * :doc:`neb/spin <neb_spin>`
    * :doc:`neigh_modify <neigh_modify>`
    * :doc:`neighbor <neighbor>`
    * :doc:`newton <newton>`
@@ -86,11 +81,8 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
-   * :doc:`plugin <plugin>`
-   * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`
-   * :doc:`python <python>`
    * :doc:`quit <quit>`
    * :doc:`read_data <read_data>`
    * :doc:`read_dump <read_dump>`
@@ -108,14 +100,9 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`shell <shell>`
    * :doc:`special_bonds <special_bonds>`
    * :doc:`suffix <suffix>`
-   * :doc:`tad <tad>`
-   * :doc:`temper <temper>`
-   * :doc:`temper/grem <temper_grem>`
-   * :doc:`temper/npt <temper_npt>`
    * :doc:`thermo <thermo>`
    * :doc:`thermo_modify <thermo_modify>`
    * :doc:`thermo_style <thermo_style>`
-   * :doc:`third_order (k) <third_order>`
    * :doc:`timer <timer>`
    * :doc:`timestep <timestep>`
    * :doc:`uncompute <uncompute>`
@@ -128,3 +115,27 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`write_data <write_data>`
    * :doc:`write_dump <write_dump>`
    * :doc:`write_restart <write_restart>`
+
+Additional general LAMMPS commands provided by packages.  A few
+commands have accelerated versions.  This is indicated by an
+additional letter in parenthesis: k = KOKKOS.
+
+.. table_from_list::
+   :columns: 5
+
+   * :doc:`dynamical_matrix (k) <dynamical_matrix>`
+   * :doc:`group2ndx <group2ndx>`
+   * :doc:`hyper <hyper>`
+   * :doc:`kim <kim_commands>`
+   * :doc:`mdi <mdi>`
+   * :doc:`ndx2group <group2ndx>`
+   * :doc:`neb <neb>`
+   * :doc:`neb/spin <neb_spin>`
+   * :doc:`plugin <plugin>`
+   * :doc:`prd <prd>`
+   * :doc:`python <python>`
+   * :doc:`tad <tad>`
+   * :doc:`temper <temper>`
+   * :doc:`temper/grem <temper_grem>`
+   * :doc:`temper/npt <temper_npt>`
+   * :doc:`third_order (k) <third_order>`

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>`
@@ -74,6 +76,7 @@ OPT.
    *
    *
    *
+   * :doc:`amoeba <angle_amoeba>`
    * :doc:`charmm (iko) <angle_charmm>`
    * :doc:`class2 (ko) <angle_class2>`
    * :doc:`class2/p6 <angle_class2>`
@@ -88,11 +91,12 @@ OPT.
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
-   * :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
+   * :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:
@@ -152,6 +156,7 @@ OPT.
    *
    *
    *
+   * :doc:`amoeba <improper_amoeba>`
    * :doc:`class2 (ko) <improper_class2>`
    * :doc:`cossq (o) <improper_cossq>`
    * :doc:`cvff (io) <improper_cvff>`

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
 ============
@@ -28,6 +29,8 @@ OPT.
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
    * :doc:`addtorque <fix_addtorque>`
+   * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
+   * :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
    * :doc:`append/atoms <fix_append_atoms>`
    * :doc:`atc <fix_atc>`
    * :doc:`atom/swap <fix_atom_swap>`
@@ -103,7 +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>`
@@ -162,6 +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
 ======================
@@ -38,6 +39,7 @@ OPT.
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
+   * :doc:`amoeba <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -124,6 +126,7 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
+   * :doc:`hippo <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@@ -179,9 +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/sdk/coul/long (go) <pair_sdk>`
-   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/spica (gko) <pair_spica>`
+   * :doc:`lj/spica/coul/long (go) <pair_spica>`
+   * :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>`
@@ -194,10 +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>`
@@ -231,7 +235,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
-   * :doc:`pace <pair_pace>`
+   * :doc:`pace (k) <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -268,7 +272,9 @@ 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:`table (gko) <pair_table>`
    * :doc:`table/rx (k) <pair_table_rx>`
@@ -279,6 +285,7 @@ OPT.
    * :doc:`tersoff/table (o) <pair_tersoff>`
    * :doc:`tersoff/zbl (gko) <pair_tersoff_zbl>`
    * :doc:`thole <pair_thole>`
+   * :doc:`threebody/table <pair_threebody_table>`
    * :doc:`tip4p/cut (o) <pair_coul>`
    * :doc:`tip4p/long (o) <pair_coul>`
    * :doc:`tip4p/long/soft (o) <pair_fep_soft>`

doc/src/Commands_parse.rst

@@ -77,18 +77,19 @@ LAMMPS:
    so that you do not have to define (or discard) a temporary variable,
    "X" in this case.
 
-   Additionally, the "immediate" variable expression may be followed by
-   a colon, followed by a C-style format string, e.g. ":%f" or ":%.10g".
-   The format string must be appropriate for a double-precision
-   floating-point value.  The format string is used to output the result
-   of the variable expression evaluation.  If a format string is not
-   specified a high-precision "%.20g" is used as the default.
+   Additionally, the entire "immediate" variable expression may be
+   followed by a colon, followed by a C-style format string,
+   e.g. ":%f" or ":%.10g".  The format string must be appropriate for
+   a double-precision floating-point value.  The format string is used
+   to output the result of the variable expression evaluation.  If a
+   format string is not specified, a high-precision "%.20g" is used as
+   the default format.
 
    This can be useful for formatting print output to a desired precision:
 
    .. code-block:: LAMMPS
 
-      print "Final energy per atom: $(pe/atoms:%10.3f) eV/atom"
+      print "Final energy per atom: $(v_ke_per_atom+v_pe_per_atom:%10.3f) eV/atom"
 
    Note that neither the curly-bracket or immediate form of variables
    can contain nested $ characters for other variables to substitute
@@ -122,14 +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
-   single argument enclosed in single or double quotes can span multiple
-   lines if the "&" character is used, as described above.  When the
-   lines are concatenated together (and the "&" characters and line
-   breaks removed), the text will become a single line.  If you want
-   multiple lines of an argument to retain their line breaks, the text
-   can be enclosed in triple quotes, in which case "&" characters are
-   not needed.  For example:
+   can be enclosed in either single (') or double (") or triple (""")
+   quotes.  A long single argument enclosed in single or double quotes
+   can span multiple lines if the "&" character is used, as described
+   in :ref:`1 <one>` above.  When the lines are concatenated together
+   by LAMMPS (and the "&" characters and line breaks removed), the
+   combined text will become a single line.  If you want multiple lines
+   of an argument to retain their line breaks, the text can be enclosed
+   in triple quotes, in which case "&" characters are not needed and do
+   not function as line continuation character.  For example:
 
    .. code-block:: LAMMPS
 
@@ -143,8 +145,9 @@ LAMMPS:
       System temperature = $t
       """
 
-   In each case, the single, double, or triple quotes are removed when
-   the single argument they enclose is stored internally.
+   In each of these cases, the single, double, or triple quotes are
+   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_plugins.rst

@@ -276,10 +276,27 @@ Compilation of the plugin can be managed via both, CMake or traditional
 GNU makefiles.  Some examples that can be used as a template are in the
 ``examples/plugins`` folder.  The CMake script code has some small
 adjustments to allow building the plugins for running unit tests with
-them. Another example that converts the KIM package into a plugin can be
-found in the ``examples/kim/plugin`` folder.  No changes to the sources
-of the KIM package themselves are needed; only the plugin interface and
-loader code needs to be added.  This example only supports building with
-CMake, but is probably a more typical example. To compile you need to
-run CMake with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
+them.
+
+Another example that converts the KIM package into a plugin can be found
+in the ``examples/kim/plugin`` folder.  No changes to the sources of the
+KIM package themselves are needed; only the plugin interface and loader
+code needs to be added.  This example only supports building with CMake,
+but is probably a more typical example. To compile you need to run CMake
+with -DLAMMPS_SOURCE_DIR=<path/to/lammps/src/folder>.  Other
 configuration setting are identical to those for compiling LAMMPS.
+
+A second example for a plugin from a package is in the
+``examples/PACKAGES/pace/plugin`` folder that will create a plugin from
+the ML-PACE package.  In this case the bulk of the code is in a static
+external library that is being downloaded and compiled first and then
+combined with the pair style wrapper and the plugin loader.  This
+example also contains a NSIS script that can be used to create an
+Installer package for Windows (the mutual licensing terms of the
+external library and LAMMPS conflict when distributing binaries, so the
+ML-PACE package cannot be linked statically, but the LAMMPS headers
+required to build the plugin are also available under a less restrictive
+license).  This will automatically set the required environment variable
+and launching a (compatible) LAMMPS binary will load and register the
+plugin and the ML-PACE package can then be used as it was linked into
+LAMMPS.

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_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

@@ -38,11 +38,11 @@ found together with equivalent examples in C and C++ in the
 
 .. note::
 
-   A contributed (and complete!) Fortran interface that more
-   closely resembles the C-library interface is available
-   in the ``examples/COUPLE/fortran2`` folder.  Please see the
-   ``README`` file in that folder for more information about it
-   and how to contact its author and maintainer.
+   A contributed (and more complete!) Fortran interface that more
+   closely resembles the C-library interface is available in the
+   ``examples/COUPLE/fortran2`` folder.  Please see the ``README`` file
+   in that folder for more information about it and how to contact its
+   author and maintainer.
 
 ----------
 
@@ -65,8 +65,9 @@ the optional logical argument set to ``.true.``. Here is a simple example:
 
    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)
@@ -78,6 +79,41 @@ 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 similar to the standalone
+executable (it will ignore the `-in/-i` flag, though).  This allows to
+use 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
@@ -102,7 +138,7 @@ 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 +147,10 @@ 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
@@ -123,7 +159,7 @@ 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
 
@@ -137,9 +173,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
 
 .. f:type:: lammps
 
-   Derived type that is the general class of the Fortran interface.
-   It holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
-   that any of the included calls are forwarded to.
+   Derived type that is the general class of the Fortran interface.  It
+   holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>`
+   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`
@@ -202,7 +238,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    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)
 
@@ -210,4 +246,3 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    execute a block of commands from a string.
 
    :p character(len=*) str: LAMMPS input in string
-

doc/src/Howto.rst

@@ -34,6 +34,7 @@ Settings howto
    :maxdepth: 1
 
    Howto_2d
+   Howto_type_labels
    Howto_triclinic
    Howto_thermostat
    Howto_barostat
@@ -65,6 +66,7 @@ Force fields howto
    :maxdepth: 1
 
    Howto_bioFF
+   Howto_amoeba
    Howto_tip3p
    Howto_tip4p
    Howto_spc

doc/src/Howto_amoeba.rst

@@ -0,0 +1,324 @@
+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.  The LAMMPS
+implementation is based on Fortran 90 code provided by the Ponder
+group in their `Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
+
+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
+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
+in simulations of water, organic molecules, and biomolecules including
+proteins, provided that parameterizations (Tinker PRM force field
+files) are available for the systems you are interested in.  Files in
+the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
+be used.  The Tinker distribution and website have additional force
+field files as well:
+`https://github.com/TinkerTools/tinker/tree/release/params
+<https://github.com/TinkerTools/tinker/tree/release/params>`_.
+
+Note that currently, HIPPO can only be used for water systems, but
+HIPPO files for a variety of small organic and biomolecules are in
+preparation by the Ponder group.  Those force field files will be
+included in the LAMMPS distribution when available.
+
+To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
+fully periodic or fully non-periodic, and use an orthogonal (not
+triclinic) simulation box.
+
+----------
+
+The AMOEBA and HIPPO force fields contain the following terms in their
+energy (U) computation.  Further details for AMOEBA equations are in
+:ref:`(Ponder) <amoeba-Ponder>`, further details for the HIPPO
+equations are in :ref:`(Rackers) <amoeba-Rackers>`.
+
+.. math::
+
+  U & = U_{intermolecular} + U_{intramolecular} \\
+  U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
+  U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
+
+For intermolecular terms, the AMOEBA force field includes only the
+:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms.  The
+HIPPO force field includes all but the :math:`U_{hal}` term.  In
+LAMMPS, these are all computed by the :doc:`pair_style amoeba or hippo
+<pair_style>` command.  Note that the :math:`U_{multipole}` and
+:math:`U_{polar}` terms in this formula are not the same for the
+AMOEBA and HIPPO force fields.
+
+For intramolecular terms, the :math:`U_{bond}`, :math:`U_{angle}`,
+:math:`U_{torsion}`, :math:`U_{oop}` terms are computed by the
+:doc:`bond_style class2 <bond_class2>` :doc:`angle_style amoeba
+<angle_amoeba>`, :doc:`dihedral_style fourier <dihedral_fourier>`, and
+:doc:`improper_style amoeba <improper_amoeba>` commands respectively.
+The :doc:`angle_style amoeba <angle_amoeba>` command includes the
+:math:`U_{b\theta}` bond-angle cross term, and the :math:`U_{UB}` term
+for a Urey-Bradley bond contribution between the I,K atoms in the IJK
+angle.
+
+The :math:`U_{pitorsion}` term is computed by the :doc:`fix
+amoeba/pitorsion <fix_amoeba_pitorsion>` command.  It computes 6-body
+interaction between a pair of bonded atoms which each have 2
+additional bond partners.
+
+The :math:`U_{bitorsion}` term is computed by the :doc:`fix
+amoeba/bitorsion <fix_amoeba_bitorsion>` command.  It computes 5-body
+interaction between two 4-body torsions (dihedrals) which overlap,
+having 3 atoms in common.
+
+These command doc pages have additional details on the terms they
+compute:
+
+* :doc:`pair_style amoeba or hippo <pair_amoeba>`
+* :doc:`bond_style class2 <bond_class2>`
+* :doc:`angle_style amoeba <angle_amoeba>`
+* :doc:`dihedral_style fourier <dihedral_fourier>`
+* :doc:`improper_style amoeba <improper_amoeba>`
+* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
+* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
+
+----------
+
+To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
+the following appropriately in your input script.  The only change
+needed for AMOEBA vs HIPPO simulation is for the :doc:`pair_style
+<pair_style>` and :doc:`pair_coeff <pair_coeff>` commands, as shown
+below.  See examples/amoeba for example input scripts for both AMOEBA
+and HIPPO.
+
+.. code-block:: LAMMPS
+
+   units              real                           # required
+   atom_style         amoeba
+   bond_style         class2                         # CLASS2 package
+   angle_style        amoeba
+   dihedral_style     fourier                        # EXTRA-MOLECULE package
+   improper_style     amoeba
+                                                     # required per-atom data
+   fix                amtype all property/atom i_amtype ghost yes
+   fix                extra all property/atom &
+                      i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
+   fix                polaxe all property/atom i_polaxe
+
+   fix                pit all amoeba/pitorsion       # PiTorsion terms in FF
+   fix_modify         pit energy yes
+                                                     # Bitorsion terms in FF
+   fix                bit all amoeba/bitorsion bitorsion.ubiquitin.data
+   fix_modify         bit energy yes
+
+   read_data          data.ubiquitin fix amtype NULL "Tinker Types" &
+                      fix pit "pitorsion types" "PiTorsion Coeffs" &
+                      fix pit pitorsions PiTorsions &
+                      fix bit bitorsions BiTorsions
+
+   pair_style         amoeba                          # AMOEBA FF
+   pair_coeff         * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
+
+   pair_style         hippo                           # HIPPO FF
+   pair_coeff         * * hippo_water.prm hippo_water.key
+
+   special_bonds      lj/coul 0.5 0.5 0.5 one/five yes     # 1-5 neighbors
+
+The data file read by the :doc:`read_data <read_data>` command should
+be created by the tools/tinker/tinker2lmp.py conversion program
+described below.  It will create a section in the data file with the
+header "Tinker Types".  A :doc:`fix property/atom <fix_property_atom>`
+command for the data must be specified before the read_data command.
+In the example above the fix ID is *amtype*.
+
+Similarly, if the system you are simulating defines AMOEBA/HIPPO
+pitorsion or bitorsion interactions, there will be entries in the data
+file for those interactions.  They require a :doc:`fix
+amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
+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, 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
+what is listed above.
+
+The two :doc:`fix property/atom <fix_property_atom>` commands with IDs
+(in the example above) *extra* and *polaxe* are also needed to define
+internal per-atom quantities used by the AMOEBA and HIPPO force
+fields.
+
+The :doc:`pair_coeff <pair_coeff>` command used for either the AMOEBA
+or HIPPO force field takes two arguments for Tinker force field files,
+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 specifics below.
+
+A :doc:`special_bonds <special_bonds>` command with the *one/five*
+option is required, since the AMOEBA/HIPPO force fields define
+weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
+1-5 interactions.  This command will trigger a per-atom list of 1-5
+neighbors to be generated.  The AMOEBA and HIPPO force fields define
+their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
+terms which in the Tinker PRM and KEY files; they can be different for
+different terms in the force field.
+
+In addition to the list above, these command doc pages have additional
+details:
+
+* :doc:`atom_style amoeba <atom_style>`
+* :doc:`fix property/atom <fix_property_atom>`
+* :doc:`special_bonds <special_bonds>`
+
+----------
+
+Tinker PRM and KEY files
+
+A Tinker PRM file is composed of sections, each of which has multiple
+lines.  This is the list of PRM sections LAMMPS knows how to parse and
+use.  Any other sections are skipped:
+
+* Angle Bending Parameters
+* Atom Type Definitions
+* Atomic Multipole Parameters
+* Bond Stretching Parameters
+* Charge Penetration Parameters
+* Charge Transfer Parameters
+* Dipole Polarizability Parameters
+* Dispersion Parameters
+* Force Field Definition
+* Literature References
+* Out-of-Plane Bend Parameters
+* Pauli Repulsion Parameters
+* Pi-Torsion Parameters
+* Stretch-Bend Parameters
+* Torsion-Torsion Parameters
+* Torsional Parameters
+* Urey-Bradley Parameters
+* Van der Waals Pair Parameters
+* Van der Waals Parameters
+
+A Tinker KEY file is composed of lines, each of which has a keyword
+followed by zero or more parameters.  This is the list of keywords
+LAMMPS knows how to parse and use in the same manner Tinker does.  Any
+other keywords are skipped.  The value in parenthesis is the default
+value for the keyword if it is not specified, or if the keyfile in the
+:doc:`pair_coeff <pair_coeff>` command is specified as NULL:
+
+* a-axis (0.0)
+* b-axis (0.0)
+* c-axis (0.0)
+* ctrn-cutoff (6.0)
+* ctrn-taper (0.9 * ctrn-cutoff)
+* cutoff
+* delta-halgren (0.07)
+* dewald (no long-range dispersion unless specified)
+* dewald-alpha (0.4)
+* dewald-cutoff (7.0)
+* dispersion-cutoff (9.0)
+* dispersion-taper (9.0 * dispersion-cutoff)
+* dpme-grid
+* dpme-order (4)
+* ewald (no long-range electrostatics unless specified)
+* ewald-alpha (0.4)
+* ewald-cutoff (7.0)
+* gamma-halgren (0.12)
+* mpole-cutoff (9.0)
+* mpole-taper (0.65 * mpole-cutoff)
+* pcg-guess (enabled by default)
+* pcg-noguess (disable pcg-guess if specified)
+* pcg-noprecond (disable pcg-precond if specified)
+* pcg-peek (1.0)
+* pcg-precond (enabled by default)
+* pewald-alpha (0.4)
+* pme-grid
+* pme-order (5)
+* polar-eps (1.0e-6)
+* polar-iter (100)
+* polar-predict (no prediction operation unless specified)
+* ppme-order (5)
+* repulsion-cutoff (6.0)
+* repulsion-taper (0.9 * repulsion-cutoff)
+* taper
+* usolve-cutoff (4.5)
+* usolve-diag (2.0)
+* vdw-cutoff (9.0)
+* vdw-taper (0.9 * vdw-cutoff)
+
+----------
+
+Tinker2lmp.py tool
+
+This conversion tool is found in the tools/tinker directory.
+As shown in examples/amoeba/README, these commands produce
+the data files found in examples/amoeba, and also illustrate
+all the options available to use with the tinker2lmp.py script:
+
+.. code-block:: bash
+
+   % python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba                # AMOEBA non-periodic system
+   % python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo                   # HIPPO non-periodic system
+   % python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643    # AMOEBA periodic system
+   % python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643       # HIPPO periodic system
+   % python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new   # system with bitorsions
+
+Switches and their arguments may be specified in any order.
+
+The -xyz switch is required and specifies an input XYZ file as an
+argument.  The format of this file is an extended XYZ format defined
+and used by Tinker for its input.  Example \*.xyz files are in the
+examples/amoeba directory.  The file lists the atoms in the system.
+Each atom has the following information: Tinker species name (ignored
+by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
+IDs the atom is bonded to.
+
+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://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>`_
+
+The -amoeba or -hippo switch is required.  It specifies an input
+AMOEBA or HIPPO PRM force field file as an argument.  This should be
+the same file used by the :doc:`pair_style <pair_style>` command in
+the input script.
+
+The -data switch is required.  It specifies an output file name for
+the LAMMPS data file that will be produced.
+
+For periodic systems, the -pbc switch is required.  It specifies the
+periodic box size for each dimension (x,y,z).  For a Tinker simulation
+these are specified in the KEY file.
+
+The -bitorsion switch is only needed if the system contains Tinker
+bitorsion interactions.  The data for each type of bitorsion
+interaction will be written to the specified file, and read by the
+:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>` command.  The data
+includes 2d arrays of values to which splines are fit, and thus is not
+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).
+
+.. _howto-Rackers:
+
+**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
+
+.. _howto-Ren:
+
+**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
+
+.. _howto-Shi:
+
+**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
+

doc/src/Howto_body.rst

@@ -239,7 +239,7 @@ is consistent with the 6 moments of inertia: ixx iyy izz ixy ixz iyz =
 
 .. parsed-literal::
 
-   3 1 27
+   3 1 19
    4
    1 1 4 0 0 0
    -0.7071 -0.7071 0

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
-does this by using the `MolSSI Driver Interface (MDI) library
-<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_,
+a simulation.  In this context, LAMMPS can act as either a client or
+server code.  It does this by using the `MolSSI Driver Interface (MDI)
+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
-LAMMPS operates as an MDI driver to perform *ab initio* MD simulations
-in conjunction with a quantum mechanics code.  Its post_force() method
-illustrates how a driver issues MDI commands to another code.  This
-command can be used to couple to an MDI engine which is either a
-stand-alone code or a plugin library.
+The package also has a `fix mdi/qm <fix_mdi_qm>` command in which
+LAMMPS operates as an MDI driver in conjunction with a quantum
+mechanics code as an MDI engine.  The post_force() method of the
+fix_mdi_qm.cpp file shows how a driver issues MDI commands to another
+code.  This command can be used to couple to an MDI engine which is
+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
-  and one as an engine.  As an engine, LAMMPS is a surrogate for a
-  quantum code.
+* Run ab initio MD (AIMD) using 2 instances of LAMMPS.  As a driver
+  LAMMPS performs the timestepping in either NVE or NPT mode.  As an
+  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
-the QM code.
+without modifying the input scripts or launch commands, except to
+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
-support, `Quantum ESPRESSO (QE) <https://www.quantum-espresso.org/>`_
-and `INQ <https://qsg.llnl.gov/node/101.html>`_.  There are also
-several QM codes which have indirect support through QCEngine or i-PI.
-The former means they require a wrapper program (QCEngine) with MDI
+Currently there are at least two quantum DFT codes which have direct
+MDI support, `Quantum ESPRESSO (QE)
+<https://www.quantum-espresso.org/>`_ and `INQ
+<https://qsg.llnl.gov/node/101.html>`_.  There are also several QM
+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

@@ -19,7 +19,7 @@ atoms and the water molecule to run a rigid SPC model.
 | LJ :math:`\sigma` of OO = 3.166
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 | :math:`r_0` of OH bond = 1.0
-| :math:`\theta` of HOH angle = 109.47\ :math:`^{\circ}`
+| :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
 |
 
 Note that as originally proposed, the SPC model was run with a 9

doc/src/Howto_structured_data.rst

@@ -184,7 +184,7 @@ frame.
 
 .. code-block:: python
 
-   import re, yaml
+   import yaml
    import pandas as pd
 
    try:
@@ -193,7 +193,7 @@ frame.
        from yaml import SafeLoader as Loader
 
    with open("ave.yaml") as f:
-       ave = yaml.load(docs, Loader=Loader)
+       ave = yaml.load(f, Loader=Loader)
 
    keys = ave['keywords']
    df = {}

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
-   fix          NVT all nvt temp $T $T 10 drag 0.2
+   velocity     all create ${Tinit} 102486 mom yes rot yes dist gaussian
+   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.
-However, instead of measure the momentum flux in response of applied velocity gradient,
-it measures the velocity profile in response of applied stress.
+The sixth is the periodic perturbation method, which is also a non-equilibrium MD method.
+However, instead of measuring the momentum flux in response to an applied velocity gradient,
+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/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
-have more flexibility as to what features to include or exclude in the
-build.  If you plan to :doc:`modify or extend LAMMPS <Modify>`, then you
-need the source code.
+When downloading the LAMMPS source code, you also have to :doc:`build
+LAMMPS <Build>`.  But you have more flexibility as to what features to
+include or exclude in the build.  When you download and install
+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

@@ -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 Fedora Linux executables <fedora>`
-| :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
-| :ref:`Pre-built OpenSuse Linux executables <opensuse>`
-| :ref:`Gentoo Linux executable <gentoo>`
-| :ref:`Arch Linux build-script <arch>`
-|
+- :ref:`Pre-built Ubuntu Linux executables <ubuntu>`
+- :ref:`Pre-built Fedora Linux executables <fedora>`
+- :ref:`Pre-built EPEL Linux executables (RHEL, CentOS) <epel>`
+- :ref:`Pre-built OpenSuse Linux executables <opensuse>`
+- :ref:`Gentoo Linux executable <gentoo>`
+- :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
-Ubuntu Linux versions, can be downloaded as a Debian package.  This
-allows you to install LAMMPS with a single command, and stay
-up-to-date with the current stable version of LAMMPS by simply updating
-your operating system.  Please note, that the repository below offers
-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
+A pre-built LAMMPS executable suitable for running on the latest Ubuntu
+Linux versions, can be downloaded as a Debian package.  This allows you
+to install LAMMPS with a single command, and stay (mostly) up-to-date
+with the current stable version of LAMMPS by simply updating your
+operating system.
 
 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
-can then be used in the usual way to run input scripts:
+This downloads an executable named ``lmp`` to your box and multiple
+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:
-
-.. code-block:: bash
-
-   $ sudo apt-get install lammps-stable-doc
-
-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
+The ``lmp`` binary is built with the :ref:`KIM package <kim>` included,
+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 also 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
-in the Fedora Linux distribution as of version 28. The packages
-can be installed via the dnf package manager. There are 3 basic
-varieties (lammps = no MPI, lammps-mpich = MPICH MPI library,
-lammps-openmpi = OpenMPI MPI library) and for each support for
-linking to the C library interface (lammps-devel, lammps-mpich-devel,
-lammps-openmpi-devel), the header for compiling programs using
-the C library interface (lammps-headers), and the LAMMPS python
-module for Python 3. All packages can be installed at the same
-time and the name of the LAMMPS executable is ``lmp`` and ``lmp_openmpi``
-or ``lmp_mpich`` respectively.  By default, ``lmp`` will refer to the
-serial executable, unless one of the MPI environment modules is loaded
-(``module load mpi/mpich-x86_64`` or ``module load mpi/openmpi-x86_64``).
-Then the corresponding parallel LAMMPS executable can be used.
-The same mechanism applies when loading the LAMMPS python module.
+Pre-built LAMMPS packages for stable releases are available in the
+Fedora Linux distribution as of Fedora version 28. The packages can be
+installed via the dnf package manager. There are 3 basic varieties
+(lammps = no MPI, lammps-mpich = MPICH MPI library, lammps-openmpi =
+OpenMPI MPI library) and for each support for linking to the C library
+interface (lammps-devel, lammps-mpich-devel, lammps-openmpi-devel), the
+header for compiling programs using the C library interface
+(lammps-headers), and the LAMMPS python module for Python 3. All
+packages can be installed at the same time and the name of the LAMMPS
+executable is ``lmp`` and ``lmp_openmpi`` or ``lmp_mpich`` respectively.
+By default, ``lmp`` will refer to the serial executable, unless one of
+the MPI environment modules is loaded (``module load mpi/mpich-x86_64``
+or ``module load mpi/openmpi-x86_64``).  Then the corresponding parallel
+LAMMPS executable can be used.  The same mechanism applies when loading
+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/Intro_citing.rst

@@ -30,12 +30,12 @@ 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>`_
 
 
-DOI for the LAMMPS code
-^^^^^^^^^^^^^^^^^^^^^^^
+DOI for the LAMMPS source code
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
-to create digital object identifies (DOI) for stable releases of the
-LAMMPS source code. There are two types of DOIs for the LAMMPS source code.
+The LAMMPS developers use the `Zenodo service at CERN <https://zenodo.org/>`_
+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.
 
 The canonical DOI for **all** versions of LAMMPS, which will always
 point to the **latest** stable release version is:

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
-documentation shall be written in American English and the .rst file
-must use only ASCII characters so it can be cleanly translated to PDF
-files (via `sphinx <sphinx>`_ and PDFLaTeX).  Special characters may be included via
-embedded math expression typeset in a LaTeX subset.
+`ReStructuredText format <rst_>`_ (.rst files in the ``doc/src/``
+folder). The documentation shall be written in American English and the
+.rst file must use only ASCII characters so it can be cleanly translated
+to PDF files (via `sphinx <https://www.sphinx-doc.org>`_ and PDFLaTeX).
+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

@@ -27,6 +27,7 @@ page gives those details.
    :columns: 6
 
    * :ref:`ADIOS <PKG-ADIOS>`
+   * :ref:`AMOEBA <PKG-AMOEBA>`
    * :ref:`ASPHERE <PKG-ASPHERE>`
    * :ref:`ATC <PKG-ATC>`
    * :ref:`AWPMD <PKG-AWPMD>`
@@ -35,7 +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>`
@@ -149,6 +150,38 @@ This package has :ref:`specific installation instructions <adios>` on the :doc:`
 
 ----------
 
+.. _PKG-AMOEBA:
+
+AMOEBA package
+---------------
+
+**Contents:**
+
+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
+
+----------
+
 .. _PKG-ASPHERE:
 
 ASPHERE package
@@ -181,9 +214,10 @@ 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
-continuum finite element equations or perform on-the-fly conversion of
-atomic information to continuum fields.
+ATC stands for atoms-to-continuum.  This package implements a
+:doc:`fix atc <fix_atc>` command to either couple molecular dynamics
+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).
 
@@ -242,7 +276,7 @@ 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)
@@ -298,6 +332,8 @@ 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
@@ -365,28 +401,30 @@ 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
-simulation of ionic liquids, electrolytes, lipids and charged amino
-acids.
+coarse-grained SPICA (formerly called SDK) model which enables
+simulation of biological or soft material systems.
 
-**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-SDK/README
-* :doc:`pair_style lj/sdk/\* <pair_sdk>`
-* :doc:`angle_style sdk <angle_sdk>`
-* examples/PACKAGES/cgsdk
+* src/CG-SPICA: filenames -> commands
+* src/CG-SPICA/README
+* :doc:`pair_style lj/spica/\* <pair_spica>`
+* :doc:`angle_style spica <angle_spica>`
+* examples/PACKAGES/cgspica
 * https://www.lammps.org/pictures.html#cg
+* https://www.spica-ff.org/
 
 ----------
 
@@ -614,7 +652,7 @@ 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
 
 ----------
@@ -657,7 +695,7 @@ advection-diffusion-reaction systems. The equations of motion of these
 DPD extensions are integrated through a modified velocity-Verlet (MVV)
 algorithm.
 
-**Author:** Zhen Li (Division of Applied Mathematics, Brown University)
+**Author:** Zhen Li (Department of Mechanical Engineering, Clemson University)
 
 **Supporting info:**
 
@@ -824,6 +862,8 @@ 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
@@ -892,6 +932,10 @@ 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
@@ -1364,7 +1408,7 @@ 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
 
@@ -1479,7 +1523,7 @@ 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
 
 ----------
@@ -1516,31 +1560,40 @@ MESONT package
 
 **Contents:**
 
-MESONT is a LAMMPS package for simulation of nanomechanics of
-nanotubes (NTs). The model is based on a coarse-grained representation
-of NTs as "flexible cylinders" consisting of a variable number of
+MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
+(NTs). The model is based on a coarse-grained representation of NTs as
+"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
-independent implementations of this model: :doc:`pair_style mesocnt
-<pair_mesocnt>` is a (minimal) C++ implementation, and :doc:`pair_style
-mesont/tpm <pair_mesont_tpm>` is a more general and feature rich
-implementation based on a Fortran library in the ``lib/mesont`` folder.
+provided in the papers listed below.
+
+This package contains two independent implementations of this model:
+:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
+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
-are not included in the regular downloaded packages of LAMMPS or the
-git repositories.  Instead, they will be automatically downloaded
-from a web server when the package is installed for the first time.
+The potential files for these pair styles are *very* large and thus are
+not included in the regular downloaded packages of LAMMPS or the git
+repositories.  Instead, they will be automatically downloaded from a web
+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)
 
 **Supporting info:**
@@ -1550,6 +1603,8 @@ 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
@@ -1801,6 +1856,8 @@ 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
@@ -2650,7 +2707,7 @@ 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
 

doc/src/Packages_list.rst

@@ -33,6 +33,11 @@ whether an extra library is needed to build and use the package:
      - :doc:`dump adios <dump_adios>`
      - PACKAGES/adios
      - ext
+   * - :ref:`AMOEBA <PKG-AMOEBA>`
+     - AMOEBA and HIPPO force fields
+     - :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
+     - amoeba
+     - no
    * - :ref:`ASPHERE <PKG-ASPHERE>`
      - aspherical particle models
      - :doc:`Howto spherical <Howto_spherical>`
@@ -73,10 +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>`
-     - SDK coarse-graining model
-     - :doc:`pair_style lj/sdk <pair_sdk>`
-     - PACKAGES/cgsdk
+   * - :ref:`CG-SPICA <PKG-CG-SPICA>`
+     - SPICA (SDK) coarse-graining model
+     - :doc:`pair_style lj/spica <pair_spica>`
+     - PACKAGES/cgspica
      - no
    * - :ref:`CLASS2 <PKG-CLASS2>`
      - class 2 force fields

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/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., 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_measure.rst

@@ -42,5 +42,4 @@ inaccurate relative timing data, because processors have to wait when
 communication occurs for other processors to catch up.  Thus the
 reported times for "Communication" or "Other" may be higher than they
 really are, due to load-imbalance.  If this is an issue, you can
-uncomment the MPI_Barrier() lines in src/timer.cpp, and re-compile
-LAMMPS, to obtain synchronized timings.
+use the :doc:`timer sync <timer>` command to obtain synchronized timings.

doc/src/Tools.rst

@@ -56,6 +56,7 @@ Pre-processing tools
    * :ref:`moltemplate <moltemplate>`
    * :ref:`msi2lmp <msi>`
    * :ref:`polybond <polybond>`
+   * :ref:`stl_bin2txt <stlconvert>`
 
 
 Post-processing tools
@@ -94,7 +95,7 @@ Miscellaneous tools
    * :ref:`LAMMPS shell <lammps_shell>`
    * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`Offline build tool <offline>`
-   * :ref:`singularity <singularity_tool>`
+   * :ref:`singularity/apptainer <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
 
@@ -1006,14 +1007,37 @@ Ivanov, at University of Iceland (ali5 at hi.is).
 
 .. _singularity_tool:
 
-singularity tool
-----------------------------------------
+singularity/apptainer tool
+--------------------------
 
-The singularity sub-directory contains container definitions files
-that can be used to build container images for building and testing
-LAMMPS on specific OS variants using the `Singularity <https://sylabs.io>`_
-container software. Contributions for additional variants are welcome.
-For more details please see the README.md file in that folder.
+The singularity sub-directory contains container definitions files that
+can be used to build container images for building and testing LAMMPS on
+specific OS variants using the `Apptainer <https://apptainer.org>`_ or
+`Singularity <https://sylabs.io>`_ container software. Contributions for
+additional variants are welcome.  For more details please see the
+README.md file in that folder.
+
+----------
+
+.. _stlconvert:
+
+stl_bin2txt tool
+----------------
+
+The file stl_bin2txt.cpp converts binary STL files - like they are
+frequently offered for download on the web - into ASCII format STL files
+that LAMMPS can read with the :doc:`create_atoms mesh <create_atoms>` or
+the :doc:`fix smd/wall_surface <fix_smd_wall_surface>` commands.  The syntax
+for running the tool is
+
+.. code-block:: bash
+
+   stl_bin2txt infile.stl outfile.stl
+
+which creates outfile.stl from infile.stl.  This tool must be compiled
+on a platform compatible with the byte-ordering that was used to create
+the binary file.  This usually is a so-called little endian hardware
+(like x86).
 
 ----------
 

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

@@ -0,0 +1,138 @@
+.. index:: angle_style amoeba
+
+angle_style amoeba command
+==========================
+
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style amoeba
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style amoeba
+   angle_coeff * 75.0 -25.0 1.0 0.3 0.02 0.003
+   angle_coeff * ba 3.6551 24.895 1.0119 1.5228
+   angle_coeff * ub -7.6 1.5537
+
+Description
+"""""""""""
+
+The *amoeba* angle style uses the potential
+
+.. math::
+
+   E & = E_a + E_{ba} + E_{ub} \\
+   E_a & = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 \\
+   E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) \\
+   E_{UB} & = K_{ub} (r_{ik} - r_{ub})^2
+
+where :math:`E_a` is the angle term, :math:`E_{ba}` is a bond-angle
+term, :math:`E_{UB}` is a Urey-Bradley bond term, :math:`\theta_0` is
+the equilibrium angle, :math:`r_1` and :math:`r_2` are the equilibrium
+bond lengths, and :math:`r_{ub}` is the equilibrium Urey-Bradley bond
+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_amoeba>` page for more information about
+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>`
+command, however there is no bond-bond cross term formula for
+:math:`E_{bb}`.  Additionally, there is a :math:`E_{UB}` term for a
+Urey-Bradley bond.  It is effectively a harmonic bond between the I
+and K atoms of angle IJK, even though that bond is not enumerated in
+the "Bonds" section of the data file.
+
+There are also two ways that Tinker computes the angle :math:`\theta`
+in the :math:`E_a` formula.  The first is the standard way of treating
+IJK as an "in-plane" angle.  The second is an "out-of-plane" method
+which Tinker may use if the center atom J in the angle is bonded to
+one additional atom in addition to I and K.  In this case, all 4 atoms
+are used to compute the :math:`E_a` formula, resulting in forces on
+all 4 atoms.  In the Tinker PRM file, these 2 options are denoted by
+*angle* versus *anglep* entries in the "Angle Bending Parameters"
+section of the PRM force field file.  The *pflag* coefficient
+described below selects between the 2 options.
+
+----------
+
+
+Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ub}`
+formulas must be defined for each angle type via the :doc:`angle_coeff
+<angle_coeff>` command as in the example above, or in the data file or
+restart files read by the :doc:`read_data <read_data>` or
+:doc:`read_restart <read_restart>` commands.
+
+These are the 8 coefficients for the :math:`E_a` formula:
+
+* pflag = 0 or 1
+* ubflag = 0 or 1
+* :math:`\theta_0` (degrees)
+* :math:`K_2` (energy)
+* :math:`K_3` (energy)
+* :math:`K_4` (energy)
+* :math:`K_5` (energy)
+* :math:`K_6` (energy)
+
+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` values are effectively
+energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or
+radian\^6.
+
+For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
+<angle_coeff>` command in the input script lists 5 coefficients, the
+first of which is "ba" to indicate they are BondAngle coefficients.
+In a data file, these coefficients should be listed under a "BondAngle
+Coeffs" heading and you must leave out the "ba", i.e. only list 4
+coefficients after the angle type.
+
+* ba
+* :math:`N_1` (energy/distance\^2)
+* :math:`N_2` (energy/distance\^2)
+* :math:`r_1` (distance)
+* :math:`r_2` (distance)
+
+The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
+since it is the same value from the :math:`E_a` formula.
+
+For the :math:`E_{ub}` formula, each line in a :doc:`angle_coeff
+<angle_coeff>` command in the input script lists 3 coefficients, the
+first of which is "ub" to indicate they are UreyBradley coefficients.
+In a data file, these coefficients should be listed under a
+"UreyBradley Coeffs" heading and you must leave out the "ub",
+i.e. only list 2 coefficients after the angle type.
+
+* ub
+* :math:`K_{ub}` (energy/distance\^2)
+* :math:`r_{ub}` (distance)
+
+----------
+
+Restrictions
+""""""""""""
+
+This angle style can only be used if LAMMPS was built with the AMOEBA
+package.  See the :doc:`Build package <Build_package>` doc page for
+more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none

doc/src/angle_class2.rst

@@ -24,7 +24,7 @@ Examples
 .. code-block:: LAMMPS
 
    angle_style class2
-   angle_coeff * 75.0
+   angle_coeff * 75.0 25.0 0.3 0.002
    angle_coeff 1 bb 10.5872 1.0119 1.5228
    angle_coeff * ba 3.6551 24.895 1.0119 1.5228
 

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
-be used, as in the first example above.  Or a wild-card asterisk can be
-used to set the coefficients for multiple angle types.  This takes the
-form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of angle types,
-then an asterisk with no numeric values means all types from 1 to N.  A
-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).
+:math:`N` can be specified in one of two ways.  An explicit numeric
+value can be used, as in the first example above.  Or :math:`N` can be a
+type label, which is an alphanumeric string defined by the
+:doc:`labelmap <labelmap>` command or in a section of a data file read
+by the :doc:`read_data <read_data>` command.
 
-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:
+For numeric values only, a wild-card asterisk can be used to set the
+coefficients for multiple angle types.  This takes the form "\*" or
+"\*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
-script, except that wild-card asterisks should not be used since
-coefficients for all N types must be listed in the file.  For example,
-under the "Angle Coeffs" section of a data file, the line that
-corresponds to the first example above would be listed as
+same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
+command in an input script, except that wild-card asterisks should not
+be used since coefficients for all :math:`N` types must be listed in the
+file.  For example, under the "Angle Coeffs" section of a data file, the
+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
-doc page for details.
+allow specification of the cross-term coefficients.  See its doc page
+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
-page.
+compact form on the :ref:`Commands angle <angle>` doc 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 sdk/omp
+.. index:: angle_style spica
+.. 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
-intended for coarse grained MD simulations with the CMM parameterization
-using the :doc:`pair_style lj/sdk <pair_sdk>`.  Relative to the
-pair_style *lj/sdk*, however, the energy is shifted by
+*lj/spica* pair style between the atoms 1 and 3.  This angle potential is
+intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
+using the :doc:`pair_style lj/spica <pair_spica>`.  Relative to the
+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:`pair_style lj/sdk/coul/long <pair_sdk>`
+:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
+: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
 """"""""
@@ -73,6 +73,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`zero <angle_zero>` - topology but no interactions
 * :doc:`hybrid <angle_hybrid>` - define multiple styles of angle interactions
 
+* :doc:`amoeba <angle_amoeba>` - AMOEBA angle
 * :doc:`charmm <angle_charmm>` - CHARMM angle
 * :doc:`class2 <angle_class2>` - COMPASS (class 2) angle
 * :doc:`class2/p6 <angle_class2>` - COMPASS (class 2) angle expanded to 6th order
@@ -87,11 +88,12 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
 * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
-* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
+* :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
 
 ----------

doc/src/angle_zero.rst

@@ -8,7 +8,10 @@ Syntax
 
 .. code-block:: LAMMPS
 
-   angle_style zero *nocoeff*
+   angle_style zero keyword
+
+* zero or more keywords may be appended
+* keyword = *nocoeff*
 
 Examples
 """"""""

doc/src/atom_style.rst

@@ -10,7 +10,7 @@ Syntax
 
    atom_style style args
 
-* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
+* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or  *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *mesont* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
 
   .. parsed-literal::
 
@@ -78,6 +78,8 @@ coordinates, velocities, atom IDs and types.  See the
 :doc:`set <set>` commands for info on how to set these various
 quantities.
 
++--------------+-----------------------------------------------------+--------------------------------------+
+| *amoeba*     | molecular + charge + 1/5 neighbors                  | AMOEBA/HIPPO polarized force fields  |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *angle*      | bonds and angles                                    | bead-spring polymers with stiffness  |
 +--------------+-----------------------------------------------------+--------------------------------------+
@@ -137,11 +139,13 @@ quantities.
 .. note::
 
    It is possible to add some attributes, such as a molecule ID, to
-   atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command.  This command also
-   allows new custom attributes consisting of extra integer or
-   floating-point values to be added to atoms.  See the :doc:`fix property/atom <fix_property_atom>` page for examples of cases
-   where this is useful and details on how to initialize, access, and
-   output the custom values.
+   atom styles that do not have them via the :doc:`fix property/atom
+   <fix_property_atom>` command.  This command also allows new custom
+   attributes consisting of extra integer or floating-point values to
+   be added to atoms.  See the :doc:`fix property/atom
+   <fix_property_atom>` page for examples of cases where this is
+   useful and details on how to initialize, access, and output the
+   custom values.
 
 All of the above styles define point particles, except the *sphere*,
 *bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
@@ -154,19 +158,20 @@ per-type basis, using the :doc:`mass <mass>` command, The finite-size
 particle styles assign mass to individual particles on a per-particle
 basis.
 
-For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a
-per-particle diameter and mass.  If the diameter > 0.0, the particle
-is a finite-size sphere.  If the diameter = 0.0, it is a point
-particle.  Note that by use of the *disc* keyword with the :doc:`fix
-nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
-:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
-<fix_npt_sphere>` commands for the *sphere* style, spheres can be effectively treated as 2d
-discs for a 2d simulation if desired.  See also the :doc:`set
-density/disc <set>` command.  The *sphere* and *bpm/sphere* styles take an optional 0
-or 1 argument.  A value of 0 means the radius of each sphere is
-constant for the duration of the simulation.  A value of 1 means the
-radii may vary dynamically during the simulation, e.g. due to use of
-the :doc:`fix adapt <fix_adapt>` command.
+For the *sphere* and *bpm/sphere* styles, the particles are spheres
+and each stores a per-particle diameter and mass.  If the diameter >
+0.0, the particle is a finite-size sphere.  If the diameter = 0.0, it
+is a point particle.  Note that by use of the *disc* keyword with the
+:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
+<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
+npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
+can be effectively treated as 2d discs for a 2d simulation if desired.
+See also the :doc:`set density/disc <set>` command.  The *sphere* and
+*bpm/sphere* styles take an optional 0 or 1 argument.  A value of 0
+means the radius of each sphere is constant for the duration of the
+simulation.  A value of 1 means the radii may vary dynamically during
+the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
+command.
 
 For the *ellipsoid* style, the particles are ellipsoids and each
 stores a flag which indicates whether it is a finite-size ellipsoid or
@@ -175,15 +180,16 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
 with its orientation.
 
 For the *dielectric* style, each particle can be either a physical
-particle (e.g. an ion), or an interface particle representing a boundary
-element. For physical particles, the per-particle properties are
-the same as atom_style full.  For interface particles, in addition to
-these properties, each particle also has an area, a normal unit vector,
-a mean local curvature, the mean and difference of the dielectric constants
-of two sides of the interface, and the local dielectric constant at the
-boundary element.  The distinction between the physical and interface
-particles is only meaningful when :doc:`fix polarize <fix_polarize>`
-commands are applied to the interface particles.
+particle (e.g. an ion), or an interface particle representing a
+boundary element. For physical particles, the per-particle properties
+are the same as atom_style full.  For interface particles, in addition
+to these properties, each particle also has an area, a normal unit
+vector, a mean local curvature, the mean and difference of the
+dielectric constants of two sides of the interface, and the local
+dielectric constant at the boundary element.  The distinction between
+the physical and interface particles is only meaningful when :doc:`fix
+polarize <fix_polarize>` commands are applied to the interface
+particles.
 
 For the *dipole* style, a point dipole is defined for each point
 particle.  Note that if you wish the particles to be finite-size
@@ -272,16 +278,17 @@ showing the use of the *template* atom style versus *molecular*.
 
 .. note::
 
-   When using the *template* style with a :doc:`molecule template <molecule>` that contains multiple molecules, you should
-   insure the atom types, bond types, angle_types, etc in all the
-   molecules are consistent.  E.g. if one molecule represents H2O and
-   another CO2, then you probably do not want each molecule file to
-   define 2 atom types and a single bond type, because they will conflict
-   with each other when a mixture system of H2O and CO2 molecules is
-   defined, e.g. by the :doc:`read_data <read_data>` command.  Rather the
-   H2O molecule should define atom types 1 and 2, and bond type 1.  And
-   the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
-   2 if a single oxygen type is desired), and bond type 2.
+   When using the *template* style with a :doc:`molecule template
+   <molecule>` that contains multiple molecules, you should insure the
+   atom types, bond types, angle_types, etc in all the molecules are
+   consistent.  E.g. if one molecule represents H2O and another CO2,
+   then you probably do not want each molecule file to define 2 atom
+   types and a single bond type, because they will conflict with each
+   other when a mixture system of H2O and CO2 molecules is defined,
+   e.g. by the :doc:`read_data <read_data>` command.  Rather the H2O
+   molecule should define atom types 1 and 2, and bond type 1.  And
+   the CO2 molecule should define atom types 3 and 4 (or atom types 3
+   and 2 if a single oxygen type is desired), and bond type 2.
 
 For the *body* style, the particles are arbitrary bodies with internal
 attributes defined by the "style" of the bodies, which is specified by
@@ -339,6 +346,8 @@ Many of the styles listed above are only enabled if LAMMPS was built
 with a specific package, as listed below.  See the :doc:`Build package
 <Build_package>` page for more info.
 
+The *amoeba* style is part of the AMOEBA package.
+
 The *angle*, *bond*, *full*, *molecular*, and *template* styles are
 part of the MOLECULE package.
 
@@ -350,9 +359,11 @@ The *dipole* style is part of the DIPOLE package.
 
 The *peri* style is part of the PERI package for Peridynamics.
 
-The *oxdna* style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA.
+The *oxdna* style is part of the CG-DNA package for coarse-grained
+simulation of DNA and RNA.
 
-The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
+The *electron* style is part of the EFF package for :doc:`electronic
+force fields <pair_eff>`.
 
 The *dpd* style is part of the DPD-REACT package for dissipative
 particle dynamics (DPD).
@@ -363,7 +374,8 @@ dissipative particle dynamics (mDPD), and transport dissipative particle
 dynamics (tDPD), respectively.
 
 The *sph* style is part of the SPH package for smoothed particle
-hydrodynamics (SPH).  See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
+hydrodynamics (SPH).  See `this PDF guide
+<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
 
 The *mesont* style is part of the MESONT package.
 

doc/src/balance.rst

@@ -6,7 +6,7 @@ balance command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    balance thresh style args ... keyword args ...
 

doc/src/bond_bpm_rotational.rst

@@ -38,8 +38,7 @@ Examples
    bond_style bpm/rotational
    bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
 
-   bond_style bpm/rotational myfix 1000 time id1 id2
-   fix myfix all store/local 1000 3
+   bond_style bpm/rotational store/local myfix 1000 time id1 id2
    dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
    dump_modify 1 write_header no
 

doc/src/bond_coeff.rst

@@ -10,7 +10,7 @@ Syntax
 
    bond_coeff N args
 
-* N = bond type (see asterisk form below)
+* N = numeric bond type (see asterisk form below), or type label
 * args = coefficients for one or more bond types
 
 Examples
@@ -21,7 +21,10 @@ Examples
    bond_coeff 5 80.0 1.2
    bond_coeff * 30.0 1.5 1.0 1.0
    bond_coeff 1*4 30.0 1.5 1.0 1.0
-   bond_coeff 1 harmonic 200.0 1.0
+   bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
+
+   labelmap bond 5 carbonyl
+   bond_coeff carbonyl 80.0 1.2
 
 Description
 """""""""""
@@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
 Bond 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
-be used, as in the first example above.  Or a wild-card asterisk can be
-used to set the coefficients for multiple bond types.  This takes the
-form "\*" or "\*n" or "n\*" or "m\*n".  If N = the number of bond types,
-then an asterisk with no numeric values means all types from 1 to N.  A
+:math:`N` can be specified in one of several ways.  An explicit numeric
+value can be used, as in the first example above.  Or :math:`N` can be a
+type label, which is an alphanumeric string defined by the
+:doc:`labelmap <labelmap>` command or in a section of a data file read
+by the :doc:`read_data <read_data>` command.
+
+For numeric values only, a wild-card asterisk can be used to set the
+coefficients for multiple bond types.  This takes the form "\*" or "\*n"
+or "n\*" or "m\*n".  If :math:`N` is the number of bond 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 N (inclusive).  A middle asterisk
-means all types from m to n (inclusive).
+asterisk means all types from n to :math:`N` (inclusive).  A middle
+asterisk means all types from m to n (inclusive).
 
 Note that using a bond_coeff command can override a previous setting
 for the same bond type.  For example, these commands set the coeffs
@@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
 A line in a data file that specifies bond coefficients uses the exact
 same format as the arguments of the bond_coeff command in an input
 script, except that wild-card asterisks should not be used since
-coefficients for all N types must be listed in the file.  For example,
-under the "Bond Coeffs" section of a data file, the line that
+coefficients for all :math:`N` types must be listed in the file.  For
+example, under the "Bond Coeffs" section of a data file, the line that
 corresponds to the first example above would be listed as
 
 .. parsed-literal::

doc/src/bond_mesocnt.rst

@@ -0,0 +1,84 @@
+.. index:: bond_style mesocnt
+
+bond_style mesocnt command
+===========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style mesocnt
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style mesocnt
+   bond_coeff 1 C 10 10 20.0
+   bond_coeff 4 custom 800.0 10.0
+
+Description
+"""""""""""
+
+.. versionadded:: 15Sep2022
+
+The *mesocnt* bond style is a wrapper for the :doc:`harmonic
+<bond_harmonic>` style, and uses the potential
+
+.. math::
+
+   E = K (r - r_0)^2
+
+where :math:`r_0` is the equilibrium bond distance.  Note that the
+usual 1/2 factor is included in :math:`K`.  The style implements
+parameterization presets of :math:`K` for mesoscopic simulations of
+carbon nanotubes based on the atomistic simulations of
+:ref:`(Srivastava) <Srivastava_1>`.
+
+Other presets can be readily implemented in the future.
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands:
+
+* preset = *C* or *custom*
+* additional parameters depending on preset
+
+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)
+
+Preset *custom* is simply a direct wrapper for the :doc:`harmonic
+<bond_harmonic>` style, and the additional parameters are:
+
+* :math:`K` (energy/distance\^2)
+* :math:`r_0` (distance)
+
+Restrictions
+""""""""""""
+
+This bond style can only be used if LAMMPS was built with the MOLECULE
+and MESONT packages.  See the :doc:`Build package <Build_package>`
+page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`bond_coeff <bond_coeff>`, :doc:`delete_bonds <delete_bonds>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Srivastava_1:
+
+**(Srivastava)** Zhigilei, Wei and Srivastava, Phys. Rev. B 71, 165417
+(2005).