Merge pull request #3460 from akohlmey/maintenance-2022-06-23

Second round of maintenance fixes and backports for the stable release

.gitattributes

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

.github/CODEOWNERS

@@ -13,45 +13,39 @@ lib/kim/*             @ellio167
 lib/mesont/*          @iafoss
 
 # whole packages
-src/ADIOS/*           @pnorbert
-src/AMOEBA/*          @sjplimp
-src/BPM/*             @jtclemm
+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-SPICA/*        @yskmiyazaki
+src/CG-SDK/*          @akohlmey
 src/COLVARS/*         @giacomofiorin
-src/COMPRESS/*        @rbberger
 src/DIELECTRIC/*      @ndtrung81
-src/ELECTRODE/*       @ludwig-ahrens
 src/FEP/*             @agiliopadua
-src/GPU/*             @ndtrung81
-src/GRANULAR/*        @jtclemm @dsbolin
+src/ML-HDNNP/*        @singraber
 src/INTEL/*           @wmbrownintel
-src/KIM/*             @ellio167
-src/KOKKOS/*          @stanmoore1
-src/LATTE/*           @cnegre
 src/MANIFOLD/*        @Pakketeretet2
-src/MDI/*             @taylor-a-barnes @sjplimp
+src/MDI/*             @taylor-a-barnes
 src/MEAM/*            @martok
 src/MESONT/*          @iafoss
-src/ML-HDNNP/*        @singraber
-src/ML-IAP/*          @athomps
-src/ML-PACE/*         @yury-lysogorskiy
-src/ML-POD/*          @exapde @rohskopf
 src/MOFFF/*           @hheenen
 src/MOLFILE/*         @akohlmey
 src/NETCDF/*          @pastewka
-src/OPENMP/*          @akohlmey
-src/PHONON/*          @lingtikong
-src/PLUGIN/*          @akohlmey
+src/ML-PACE/*         @yury-lysogorskiy
 src/PLUMED/*          @gtribello
+src/PHONON/*          @lingtikong
 src/PTM/*             @pmla
+src/OPENMP/*          @akohlmey
 src/QMMM/*            @akohlmey
-src/REACTION/*        @jrgissing
 src/REAXFF/*          @hasanmetin @stanmoore1
+src/REACTION/*        @jrgissing
 src/SCAFACOS/*        @rhalver
-src/SNAP/*            @athomps
-src/SPIN/*            @julient31
 src/TALLY/*           @akohlmey
 src/UEF/*             @danicholson
 src/VTK/*             @rbberger
@@ -63,10 +57,7 @@ src/MANYBODY/pair_vashishta_table.* @andeplane
 src/MANYBODY/pair_atm.*             @sergeylishchuk
 src/REPLICA/*_grem.*                @dstelter92
 src/EXTRA-COMPUTE/compute_stress_mop*.* @RomainVermorel
-src/EXTRA-COMPUTE/compute_born_matrix.* @Bibobu @athomps
 src/MISC/*_tracker.*                @jtclemm
-src/MC/fix_gcmc.*                   @athomps
-src/MC/fix_sgcmc.*                  @athomps
 
 # core LAMMPS classes
 src/lammps.*              @sjplimp
@@ -128,32 +119,26 @@ src/dump_movie.*          @akohlmey
 src/exceptions.h          @rbberger
 src/fix_nh.*              @athomps
 src/info.*                @akohlmey @rbberger
-src/min*                  @sjplimp @stanmoore1
-src/platform.*            @akohlmey
 src/timer.*               @akohlmey
+src/min*                  @sjplimp @stanmoore1
 src/utils.*               @akohlmey @rbberger
 src/verlet.*              @sjplimp @stanmoore1
 src/math_eigen_impl.h     @jewettaij
 
 # tools
-tools/coding_standard/* @akohlmey @rbberger
-tools/emacs/*         @HaoZeke
-tools/lammps-shell/*  @akohlmey
 tools/msi2lmp/*       @akohlmey
-tools/offline/*       @rbberger
+tools/emacs/*         @HaoZeke
 tools/singularity/*   @akohlmey @rbberger
-tools/swig/*          @akohlmey
+tools/coding_standard/* @rbberger
 tools/valgrind/*      @akohlmey
-tools/vim/*           @hammondkd
+tools/swig/*          @akohlmey
+tools/offline/*       @rbberger
 
 # tests
-unittest/*            @akohlmey
+unittest/*            @akohlmey @rbberger
 
 # cmake
 cmake/*               @junghans @rbberger
-cmake/Modules/LAMMPSInterfacePlugin.cmake @akohlmey
-cmake/Modules/MPI4WIN.cmake @akohlmey
-cmake/Modules/OpenCLLoader.cmake @akohlmey
 cmake/Modules/Packages/COLVARS.cmake @junghans @rbberger @giacomofiorin
 cmake/Modules/Packages/KIM.cmake @junghans @rbberger @ellio167
 cmake/presets/*.cmake @akohlmey
@@ -162,12 +147,13 @@ cmake/presets/*.cmake @akohlmey
 python/*              @rbberger
 
 # fortran
-fortran/*             @akohlmey @hammondkd
+fortran/*             @akohlmey
 
 # docs
-doc/*                 @akohlmey
+doc/utils/*/*         @rbberger
+doc/Makefile          @rbberger
+doc/README            @rbberger
 examples/plugin/*     @akohlmey
-examples/PACKAGES/pace/plugin/*     @akohlmey
 
 # for releases
 src/version.h         @sjplimp

.github/ISSUE_TEMPLATE/help_request.md

@@ -1,6 +1,6 @@
 ---
 name: Request for Help
-about: "Don't post help requests here, post in the LAMMPS forum"
+about: "Don't post help requests here, email the lammps-users mailing list"
 title: ""
 labels: invalid
 assignees: ''
@@ -8,9 +8,8 @@ assignees: ''
 ---
 
 Please **do not** post requests for help (e.g. with installing or using LAMMPS) here.
-Instead, you can post to the LAMMPS category in the Materials Science Community
-Discourse forum at: https://matsci.org/lammps/
+Instead send an e-mail to the lammps-users mailing list.
 
 This issue tracker is for tracking LAMMPS development related issues only.
 
-Thank you in advance for your cooperation.
+Thanks for your cooperation.

.github/codecov.yml

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

.github/workflows/codeql-analysis.yml

@@ -49,9 +49,7 @@ jobs:
       shell: bash
       working-directory: build
       run: |
-        cmake -C ../cmake/presets/most.cmake \
-              -D DOWNLOAD_POTENTIALS=off \
-              ../cmake
+        cmake -C ../cmake/presets/most.cmake ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/compile-msvc.yml

@@ -3,11 +3,7 @@ name: "Native Windows Compilation and Unit Tests"
 
 on:
   push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
+    branches: [develop]
 
   workflow_dispatch:
 
@@ -26,25 +22,20 @@ jobs:
     - name: Select Python version
       uses: actions/setup-python@v4
       with:
-        python-version: '3.11'
+        python-version: '3.10'
 
     - name: Building LAMMPS via CMake
       shell: bash
       run: |
         python3 -m pip install numpy
         python3 -m pip install pyyaml
-        nuget install MSMPIsdk
-        nuget install MSMPIDIST
         cmake -C cmake/presets/windows.cmake \
-              -D DOWNLOAD_POTENTIALS=off \
               -D PKG_PYTHON=on \
-              -D WITH_PNG=off \
-              -D WITH_JPEG=off \
               -S cmake -B build \
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \
               -D ENABLE_TESTING=on
-        cmake --build build --config Release --parallel 2
+        cmake --build build --config Release
 
     - name: Run LAMMPS executable
       shell: bash
@@ -55,4 +46,4 @@ jobs:
     - name: Run Unit Tests
       working-directory: build
       shell: bash
-      run: ctest -V -C Release -E FixTimestep:python_move_nve
+      run: ctest -V -C Release

.github/workflows/coverity.yml

@@ -1,103 +0,0 @@
-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

@@ -3,11 +3,7 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches:
-      - develop
-  pull_request:
-    branches:
-      - develop
+    branches: [develop]
 
   workflow_dispatch:
 
@@ -43,11 +39,9 @@ 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 \
-              -D DOWNLOAD_POTENTIALS=off \
               -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
               -D CMAKE_C_COMPILER_LAUNCHER=ccache \
               -D ENABLE_TESTING=on \

.gitignore

@@ -55,5 +55,3 @@ out/RelWithDebInfo
 out/Release
 out/x86
 out/x64
-src/Makefile.package-e
-src/Makefile.package.settings-e

CITATION.cff

@@ -1,91 +0,0 @@
-# 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"

README

@@ -16,8 +16,8 @@ National Laboratories, a US Department of Energy facility, with
 funding from the DOE.  It is an open-source code, distributed freely
 under the terms of the GNU Public License (GPL) version 2.
 
-The code is maintained by the LAMMPS development team who can be emailed
-at developers@lammps.org.  The LAMMPS WWW Site at www.lammps.org has
+The primary author of the code is Steve Plimpton, who can be emailed
+at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
 more information about the code and its uses.
 
 The LAMMPS distribution includes the following files and directories:

SECURITY.md

@@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
 behavior from calling functions in one of those libraries.
 
 Thus is is quite easy to crash LAMMPS through malicious input and do all
-kinds of file system manipulations.  And because of that LAMMPS should
+kinds of filesystem manipulations.  And because of that LAMMPS should
 **NEVER** be compiled or **run** as superuser, either from a "root" or
 "administrator" account directly or indirectly via "sudo" or "su".
 
 Therefore what could be seen as a security vulnerability is usually
-either a user mistake or a bug in the code.  Bugs can be reported in the
-LAMMPS project [issue tracker on
-GitHub](https://github.com/lammps/lammps/issues).
+either a user mistake or a bug in the code.  Bugs can be reported in
+the LAMMPS project
+[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
 
 To mitigate issues with using homoglyphs or bidirectional reordering in
 unicode, which have been demonstrated as a vector to obfuscate and hide
@@ -30,19 +30,10 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows a continuous release development model.  We aim to keep
-the development version (`develop` branch) always fully functional and
-employ a variety of automatic testing procedures to detect failures
-of existing functionality from adding or modifying features.  Most of
-those tests are run on pull requests *before* merging to the `develop`
-branch.  The `develop` branch is protected, so all changes *must* be
-submitted as a pull request and thus cannot avoid the automated tests.
-
-Additional tests are run *after* merging.  Before releases are made
-*all* tests must have cleared.  Then a release tag is applied and the
-`release` branch is fast-forwarded to that tag.  This is often referred
-to as a patch release. Bug fixes and updates are
-applied first to the `develop` branch.  Later, they appear in the `release`
-branch when the next patch release occurs.
-For stable releases, selected bug fixes, updates, and new functionality
-are pushed to the `stable` branch and a new stable tag is applied.
+LAMMPS follows continuous release development model.  We aim to keep all
+release versions (stable or patch) fully functional and employ a variety
+of automatic testing procedures to detect failures of existing
+functionality from adding new features before releases are made.  Thus
+bugfixes and updates are only integrated into the current development
+branch and thus the next (patch) release and users are recommended to
+update regularly.

cmake/CMakeLists.txt

@@ -3,7 +3,6 @@
 # This file is part of LAMMPS
 # Created by Christoph Junghans and Richard Berger
 cmake_minimum_required(VERSION 3.10)
-########################################
 # set policy to silence warnings about ignoring <PackageName>_ROOT but use it
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
@@ -17,17 +16,6 @@ endif()
 if(POLICY CMP0109)
   cmake_policy(SET CMP0109 OLD)
 endif()
-# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
-if(POLICY CMP0135)
-  cmake_policy(SET CMP0135 OLD)
-endif()
-########################################
-# Use CONFIGURE_DEPENDS as option for file(GLOB...) when available
-if(CMAKE_VERSION VERSION_LESS 3.12)
-  unset(CONFIGURE_DEPENDS)
-else()
-  set(CONFIGURE_DEPENDS CONFIGURE_DEPENDS)
-endif()
 ########################################
 
 project(lammps CXX)
@@ -116,7 +104,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
+      set(CMAKE_TUNE_DEFAULT "-xHost")
     endif()
   endif()
 endif()
@@ -151,11 +139,13 @@ set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
 # ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 # and prints lots of pointless warnings about "unsafe" functions
 if(MSVC)
-  if((CMAKE_CXX_COMPILER_ID STREQUAL "MSVC") OR (CMAKE_CXX_COMPILER_ID STREQUAL "Intel"))
+  if(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
     add_compile_options(/Zc:__cplusplus)
     add_compile_options(/wd4244)
     add_compile_options(/wd4267)
-    add_compile_options(/EHsc)
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
   endif()
   add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
@@ -168,19 +158,6 @@ endif()
 ########################################################################
 # User input options                                                   #
 ########################################################################
-# set path to python interpreter and thus enforcing python version 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)
@@ -202,8 +179,8 @@ else()
 endif()
 
 include(GNUInstallDirs)
-file(GLOB ALL_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
-file(GLOB MAIN_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/main.cpp)
+file(GLOB ALL_SOURCES ${LAMMPS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB MAIN_SOURCES ${LAMMPS_SOURCE_DIR}/main.cpp)
 list(REMOVE_ITEM ALL_SOURCES ${MAIN_SOURCES})
 add_library(lammps ${ALL_SOURCES})
 
@@ -221,7 +198,6 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES
   ADIOS
-  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -230,7 +206,7 @@ set(STANDARD_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -258,7 +234,6 @@ set(STANDARD_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
-  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -274,7 +249,6 @@ set(STANDARD_PACKAGES
   ML-QUIP
   ML-RANN
   ML-SNAP
-  ML-POD
   MOFFF
   MOLECULE
   MOLFILE
@@ -325,15 +299,6 @@ if(PKG_ADIOS)
   # script that defines the MPI::MPI_C target
   enable_language(C)
   find_package(ADIOS2 REQUIRED)
-  if(BUILD_MPI)
-    if(NOT ADIOS2_HAVE_MPI)
-      message(FATAL_ERROR "ADIOS2 must be built with MPI support when LAMMPS has MPI enabled")
-    endif()
-  else()
-    if(ADIOS2_HAVE_MPI)
-      message(FATAL_ERROR "ADIOS2 must be built without MPI support when LAMMPS has MPI disabled")
-    endif()
-  endif()
   target_link_libraries(lammps PRIVATE adios2::adios2)
 endif()
 
@@ -397,13 +362,11 @@ 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)
@@ -441,19 +404,21 @@ if(BUILD_OMP)
   target_link_libraries(lmp PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_ML-POD OR PKG_LATTE OR PKG_ELECTRODE)
+if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
-  if (NOT USE_INTERNAL_LINALG)
-    find_package(LAPACK)
-    find_package(BLAS)
-  endif()
-  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
-    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.cpp)
-    add_library(linalg STATIC ${LINALG_SOURCES})
+  find_package(LAPACK)
+  find_package(BLAS)
+  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+    include(CheckGeneratorSupport)
+    if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
+      status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
+    endif()
+    enable_language(Fortran)
+    file(GLOB LAPACK_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
+    add_library(linalg STATIC ${LAPACK_SOURCES})
     set_target_properties(linalg PROPERTIES OUTPUT_NAME lammps_linalg${LAMMPS_MACHINE})
     set(BLAS_LIBRARIES "$<TARGET_FILE:linalg>")
     set(LAPACK_LIBRARIES "$<TARGET_FILE:linalg>")
-    target_link_libraries(lammps PRIVATE linalg)
   else()
     list(APPEND LAPACK_LIBRARIES ${BLAS_LIBRARIES})
   endif()
@@ -521,7 +486,7 @@ else()
 endif()
 
 foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
-        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
+        PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -566,8 +531,6 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
 ########################################################
 # Fetch missing external files and archives for packages
 ########################################################
-option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
-mark_as_advanced(DOWNLOAD_POTENTIALS)
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   if(PKG_${PKG})
     FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
@@ -580,8 +543,8 @@ endforeach()
 foreach(PKG ${STANDARD_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -608,8 +571,8 @@ endforeach()
 foreach(PKG ${SUFFIX_PACKAGES})
   set(${PKG}_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/${PKG})
 
-  file(GLOB ${PKG}_SOURCES ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
-  file(GLOB ${PKG}_HEADERS ${CONFIGURE_DEPENDS} ${${PKG}_SOURCES_DIR}/[^.]*.h)
+  file(GLOB ${PKG}_SOURCES ${${PKG}_SOURCES_DIR}/[^.]*.cpp)
+  file(GLOB ${PKG}_HEADERS ${${PKG}_SOURCES_DIR}/[^.]*.h)
 
   # check for package files in src directory due to old make system
   DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${${PKG}_SOURCES} ${${PKG}_HEADERS})
@@ -620,11 +583,18 @@ endforeach()
 ##############################################
 # add lib sources of (simple) enabled packages
 ############################################
-foreach(PKG_LIB POEMS ATC AWPMD H5MD)
+foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
   if(PKG_${PKG_LIB})
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
-    file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
-      ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
+    if(PKG_LIB STREQUAL "mesont")
+      enable_language(Fortran)
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
+    else()
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
+        ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
+    endif()
     add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})
     set_target_properties(${PKG_LIB} PROPERTIES OUTPUT_NAME lammps_${PKG_LIB}${LAMMPS_MACHINE})
     target_link_libraries(lammps PRIVATE ${PKG_LIB})
@@ -638,7 +608,7 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD)
   endif()
 endforeach()
 
-if(PKG_ELECTRODE OR PKG_ML-POD)
+if(PKG_ELECTRODE)
   target_link_libraries(lammps PRIVATE ${LAPACK_LIBRARIES})
 endif()
 
@@ -667,7 +637,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MC MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -740,17 +710,18 @@ list(FIND LANGUAGES "Fortran" _index)
 if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
-  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
-  library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
-  platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
-set(LAMMPS_FMT_HEADERS core.h format.h)
+set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
+  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
+  pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
+if(LAMMPS_EXCEPTIONS)
+  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
+endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
 set_target_properties(lammps PROPERTIES PREFIX "lib")
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@@ -759,14 +730,6 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
     install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   endif()
 endforeach()
-foreach(_HEADER ${LAMMPS_FMT_HEADERS})
-  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
-  add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
-  add_dependencies(lammps fmt_${_HEADER})
-  if(BUILD_SHARED_LIBS)
-    install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
-  endif()
-endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
 get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@@ -821,13 +784,9 @@ 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)
@@ -860,25 +819,16 @@ 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)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
-    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
-    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
+    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
   endif()
 endif()
 
@@ -893,23 +843,6 @@ if(ClangFormat_FOUND)
     WORKING_DIRECTORY ${LAMMPS_SOURCE_DIR})
 endif()
 
-# extract Kokkos compilation settings
-get_cmake_property(_allvars VARIABLES)
-foreach(_var ${_allvars})
-  if(${_var})
-    string(REGEX MATCH "Kokkos_ENABLE_(SERIAL|THREADS|OPENMP|CUDA|HIP|SYCL|OPENMPTARGET|HPX)" _match ${_var})
-    if(_match)
-      string(REGEX REPLACE "Kokkos_ENABLE_(OPENMP|SERIAL|CUDA|HIP|SYCL)" "\\1" _match ${_var})
-      list(APPEND KOKKOS_DEVICE ${_match})
-    endif()
-    string(REGEX MATCH "Kokkos_ARCH" _match ${_var})
-    if(_match)
-      string(REGEX REPLACE "Kokkos_ARCH_(.*)" "\\1" _match ${_var})
-      list(APPEND KOKKOS_ARCH ${_match})
-    endif()
-  endif()
-endforeach()
-
 get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 if(BUILD_IS_MULTI_CONFIG)
   set(LAMMPS_BUILD_TYPE "Multi-Config")
@@ -921,7 +854,6 @@ feature_summary(DESCRIPTION "The following tools and libraries have been found a
 message(STATUS "<<< Build configuration >>>
    LAMMPS Version:   ${PROJECT_VERSION}
    Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
-   CMake Version:    ${CMAKE_VERSION}
    Build type:       ${LAMMPS_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -1008,10 +940,7 @@ if(PKG_GPU)
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
-  message(STATUS "Kokkos Devices: ${KOKKOS_DEVICE}")
-  if(KOKKOS_ARCH)
-    message(STATUS "Kokkos Architecture: ${KOKKOS_ARCH}")
-  endif()
+  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
 endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>

cmake/CMakeSettings.json

@@ -72,7 +72,7 @@
       "configurationType": "Debug",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
       "buildCommandArgs": "",
       "ctestCommandArgs": "",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -105,7 +105,7 @@
       "configurationType": "Release",
       "buildRoot": "${workspaceRoot}\\build\\${name}",
       "installRoot": "${workspaceRoot}\\install\\${name}",
-      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe -DBUILD_MPI=off",
+      "cmakeCommandArgs": "-C ${workspaceRoot}\\cmake\\presets\\windows.cmake -DCMAKE_C_COMPILER=clang-cl.exe -DCMAKE_CXX_COMPILER=clang-cl.exe",
       "buildCommandArgs": "",
       "ctestCommandArgs": "-V",
       "inheritEnvironments": [ "clang_cl_x64" ],
@@ -305,4 +305,4 @@
       ]
     }
   ]
-}
+}

cmake/Modules/Documentation.cmake

@@ -17,7 +17,7 @@ if(BUILD_DOC)
   endif()
   find_package(Doxygen 1.8.10 REQUIRED)
 
-  file(GLOB DOC_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
+  file(GLOB DOC_SOURCES ${LAMMPS_DOC_DIR}/src/[^.]*.rst)
 
 
   add_custom_command(
@@ -56,27 +56,16 @@ if(BUILD_DOC)
   )
 
   set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "b81661c6e6ba06278e6ae37b30b0c492" CACHE STRING "MD5 checksum of MathJax tarball")
+  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
-  GetFallbackURL(MATHJAX_URL MATHJAX_FALLBACK)
 
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    if(EXISTS ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
-      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz)
-    endif()
-    if(NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}")
-      file(DOWNLOAD ${MATHJAX_URL} "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz" STATUS DL_STATUS SHOW_PROGRESS)
-      file(MD5 ${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz DL_MD5)
-      if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${MATHJAX_MD5}"))
-        message(WARNING "Download from primary URL ${MATHJAX_URL} failed\nTrying fallback URL ${MATHJAX_FALLBACK}")
-        file(DOWNLOAD ${MATHJAX_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${MATHJAX_MD5} SHOW_PROGRESS)
-      endif()
-    else()
-      message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-    endif()
+    file(DOWNLOAD ${MATHJAX_URL}
+      "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
+      EXPECTED_MD5 ${MATHJAX_MD5})
     execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf mathjax.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    file(GLOB MATHJAX_VERSION_DIR ${CONFIGURE_DEPENDS} ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
+    file(GLOB MATHJAX_VERSION_DIR ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)
   endif()
 

cmake/Modules/ExternalCMakeProject.cmake

@@ -9,22 +9,8 @@ function(ExternalCMakeProject target url hash basedir cmakedir cmakefile)
 
   get_filename_component(archive ${url} NAME)
   file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)
-  if(EXISTS ${CMAKE_BINARY_DIR}/_deps/${archive})
-    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
-  endif()
-  if(NOT "${DL_MD5}" STREQUAL "${hash}")
-    message(STATUS "Downloading ${url}")
-    file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} STATUS DL_STATUS SHOW_PROGRESS)
-    file(MD5 ${CMAKE_BINARY_DIR}/_deps/${archive} DL_MD5)
-    if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${hash}"))
-      set(${target}_URL ${url})
-      GetFallbackURL(${target}_URL fallback)
-      message(WARNING "Download from primary URL ${url} failed\nTrying fallback URL ${fallback}")
-      file(DOWNLOAD ${fallback} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
-    endif()
-  else()
-    message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/_deps/${archive}")
-  endif()
+  message(STATUS "Downloading ${url}")
+  file(DOWNLOAD ${url} ${CMAKE_BINARY_DIR}/_deps/${archive} EXPECTED_HASH MD5=${hash} SHOW_PROGRESS)
   message(STATUS "Unpacking and configuring ${archive}")
   execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf ${CMAKE_BINARY_DIR}/_deps/${archive}
     WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src)

cmake/Modules/FindClangFormat.cmake

@@ -1,10 +1,5 @@
 # Find clang-format
 find_program(ClangFormat_EXECUTABLE NAMES clang-format
-                                          clang-format-15.0
-                                          clang-format-14.0
-                                          clang-format-13.0
-                                          clang-format-12.0
-                                          clang-format-11.0
                                           clang-format-10.0
                                           clang-format-9.0
                                           clang-format-8.0
@@ -19,27 +14,19 @@ if(ClangFormat_EXECUTABLE)
                   OUTPUT_VARIABLE clang_format_version
                   ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE)
 
-  if(clang_format_version MATCHES "^(Ubuntu |)clang-format version .*")
-    # Arch Linux output:
+
+  if(clang_format_version MATCHES "^clang-format version .*")
+    # Arch Linux
     # clang-format version 10.0.0
-    #
-    # Ubuntu 18.04 LTS output:
+
+    # Ubuntu 18.04 LTS Output
     # clang-format version 6.0.0-1ubuntu2 (tags/RELEASE_600/final)
-    #
-    # Ubuntu 20.04 LTS output:
-    # clang-format version 10.0.0-4ubuntu1
-    #
-    # Ubuntu 22.04 LTS output:
-    # Ubuntu clang-format version 14.0.0-1ubuntu1
-    #
-    # Fedora 36 output:
-    # clang-format version 14.0.5 (Fedora 14.0.5-1.fc36)
-    string(REGEX REPLACE "^(Ubuntu |)clang-format version ([0-9.]+).*"
-                         "\\2"
+    string(REGEX REPLACE "clang-format version ([0-9.]+).*"
+                         "\\1"
                          ClangFormat_VERSION
                          "${clang_format_version}")
   elseif(clang_format_version MATCHES ".*LLVM version .*")
-    # CentOS 7 output:
+    # CentOS 7 Output
     # LLVM (http://llvm.org/):
     #   LLVM version 3.4.2
     #   Optimized build.

cmake/Modules/FindZMQ.cmake

@@ -0,0 +1,19 @@
+find_path(ZMQ_INCLUDE_DIR zmq.h)
+find_library(ZMQ_LIBRARY NAMES zmq)
+
+include(FindPackageHandleStandardArgs)
+find_package_handle_standard_args(ZMQ DEFAULT_MSG ZMQ_LIBRARY ZMQ_INCLUDE_DIR)
+
+# Copy the results to the output variables and target.
+if(ZMQ_FOUND)
+  set(ZMQ_LIBRARIES ${ZMQ_LIBRARY})
+  set(ZMQ_INCLUDE_DIRS ${ZMQ_INCLUDE_DIR})
+
+  if(NOT TARGET ZMQ::ZMQ)
+    add_library(ZMQ::ZMQ UNKNOWN IMPORTED)
+    set_target_properties(ZMQ::ZMQ PROPERTIES
+      IMPORTED_LINK_INTERFACE_LANGUAGES "C"
+      IMPORTED_LOCATION "${ZMQ_LIBRARY}"
+      INTERFACE_INCLUDE_DIRECTORIES "${ZMQ_INCLUDE_DIR}")
+  endif()
+endif()

cmake/Modules/LAMMPSInterfacePlugin.cmake

@@ -65,7 +65,7 @@ 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 ${CONFIGURE_DEPENDS} ${path})
+  file(GLOB _dirs ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -112,76 +112,45 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure MinGW compatible MPICH development files for Windows
-    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
-    if(USE_MSMPI)
-      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-      set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-      mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
+    # 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 ${MPICH2_WIN64_DEVEL_MD5}
-          CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-          BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
-      else()
-        message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
-      endif()
-
-      ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-      file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-      add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-      set_target_properties(MPI::MPI_CXX PROPERTIES
-        IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-        INTERFACE_INCLUDE_DIRECTORIES "${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/libmsmpi.a")
+    include(ExternalProject)
+    if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+      ExternalProject_Add(mpi4win_build
+        URL     ${MPICH2_WIN64_DEVEL_URL}
+        URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+        CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+        BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
     else()
-      # Download and configure custom MPICH files for Windows
-      message(STATUS "Downloading and configuring MPICH-1.4.1 for Windows")
-      set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/mpich2-win64-devel.tar.gz" CACHE STRING "URL for MPICH2 (win64) tarball")
-      set(MPICH2_WIN64_DEVEL_MD5 "4939fdb59d13182fd5dd65211e469f14" CACHE STRING "MD5 checksum of MPICH2 (win64) tarball")
-      mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-      mark_as_advanced(MPICH2_WIN64_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")
+      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)

cmake/Modules/LAMMPSUtils.cmake

@@ -41,7 +41,7 @@ endfunction()
 
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
-  file(GLOB _dirs ${CONFIGURE_DEPENDS} ${path})
+  file(GLOB _dirs ${path})
   set(_besttime 2000-01-01T00:00:00)
   set(_bestfile "<unknown>")
   foreach(_dir ${_dirs})
@@ -80,8 +80,8 @@ endfunction()
 
 function(check_for_autogen_files source_dir)
     message(STATUS "Running check for auto-generated files from make-based build system")
-    file(GLOB SRC_AUTOGEN_FILES ${CONFIGURE_DEPENDS} ${source_dir}/style_*.h)
-    file(GLOB SRC_AUTOGEN_PACKAGES ${CONFIGURE_DEPENDS} ${source_dir}/packages_*.h)
+    file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
+    file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
@@ -99,15 +99,8 @@ function(check_for_autogen_files source_dir)
 endfunction()
 
 macro(pkg_depends PKG1 PKG2)
-  if(DEFINED BUILD_${PKG2})
-    if(PKG_${PKG1} AND NOT BUILD_${PKG2})
-      message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with -D BUILD_${PKG2}=ON")
-    endif()
-  elseif(DEFINED PKG_${PKG2})
-    if(PKG_${PKG1} AND NOT PKG_${PKG2})
-      message(WARNING "The ${PKG1} package depends on the ${PKG2} package. Enabling it.")
-      set(PKG_${PKG2} ON CACHE BOOL "" FORCE)
-    endif()
+  if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
+    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
   endif()
 endmacro()
 
@@ -125,27 +118,25 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
-  if(DOWNLOAD_POTENTIALS)
-    if(EXISTS "${pkgfolder}/potentials.txt")
-      file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
-      foreach(line ${linelist})
-        string(FIND ${line} " " blank)
-        math(EXPR plusone "${blank}+1")
-        string(SUBSTRING ${line} 0 ${blank} pot)
-        string(SUBSTRING ${line} ${plusone} -1 sum)
-        if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
-          file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
-        endif()
-        if(NOT sum STREQUAL oldsum)
-          message(STATUS "Downloading external potential ${pot} from ${LAMMPS_POTENTIALS_URL}")
-          string(RANDOM LENGTH 10 TMP_EXT)
-          file(DOWNLOAD "${LAMMPS_POTENTIALS_URL}/${pot}.${sum}" "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}"
-            EXPECTED_HASH MD5=${sum} SHOW_PROGRESS)
-          file(COPY "${CMAKE_BINARY_DIR}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
-          file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
-        endif()
-      endforeach()
-    endif()
+  if(EXISTS "${pkgfolder}/potentials.txt")
+    file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
+    foreach(line ${linelist})
+      string(FIND ${line} " " blank)
+      math(EXPR plusone "${blank}+1")
+      string(SUBSTRING ${line} 0 ${blank} pot)
+      string(SUBSTRING ${line} ${plusone} -1 sum)
+      if(EXISTS "${LAMMPS_POTENTIALS_DIR}/${pot}")
+        file(MD5 "${LAMMPS_POTENTIALS_DIR}/${pot}" oldsum)
+      endif()
+      if(NOT sum STREQUAL oldsum)
+        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}/${pot}.${TMP_EXT}" DESTINATION "${LAMMPS_POTENTIALS_DIR}")
+        file(RENAME "${LAMMPS_POTENTIALS_DIR}/${pot}.${TMP_EXT}" "${LAMMPS_POTENTIALS_DIR}/${pot}")
+      endif()
+    endforeach()
   endif()
 endfunction(FetchPotentials)
 
@@ -158,14 +149,3 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   set(CMAKE_LINUX_DISTRO ${distro})
   set(CMAKE_DISTRO_VERSION ${disversion})
 endif()
-
-function(GetFallbackURL input output)
-  string(REPLACE "_URL" "" _tmp ${input})
-  string(TOLOWER ${_tmp} libname)
-  string(REGEX REPLACE "^https://.*/([^/]+gz)" "${LAMMPS_THIRDPARTY_URL}/${libname}-\\1" newurl "${${input}}")
-  if ("${newurl}" STREQUAL "${${input}}")
-    set(${output} "" PARENT_SCOPE)
-  else()
-    set(${output} ${newurl} PARENT_SCOPE)
-  endif()
-endfunction(GetFallbackURL)

cmake/Modules/MPI4WIN.cmake

@@ -1,74 +1,39 @@
-# Download and configure MinGW compatible MPICH development files for Windows
-option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
+# 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)
 
-if(USE_MSMPI)
-  message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-  set(MPICH2_WIN64_DEVEL_URL "${LAMMPS_THIRDPARTY_URL}/msmpi-win64-devel.tar.gz" CACHE STRING "URL for MS-MPI (win64) tarball")
-  set(MPICH2_WIN64_DEVEL_MD5 "86314daf1bffb809f1fcbefb8a547490" CACHE STRING "MD5 checksum of MS-MPI (win64) tarball")
-  mark_as_advanced(MPICH2_WIN64_DEVEL_URL)
-  mark_as_advanced(MPICH2_WIN64_DEVEL_MD5)
-
-  include(ExternalProject)
-  if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
-    ExternalProject_Add(mpi4win_build
-      URL     ${MPICH2_WIN64_DEVEL_URL}
-      URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
-      CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
-      BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmsmpi.a)
-  else()
-    message(FATAL_ERROR "Only x86 64-bit builds are supported with MS-MPI")
-  endif()
-
-  ExternalProject_get_property(mpi4win_build SOURCE_DIR)
-  file(MAKE_DIRECTORY "${SOURCE_DIR}/include")
-  add_library(MPI::MPI_CXX UNKNOWN IMPORTED)
-  set_target_properties(MPI::MPI_CXX PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/lib/libmsmpi.a"
-    INTERFACE_INCLUDE_DIRECTORIES "${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/libmsmpi.a")
+include(ExternalProject)
+if(CMAKE_SYSTEM_PROCESSOR STREQUAL "x86_64")
+  ExternalProject_Add(mpi4win_build
+    URL     ${MPICH2_WIN64_DEVEL_URL}
+    URL_MD5 ${MPICH2_WIN64_DEVEL_MD5}
+    CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS <SOURCE_DIR>/lib/libmpi.a)
 else()
-  message(STATUS "Downloading and configuring MPICH2-1.4.1 for Windows cross-compilation")
-  set(MPICH2_WIN64_DEVEL_URL "${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")
+  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")

cmake/Modules/Packages/COLVARS.cmake

@@ -1,15 +1,20 @@
 set(COLVARS_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars)
 
-file(GLOB COLVARS_SOURCES ${CONFIGURE_DEPENDS} ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
+file(GLOB COLVARS_SOURCES ${COLVARS_SOURCE_DIR}/[^.]*.cpp)
 
-option(COLVARS_DEBUG "Enable debugging messages for Colvars (quite verbose)" OFF)
+option(COLVARS_DEBUG "Debugging messages for Colvars (quite verbose)" OFF)
 
-option(COLVARS_LEPTON "Use the Lepton library for custom expressions" ON)
+# Build Lepton by default
+option(COLVARS_LEPTON "Build and link the Lepton library" ON)
 
 if(COLVARS_LEPTON)
-  if(NOT LEPTON_SOURCE_DIR)
-    include(Packages/LEPTON)
-  endif()
+  set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
+  file(GLOB LEPTON_SOURCES ${LEPTON_DIR}/src/[^.]*.cpp)
+  add_library(lepton STATIC ${LEPTON_SOURCES})
+  # Change the define below to LEPTON_BUILDING_SHARED_LIBRARY when linking Lepton as a DLL with MSVC
+  target_compile_definitions(lepton PRIVATE -DLEPTON_BUILDING_STATIC_LIBRARY)
+  set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
+  target_include_directories(lepton PRIVATE ${LEPTON_DIR}/include)
 endif()
 
 add_library(colvars STATIC ${COLVARS_SOURCES})
@@ -25,11 +30,14 @@ target_include_directories(colvars PRIVATE ${LAMMPS_SOURCE_DIR})
 target_link_libraries(lammps PRIVATE colvars)
 
 if(COLVARS_DEBUG)
-  # Need to export the define publicly to be valid in interface code
+  # Need to export the macro publicly to also affect the proxy
   target_compile_definitions(colvars PUBLIC -DCOLVARS_DEBUG)
 endif()
 
 if(COLVARS_LEPTON)
+  target_link_libraries(lammps PRIVATE lepton)
   target_compile_definitions(colvars PRIVATE -DLEPTON)
-  target_link_libraries(colvars PUBLIC lepton)
+  # Disable the line below when linking Lepton as a DLL with MSVC
+  target_compile_definitions(colvars PRIVATE -DLEPTON_USE_STATIC_LIBRARIES)
+  target_include_directories(colvars PUBLIC ${LEPTON_DIR}/include)
 endif()

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,9 +1,4 @@
-find_package(ZLIB)
-if(NOT ZLIB_FOUND)
-  message(WARNING "No Zlib development support found. Disabling COMPRESS package...")
-  set(PKG_COMPRESS OFF CACHE BOOL "" FORCE)
-  return()
-endif()
+find_package(ZLIB REQUIRED)
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
 
 find_package(PkgConfig QUIET)

cmake/Modules/Packages/GPU.cmake

@@ -26,20 +26,7 @@ elseif(GPU_PREC STREQUAL "SINGLE")
   set(GPU_PREC_SETTING "SINGLE_SINGLE")
 endif()
 
-option(GPU_DEBUG "Enable debugging code of the GPU package" OFF)
-mark_as_advanced(GPU_DEBUG)
-
-if(PKG_AMOEBA AND FFT_SINGLE)
-  message(FATAL_ERROR "GPU acceleration of AMOEBA is not (yet) compatible with single precision FFT")
-endif()
-
-if (PKG_AMOEBA)
-  list(APPEND GPU_SOURCES
-              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.h
-              ${GPU_SOURCES_DIR}/amoeba_convolution_gpu.cpp)
-endif()
-
-file(GLOB GPU_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
+file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
 if(GPU_API STREQUAL "CUDA")
@@ -68,7 +55,7 @@ if(GPU_API STREQUAL "CUDA")
   set(GPU_ARCH "sm_50" CACHE STRING "LAMMPS GPU CUDA SM primary architecture (e.g. sm_60)")
 
   # ensure that no *cubin.h files exist from a compile in the lib/gpu folder
-  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
+  file(GLOB GPU_LIB_OLD_CUBIN_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/*_cubin.h)
   if(GPU_LIB_OLD_CUBIN_HEADERS)
     message(FATAL_ERROR "########################################################################\n"
       "Found file(s) generated by the make-based build system in lib/gpu\n"
@@ -78,15 +65,15 @@ if(GPU_API STREQUAL "CUDA")
       "########################################################################")
   endif()
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
   if(CUDPP_OPT)
     cuda_include_directories(${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
-    file(GLOB GPU_LIB_CUDPP_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
-    file(GLOB GPU_LIB_CUDPP_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
+    file(GLOB GPU_LIB_CUDPP_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cpp)
+    file(GLOB GPU_LIB_CUDPP_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini/[^.]*.cu)
   endif()
 
   # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
@@ -95,7 +82,6 @@ if(GPU_API STREQUAL "CUDA")
 
   # apply the following to build "fat" CUDA binaries only for known CUDA toolkits since version 8.0
   # only the Kepler achitecture and beyond is supported
-  # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
   if(CUDA_VERSION VERSION_LESS 8.0)
     message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
   elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
@@ -134,14 +120,14 @@ if(GPU_API STREQUAL "CUDA")
     if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
     endif()
-    # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
-    if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
-      string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
-    endif()
-    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
+    # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
     if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
       string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
     endif()
+    #    # Lovelace (GPU Arch 9.x) is supported by CUDA 12.0? and later
+    #if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    #  string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_9x,code=[sm_9x,compute_9x]")
+    #endif()
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
@@ -164,12 +150,7 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} ${GPU_CUDA_MPS_FLAGS})
-  if(GPU_DEBUG)
-    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
-  else()
-    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
-  endif()
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -201,7 +182,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -210,7 +191,6 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu
-    ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu
   )
 
   foreach(GPU_KERNEL ${GPU_LIB_CU})
@@ -227,7 +207,6 @@ elseif(GPU_API STREQUAL "OPENCL")
   GenerateOpenCLHeader(tersoff ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff.cu)
   GenerateOpenCLHeader(tersoff_zbl ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_zbl.cu)
   GenerateOpenCLHeader(tersoff_mod ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_tersoff_mod.cu)
-  GenerateOpenCLHeader(hippo ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h ${OCL_COMMON_HEADERS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo_extra.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_hippo.cu)
 
   list(APPEND GPU_LIB_SOURCES
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/gayberne_cl.h
@@ -237,18 +216,14 @@ elseif(GPU_API STREQUAL "OPENCL")
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_zbl_cl.h
     ${CMAKE_CURRENT_BINARY_DIR}/gpu/tersoff_mod_cl.h
-    ${CMAKE_CURRENT_BINARY_DIR}/gpu/hippo_cl.h
   )
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL -D_${GPU_PREC_SETTING})
-  if(GPU_DEBUG)
-    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
-  else()
-    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
-  endif()
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
+
   target_link_libraries(lammps PRIVATE gpu)
 
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
@@ -258,8 +233,7 @@ elseif(GPU_API STREQUAL "OPENCL")
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
-          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.")
+          set(HIP_PATH "/opt/rocm/hip" CACHE PATH "Path to HIP installation")
       else()
           set(HIP_PATH $ENV{HIP_PATH} CACHE PATH "Path to HIP installation")
       endif()
@@ -287,8 +261,6 @@ 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)")
@@ -301,7 +273,6 @@ elseif(GPU_API STREQUAL "HIP")
     else()
       # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
       # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-      # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
       set(HIP_CUDA_GENCODE "-arch=${HIP_ARCH}")
       # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
       if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))
@@ -331,22 +302,14 @@ elseif(GPU_API STREQUAL "HIP")
       if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
         string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
       endif()
-      # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
-      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
-        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
-      endif()
-      # Lovelace (GPU Arch 8.9) is supported by CUDA 11.8 and later
-      if(CUDA_VERSION VERSION_GREATER_EQUAL "11.8")
-        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
-      endif()
-      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0 and later
+      # Hopper (GPU Arch 9.0) is supported by CUDA 12.0? and later
       if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
-        string(APPEND HIP_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
+        string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_90,code=[sm_90,compute_90]")
       endif()
     endif()
   endif()
 
-  file(GLOB GPU_LIB_CU ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
+  file(GLOB GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cu ${CMAKE_CURRENT_SOURCE_DIR}/gpu/[^.]*.cu)
   list(REMOVE_ITEM GPU_LIB_CU ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_pppm.cu)
 
   set(GPU_LIB_CU_HIP "")
@@ -377,14 +340,7 @@ 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 ${CU_NAME}.cubin")
-    elseif(HIP_PLATFORM STREQUAL "spirv")
-      configure_file(${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()
+    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
@@ -398,12 +354,8 @@ elseif(GPU_API STREQUAL "HIP")
 
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -DUSE_HIP -D_${GPU_PREC_SETTING})
-  if(GPU_DEBUG)
-    target_compile_definitions(gpu PRIVATE -DUCL_DEBUG -DGERYON_KERNEL_DUMP)
-  else()
-    target_compile_definitions(gpu PRIVATE -DMPI_GERYON -DUCL_NO_EXIT)
-  endif()
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -DUSE_HIP)
   target_link_libraries(gpu PRIVATE hip::host)
 
   if(HIP_USE_DEVICE_SORT)
@@ -428,17 +380,15 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
-        # TODO: test update to current version 1.17.2
-        set(CUB_URL "https://github.com/nvidia/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
+        set(CUB_URL "https://github.com/NVlabs/cub/archive/1.12.0.tar.gz" CACHE STRING "URL for CUB tarball")
         set(CUB_MD5 "1cf595beacafff104700921bac8519f3" CACHE STRING "MD5 checksum of CUB tarball")
         mark_as_advanced(CUB_URL)
         mark_as_advanced(CUB_MD5)
-        GetFallbackURL(CUB_URL CUB_FALLBACK)
 
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          URL     ${CUB_URL} ${CUB_FALLBACK}
+          URL     ${CUB_URL}
           URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""

cmake/Modules/Packages/INTEL.cmake

@@ -112,5 +112,9 @@ if(PKG_KSPACE)
   RegisterIntegrateStyle(${INTEL_SOURCES_DIR}/verlet_lrt_intel.h)
 endif()
 
+if(PKG_ELECTRODE)
+  list(APPEND INTEL_SOURCES ${INTEL_SOURCES_DIR}/electrode_accel_intel.cpp)
+endif()
+
 target_sources(lammps PRIVATE ${INTEL_SOURCES})
 target_include_directories(lammps PRIVATE ${INTEL_SOURCES_DIR})

cmake/Modules/Packages/KOKKOS.cmake

@@ -3,7 +3,6 @@
 if(CMAKE_CXX_STANDARD LESS 14)
   message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
 endif()
-
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
@@ -49,14 +48,12 @@ 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/3.7.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "f140e02b826223b1045207d9bc10d404" 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)
-  GetFallbackURL(KOKKOS_URL KOKKOS_FALLBACK)
-
   ExternalProject_Add(kokkos_build
-    URL     ${KOKKOS_URL} ${KOKKOS_FALLBACK}
+    URL     ${KOKKOS_URL}
     URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a <INSTALL_DIR>/lib/libkokkoscontainers.a
@@ -76,7 +73,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.7.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.6.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -92,6 +89,7 @@ else()
   endif()
   add_subdirectory(${LAMMPS_LIB_KOKKOS_SRC_DIR} ${LAMMPS_LIB_KOKKOS_BIN_DIR})
 
+
   set(Kokkos_INCLUDE_DIRS ${LAMMPS_LIB_KOKKOS_SRC_DIR}/core/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/containers/src
                           ${LAMMPS_LIB_KOKKOS_SRC_DIR}/algorithms/src
@@ -126,7 +124,7 @@ set(KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/kokkos.cpp
 
 if(PKG_KSPACE)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/fft3d_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/grid3d_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/gridcomm_kokkos.cpp
                                  ${KOKKOS_PKG_SOURCES_DIR}/remap_kokkos.cpp)
   if(Kokkos_ENABLE_CUDA)
     if(NOT (FFT STREQUAL "KISS"))
@@ -141,29 +139,6 @@ if(PKG_KSPACE)
   endif()
 endif()
 
-if(PKG_ML-IAP)
-  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_python_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_unified_kokkos.cpp
-                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
-
-  # Add KOKKOS version of ML-IAP Python coupling if non-KOKKOS version is included
-  if(MLIAP_ENABLE_PYTHON AND Cythonize_EXECUTABLE)
-    file(GLOB MLIAP_KOKKOS_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/KOKKOS/*.pyx)
-    foreach(MLIAP_CYTHON_FILE ${MLIAP_KOKKOS_CYTHON_SRC})
-      get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
-      add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-              COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-              COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-              WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
-              MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
-              COMMENT "Generating C++ sources with cythonize...")
-      list(APPEND KOKKOS_PKG_SOURCES ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
-    endforeach()
-  endif()
-endif()
 
 if(PKG_PHONON)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)

cmake/Modules/Packages/LATTE.cmake

@@ -19,19 +19,17 @@ if(DOWNLOAD_LATTE)
   set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
   mark_as_advanced(LATTE_URL)
   mark_as_advanced(LATTE_MD5)
-  GetFallbackURL(LATTE_URL LATTE_FALLBACK)
 
   # 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) 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.")
+  if((NUM_BLAS GREATER 1) OR (NUM_LAPACK GREATER 1))
+    message(FATAL_ERROR "Cannot compile downloaded LATTE library due to a technical limitation")
   endif()
 
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL     ${LATTE_URL} ${LATTE_FALLBACK}
+    URL     ${LATTE_URL}
     URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib

cmake/Modules/Packages/LEPTON.cmake

@@ -1,35 +0,0 @@
-# avoid including this file twice
-if(LEPTON_SOURCE_DIR)
-   return()
-endif()
-set(LEPTON_SOURCE_DIR ${LAMMPS_LIB_SOURCE_DIR}/lepton)
-
-file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/src/[^.]*.cpp)
-
-if((CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "amd64") OR
-   (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "AMD64") OR
-   (CMAKE_HOST_SYSTEM_PROCESSOR STREQUAL "x86_64"))
-   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" ON)
-else()
-   option(LEPTON_ENABLE_JIT "Enable Just-In-Time compiler for Lepton" OFF)
-endif()
-
-if(LEPTON_ENABLE_JIT)
-  file(GLOB ASMJIT_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_SOURCE_DIR}/asmjit/*/[^.]*.cpp)
-endif()
-
-add_library(lepton STATIC ${LEPTON_SOURCES} ${ASMJIT_SOURCES})
-set_target_properties(lepton PROPERTIES OUTPUT_NAME lammps_lepton${LAMMPS_MACHINE})
-target_compile_definitions(lepton PUBLIC LEPTON_BUILDING_STATIC_LIBRARY=1)
-target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR}/include)
-if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
-  find_library(LIB_RT rt QUIET)
-  target_link_libraries(lepton PUBLIC ${LIB_RT})
-endif()
-
-if(LEPTON_ENABLE_JIT)
-  target_compile_definitions(lepton PUBLIC "LEPTON_USE_JIT=1;ASMJIT_BUILD_X86=1;ASMJIT_STATIC=1;ASMJIT_BUILD_RELEASE=1")
-  target_include_directories(lepton PUBLIC ${LEPTON_SOURCE_DIR})
-endif()
-
-target_link_libraries(lammps PRIVATE lepton)

cmake/Modules/Packages/MC.cmake

@@ -1,9 +0,0 @@
-# fix sgcmc may only be installed if also the EAM pair style from MANYBODY is installed
-if(NOT PKG_MANYBODY)
-  get_property(LAMMPS_FIX_HEADERS GLOBAL PROPERTY FIX)
-  list(REMOVE_ITEM LAMMPS_FIX_HEADERS ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.h)
-  set_property(GLOBAL PROPERTY FIX "${LAMMPS_FIX_HEADERS}")
-  get_target_property(LAMMPS_SOURCES lammps SOURCES)
-  list(REMOVE_ITEM LAMMPS_SOURCES ${LAMMPS_SOURCE_DIR}/MC/fix_sgcmc.cpp)
-  set_property(TARGET lammps PROPERTY SOURCES "${LAMMPS_SOURCES}")
-endif()

cmake/Modules/Packages/MDI.cmake

@@ -8,11 +8,10 @@ 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/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
+  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")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
-  GetFallbackURL(MDI_URL MDI_FALLBACK)
   enable_language(C)
 
   # only ON/OFF are allowed for "mpi" flag when building MDI library
@@ -27,21 +26,8 @@ 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()
@@ -50,25 +36,16 @@ if(DOWNLOAD_MDI)
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   endif()
-  # python plugins are not supported and thus must be always off on Windows
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    unset(Python_Development_FOUND)
-    set(MDI_USE_PYTHON_PLUGINS OFF)
-    if(CMAKE_CROSSCOMPILING)
-      set(CMAKE_INSTALL_LIBDIR lib)
-    endif()
-  endif()
 
   # download/ build MDI library
   # always build static library with -fpic
   # support cross-compilation and ninja-build
   include(ExternalProject)
   ExternalProject_Add(mdi_build
-    URL     ${MDI_URL} ${MDI_FALLBACK}
+    URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
-    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
-    CMAKE_ARGS
-    -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
+    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
     -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@@ -77,26 +54,25 @@ if(DOWNLOAD_MDI)
     -Dlanguage=C
     -Dlibtype=STATIC
     -Dmpi=${MDI_USE_MPI}
-    -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
-    INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
-    BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
+    INSTALL_COMMAND ""
+    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
     )
 
   # where is the compiled library?
-  ExternalProject_get_property(mdi_build PREFIX)
+  ExternalProject_get_property(mdi_build BINARY_DIR)
+  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
   # workaround for older CMake versions
-  file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
-  file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
+  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
 
   # create imported target for the MDI library
   add_library(LAMMPS::MDI UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::MDI mdi_build)
   set_target_properties(LAMMPS::MDI PROPERTIES
-    IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
-    INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
-  )
+    IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
+    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
+    )
 
   set(MDI_DEP_LIBS "")
   # if compiling with python plugins we need

cmake/Modules/Packages/MISC.cmake

@@ -1,13 +0,0 @@
-# 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

@@ -6,11 +6,10 @@ else()
 endif()
 option(DOWNLOAD_N2P2 "Download n2p2 library instead of using an already installed one)" ${DOWNLOAD_N2P2_DEFAULT})
 if(DOWNLOAD_N2P2)
-  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.2.0.tar.gz" CACHE STRING "URL for n2p2 tarball")
-  set(N2P2_MD5 "a2d9ab7f676b3a74a324fc1eda0a911d" CACHE STRING "MD5 checksum of N2P2 tarball")
+  set(N2P2_URL "https://github.com/CompPhysVienna/n2p2/archive/v2.1.4.tar.gz" CACHE STRING "URL for n2p2 tarball")
+  set(N2P2_MD5 "9595b066636cd6b90b0fef93398297a5" CACHE STRING "MD5 checksum of N2P2 tarball")
   mark_as_advanced(N2P2_URL)
   mark_as_advanced(N2P2_MD5)
-  GetFallbackURL(N2P2_URL N2P2_FALLBACK)
 
   # adjust settings from detected compiler to compiler platform in n2p2 library
   # set compiler specific flag to turn on C++11 syntax (required on macOS and CentOS 7)
@@ -73,7 +72,7 @@ if(DOWNLOAD_N2P2)
   # download compile n2p2 library. much patch MPI calls in LAMMPS interface to accommodate MPI-2 (e.g. for cross-compiling)
   include(ExternalProject)
   ExternalProject_Add(n2p2_build
-    URL     ${N2P2_URL} ${N2P2_FALLBACK}
+    URL     ${N2P2_URL}
     URL_MD5 ${N2P2_MD5}
     UPDATE_COMMAND ""
     CONFIGURE_COMMAND ""

cmake/Modules/Packages/ML-IAP.cmake

@@ -34,18 +34,16 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  file(GLOB MLIAP_CYTHON_SRC ${CONFIGURE_DEPENDS} ${LAMMPS_SOURCE_DIR}/ML-IAP/*.pyx)
+  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
+  get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
   file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
-  foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
-    get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
-    add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-            COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-            COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-            WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
-            MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
-            COMMENT "Generating C++ sources with cythonize...")
-    target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
-  endforeach()
+  add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+          COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+          COMMENT "Generating C++ sources with cythonize...")
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
+  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,25 +1,11 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2023.01.3.fix.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 "4f0b3b5b14456fe9a73b447de3765caa" 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)
-GetFallbackURL(PACELIB_URL PACELIB_FALLBACK)
 
 # download library sources to build folder
-if(EXISTS ${CMAKE_BINARY_DIR}/libpace.tar.gz)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-endif()
-if(NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}")
-  message(STATUS "Downloading ${PACELIB_URL}")
-  file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz STATUS DL_STATUS SHOW_PROGRESS)
-  file(MD5 ${CMAKE_BINARY_DIR}/libpace.tar.gz DL_MD5)
-  if((NOT DL_STATUS EQUAL 0) OR (NOT "${DL_MD5}" STREQUAL "${PACELIB_MD5}"))
-    message(WARNING "Download from primary URL ${PACELIB_URL} failed\nTrying fallback URL ${PACELIB_FALLBACK}")
-    file(DOWNLOAD ${PACELIB_FALLBACK} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5} SHOW_PROGRESS)
-  endif()
-else()
-  message(STATUS "Using already downloaded archive ${CMAKE_BINARY_DIR}/libpace.tar.gz")
-endif()
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
 
 # uncompress downloaded sources
 execute_process(
@@ -29,9 +15,23 @@ execute_process(
 )
 get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-add_subdirectory(${lib-pace} build-pace)
-set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+# 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)
 
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
+list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
+
+add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
+
+
+target_link_libraries(pace PRIVATE yaml-cpp-pace)
 if(CMAKE_PROJECT_NAME STREQUAL "lammps")
   target_link_libraries(lammps PRIVATE pace)
 endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -16,7 +16,6 @@ if(DOWNLOAD_QUIP)
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DFORTRAN_UNDERSCORE\n")
     set(temp "${temp}F95FLAGS += -fpp -free -fPIC\n")
     set(temp "${temp}F77FLAGS += -fpp -fixed -fPIC\n")
-    set(temp "${temp}F95_PRE_FILENAME_FLAG = -Tf\n")
   elseif(CMAKE_Fortran_COMPILER_ID STREQUAL GNU)
     set(temp "${temp}FPP=${CMAKE_Fortran_COMPILER} -E -x f95-cpp-input\nOPTIM=${CMAKE_Fortran_FLAGS_${BTYPE}}\n")
     set(temp "${temp}DEFINES += -DGETARG_F2003 -DGETENV_F2003 -DGFORTRAN -DFORTRAN_UNDERSCORE\n")
@@ -59,12 +58,12 @@ if(DOWNLOAD_QUIP)
     BUILD_COMMAND env QUIP_ARCH=lammps make libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
-    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
   )
   ExternalProject_get_property(quip_build SOURCE_DIR)
   add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
   set_target_properties(LAMMPS::QUIP PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}"
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
   add_dependencies(LAMMPS::QUIP quip_build)

cmake/Modules/Packages/PLUMED.cmake

@@ -59,11 +59,10 @@ if(DOWNLOAD_PLUMED)
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
-  GetFallbackURL(PLUMED_URL PLUMED_FALLBACK)
 
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL     ${PLUMED_URL} ${PLUMED_FALLBACK}
+    URL     ${PLUMED_URL}
     URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>

cmake/Modules/Packages/PYTHON.cmake

@@ -1,28 +1,8 @@
 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/Packages/SCAFACOS.cmake

@@ -18,8 +18,6 @@ if(DOWNLOAD_SCAFACOS)
   set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
   mark_as_advanced(SCAFACOS_URL)
   mark_as_advanced(SCAFACOS_MD5)
-  GetFallbackURL(SCAFACOS_URL SCAFACOS_FALLBACK)
-
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
   file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
@@ -32,7 +30,7 @@ if(DOWNLOAD_SCAFACOS)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL     ${SCAFACOS_URL} ${SCAFACOS_FALLBACK}
+    URL     ${SCAFACOS_URL}
     URL_MD5 ${SCAFACOS_MD5}
     PATCH_COMMAND patch -p1 < ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR> --disable-doc

cmake/Modules/StyleHeaderUtils.cmake

@@ -1,5 +1,5 @@
 function(FindStyleHeaders path style_class file_pattern headers)
-    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
+    file(GLOB files "${path}/${file_pattern}*.h")
     get_property(hlist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})
@@ -184,7 +184,7 @@ endfunction(DetectBuildSystemConflict)
 
 
 function(FindPackagesHeaders path style_class file_pattern headers)
-    file(GLOB files ${CONFIGURE_DEPENDS} "${path}/${file_pattern}*.h")
+    file(GLOB files "${path}/${file_pattern}*.h")
     get_property(plist GLOBAL PROPERTY ${headers})
 
     foreach(file_name ${files})

cmake/Modules/Testing.cmake

@@ -6,7 +6,7 @@ if(ENABLE_TESTING)
   find_program(VALGRIND_BINARY NAMES valgrind)
   # generate custom suppression file
   file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "\n")
-  file(GLOB VALGRIND_SUPPRESSION_FILES ${CONFIGURE_DEPENDS} ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
+  file(GLOB VALGRIND_SUPPRESSION_FILES ${LAMMPS_TOOLS_DIR}/valgrind/[^.]*.supp)
   foreach(SUPP ${VALGRIND_SUPPRESSION_FILES})
     file(READ ${SUPP} SUPPRESSIONS)
     file(APPEND ${CMAKE_CURRENT_BINARY_DIR}/lammps.supp "${SUPPRESSIONS}")

cmake/Modules/Tools.cmake

@@ -26,7 +26,7 @@ if(BUILD_TOOLS)
 
   enable_language(C)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
-  file(GLOB MSI2LMP_SOURCES ${CONFIGURE_DEPENDS} ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
+  file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
   if(STANDARD_MATH_LIB)
     target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
@@ -50,16 +50,12 @@ if(BUILD_LAMMPS_SHELL)
 
   add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
   target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
-  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
 
   # workaround for broken readline pkg-config file on FreeBSD
   if(CMAKE_SYSTEM_NAME STREQUAL "FreeBSD")
     target_include_directories(lammps-shell PRIVATE /usr/local/include)
   endif()
-  if(CMAKE_SYSTEM_NAME STREQUAL "LinuxMUSL")
-    pkg_check_modules(TERMCAP IMPORTED_TARGET REQUIRED termcap)
-    target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::TERMCAP)
-  endif()
+  target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
   install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
   install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)

cmake/presets/all_off.cmake

@@ -3,7 +3,6 @@
 
 set(ALL_PACKAGES
   ADIOS
-  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -12,7 +11,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -44,7 +43,6 @@ set(ALL_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
-  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -57,7 +55,6 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
-  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/all_on.cmake

@@ -5,7 +5,6 @@
 
 set(ALL_PACKAGES
   ADIOS
-  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -14,7 +13,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -46,7 +45,6 @@ set(ALL_PACKAGES
   KSPACE
   LATBOLTZ
   LATTE
-  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -59,7 +57,6 @@ set(ALL_PACKAGES
   ML-HDNNP
   ML-IAP
   ML-PACE
-  ML-POD
   ML-QUIP
   ML-RANN
   ML-SNAP

cmake/presets/clang.cmake

@@ -3,13 +3,6 @@
 # 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)
@@ -17,9 +10,9 @@ 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 ${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_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_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/intel.cmake

@@ -1,4 +1,4 @@
-# preset that will enable the classic Intel compilers with support for MPI and OpenMP (on Linux boxes)
+# preset that will enable Intel compilers with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "icpc" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "icc" CACHE STRING "" FORCE)
@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icc" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpc" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

cmake/presets/mingw-cross.cmake

@@ -1,5 +1,4 @@
 set(WIN_PACKAGES
-  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -8,7 +7,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -36,7 +35,6 @@ set(WIN_PACKAGES
   INTERLAYER
   KSPACE
   LATTE
-  LEPTON
   MACHDYN
   MANIFOLD
   MANYBODY
@@ -48,7 +46,6 @@ set(WIN_PACKAGES
   MISC
   ML-HDNNP
   ML-IAP
-  ML-POD
   ML-RANN
   ML-SNAP
   MOFFF

cmake/presets/most.cmake

@@ -3,14 +3,13 @@
 # are removed. The resulting binary should be able to run most inputs.
 
 set(ALL_PACKAGES
-  AMOEBA
   ASPHERE
   BOCS
   BODY
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -35,15 +34,12 @@ set(ALL_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
-  LEPTON
   MACHDYN
   MANYBODY
   MC
   MEAM
-  MESONT
   MISC
   ML-IAP
-  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

cmake/presets/nolib.cmake

@@ -13,9 +13,9 @@ set(PACKAGES_WITH_LIB
   KOKKOS
   LATBOLTZ
   LATTE
-  LEPTON
   MACHDYN
   MDI
+  MESONT
   ML-HDNNP
   ML-PACE
   ML-QUIP

cmake/presets/oneapi.cmake

@@ -18,11 +18,11 @@ set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
 set(OpenMP_C "icx" CACHE STRING "" FORCE)
-set(OpenMP_C_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
 set(OpenMP_CXX "icpx" CACHE STRING "" FORCE)
-set(OpenMP_CXX_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
-set(OpenMP_Fortran_FLAGS "-qopenmp -qopenmp-simd" CACHE STRING "" FORCE)
+set(OpenMP_Fortran_FLAGS "-qopenmp" CACHE STRING "" FORCE)
 set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
 

cmake/presets/windows.cmake

@@ -1,13 +1,11 @@
 set(WIN_PACKAGES
-  AMOEBA
   ASPHERE
-  AWPMD
   BOCS
   BODY
   BPM
   BROWNIAN
   CG-DNA
-  CG-SPICA
+  CG-SDK
   CLASS2
   COLLOID
   COLVARS
@@ -21,7 +19,6 @@ set(WIN_PACKAGES
   DPD-SMOOTH
   DRUDE
   EFF
-  ELECTRODE
   EXTRA-COMPUTE
   EXTRA-DUMP
   EXTRA-FIX
@@ -31,15 +28,12 @@ set(WIN_PACKAGES
   GRANULAR
   INTERLAYER
   KSPACE
-  LEPTON
   MANIFOLD
   MANYBODY
   MC
   MEAM
-  MESONT
   MISC
   ML-IAP
-  ML-POD
   ML-SNAP
   MOFFF
   MOLECULE

doc/Makefile

@@ -45,7 +45,7 @@ SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocess
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check role_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -86,17 +86,16 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
 		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
-		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -114,9 +113,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@mkdir -p fasthtml
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
@@ -131,8 +130,8 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ; \
-		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/;  env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		cp $(SPHINXCONFIG)/false_positives.txt $(RSTDIR)/ ; env PYTHONWARNINGS= \
 		sphinx-build -b spelling -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) spelling ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -146,9 +145,9 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@rm -f LAMMPS.epub
 	@cp src/JPG/*.* epub/JPG
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ;\
 		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -167,16 +166,15 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
 		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
-		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\
 		python utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
-		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
 		python utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
@@ -200,21 +198,21 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 
 anchor_check : $(ANCHORCHECK)
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ;\
 		rst_anchor_check src/*.rst ;\
 		deactivate ;\
 	)
 
 style_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate ;\
 		python utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
-		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \\
+		. $(VENV)/bin/activate ;\
 		python utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
@@ -222,9 +220,6 @@ package_check : $(VENV)
 char_check :
 	@( env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst && exit 1 || : )
 
-role_check :
-	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
-
 xmlgen : doxygen/xml/index.xml
 
 doxygen/Doxyfile: doxygen/Doxyfile.in
@@ -252,7 +247,7 @@ $(MATHJAX):
 
 $(ANCHORCHECK): $(VENV)
 	@( \
-		. $(VENV)/bin/activate; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
+		. $(VENV)/bin/activate; \
 		pip $(PIP_OPTIONS) install -e utils/converters;\
 		deactivate;\
 	)

doc/README

@@ -40,9 +40,8 @@ environment and local folders.
 Installing prerequisites for the documentation build
 
 To run the HTML documention build toolchain, python 3.x, doxygen, git,
-and the venv python module have to be installed if not already available.
-Also internet access is initially required to download external files
-and tools.
+and virtualenv have to be installed.  Also internet access is initially
+required to download external files and tools.
 
 Building the PDF format manual requires in addition a compatible LaTeX
 installation with support for PDFLaTeX and several add-on LaTeX packages

doc/documentation_conventions.md

@@ -4,44 +4,45 @@ This purpose of this document is to provide a point of reference
 for LAMMPS developers and contributors as to what conventions
 should be used to structure and format files in the LAMMPS manual.
 
-Last change: 2022-12-30
+Last change: 2020-04-23
 
 ## File format and tools
 
-In fall 2019, the LAMMPS documentation file format has changed from a
-home grown markup designed to generate HTML format files only, to
-[reStructuredText](https://docutils.sourceforge.io/rst.html>.  For a
-transition period all files in the old .txt format were transparently
-converted to .rst and then processed.  The `txt2rst tool` is still
-included in the distribution to obtain an initial .rst file for legacy
-integration into the manual.  Since that transition to reStructured
-text, many of the artifacts of the translation have been removed though,
-and parts of the documentation refactored and expanded to take advantage
-of the capabilities reStructuredText and associated tools.  The
-conversion from the source to the final formats (HTML, PDF, and
-optionally e-book reader formats ePUB and MOBI) is mostly automated and
-controlled by a Makefile in the `doc` folder. This makefile assumes that
-the processing is done on a Unix-like machine and Python 3.5 or later
-and a matching venv module are available.  Additional Python
-packages (like the Sphinx tool and several extensions) are transparently
-installed into a virtual environment over the internet using the `pip`
-package manager.  Further requirements and details are discussed in the
-manual.
+In fall 2019, the LAMMPS documentation file format has changed from
+a home grown minimal markup designed to generate HTML format files
+from a mostly plain text format to using the reStructuredText file
+format.  For a transition period all files in the old .txt format
+were transparently converted to .rst and then processed.  The txt2rst
+tool is still included in the distribution to obtain an initial .rst
+file for integration into the manual.  Since the transition to
+reStructured text as source format, many of the artifacts or the
+translation have been removed though and parts of the documentation
+refactored and expanded to take advantage of the capabilities
+reStructuredText and associated tools.  The conversion from the
+source to the final formats (HTML, PDF, and optionally e-book
+reader formats ePUB and MOBI) is mostly automated and controlled
+by a Makefile in the `doc` folder. This makefile assumes that the
+processing is done on a Unix-like machine and Python 3.5 or later
+and a matching virtualenv module are available.  Additional Python
+packages (like the Sphinx tool and several extensions) are
+transparently installed into a virtual environment over the
+internet using the `pip` package manager.  Further requirements
+and details are discussed in the manual.
 
 ## Work in progress
 
 The refactoring and improving of the documentation is an ongoing
 process, so statements in this document may not always be fully
-up-to-date.  When in doubt, contact the LAMMPS developers.
+up-to-date.  If in doubt, contact the LAMMPS developers.
 
 ## General structure
 
-The layout and formatting of added files should follow the example of
-the existing files.  Since many of those were initially derived from
-their former .txt format versions and the manual has been maintained in
+The layout and formatting of added files should follow the example
+of the existing files.  Since those are directly derived from their
+former .txt format versions and the manual has been maintained in
 that format for many years, there is a large degree of consistency
-already, so comparison with similar files should give you a good idea
-what kind of information and sections are needed.
+already, so comparison with similar files should give you a good
+idea what kind of information and sections are needed.
 
 ## Formatting conventions
 
@@ -51,27 +52,21 @@ It seems to be sufficient to have this consistent only within
 any single file and it is not (yet) enforced strictly, but making
 this globally consistent makes it easier to move sections around.
 
-File names, folders, paths, (shell) commands, definitions, makefile
+Filenames, folders, paths, (shell) commands, definitions, makefile
 settings and similar should be formatted as "literals" with
 double backward quotes bracketing the item: \`\`path/to/some/file\`\`
 
 Keywords and options are formatted in italics:  \*option\*
 
 Mathematical expressions, equations, symbols are typeset using
-either a `.. math:` block or the `:math:` role.
+either a `.. math:`` block or the `:math:` role.
 
-Groups of shell commands or LAMMPS input script or C/C++/Python source
+Groups of shell commands or LAMMPS input script or C/C++ source
 code should be typeset into a `.. code-block::` section. A syntax
-highlighting extension for LAMMPS input scripts is provided, so `LAMMPS`
-can be used to indicate the language in the code block in addition to
-`bash`, `c`, `c++`, `console`, `csh`, `diff', `fortran`, `json`, `make`,
-`perl`, `powershell`, `python`, `sh`, or `tcl`, `text`, or `yaml`.  When
-no syntax style is indicated, no syntax highlighting is performed.  When
-typesetting commands executed on the shell, please do not prefix
-commands with a shell prompt and use `bash` highlighting, except when
-the block also shows the output from that command.  In the latter case,
-please use a dollar sign as the shell prompt and `console` for syntax
-highlighting.
+highlighting extension for LAMMPS input scripts is provided, so
+`LAMMPS` can be used to indicate the language in the code block
+in addition to `bash`, `c`, or `python`.  When no syntax style
+is indicated, no syntax highlighting is performed.
 
 As an alternative, e.g. to typeset the syntax of file formats
 a `.. parsed-literal::` block can be used, which allows some
@@ -94,30 +89,22 @@ by `   :class: note`.
 
 ## Required steps when adding a custom style to LAMMPS
 
-When adding a new style (e.g. pair style or a compute or a fix) or a new
-command, it is **required** to include the **corresponding documentation**
-in [reStructuredText format](https://docutils.sourceforge.io/rst.html).
-Those are often new files that need to be added.  In order to be
-included in the documentation, those new files need to be referenced in a
-`.. toctree::` block.  Most of those use patterns with wild cards, so the
-addition will be automatic.  However, those additions also need to be
-added to some lists of styles or commands.  The `make style\_check`
-command when executed in the `doc` folder will perform a test and report
-any missing entries and list the affected files.  Any references defined
-with `.. \_refname:` have to be unique across all documentation files
-and this can be checked for with `make anchor\_check`.  Finally, a
-spell-check should be done, which is triggered via `make spelling`.  Any
-offenses need to be corrected and false positives should be added to the
-file `utils/sphinx-config/false\_positives.txt`.
+When adding a new style (e.g. pair style or a compute or a fix)
+or a new command, it is **required** to include the corresponding
+documentation.  Those are often new files that need to be added.
+In order to be included in the documentation, those new files
+need to be reference in a `.. toctree::` block.  Most of those
+use patterns with wildcards, so the addition will be automatic.
+However, those additions also need to be added to some lists of
+styles or commands.  The `make style\_check` command will perform
+a test and report any missing entries and list the affected files.
+Any references defined with `.. \_refname:` have to be unique
+across all documentation files and this can be checked for with
+`make anchor\_check`.  Finally, a spell-check should be done,
+which is triggered via `make spelling`.  Any offenses need to
+be corrected and false positives should be added to the file
+`utils/sphinx-config/false\_positives.txt`.
 
 ## Required additional steps when adding a new package to LAMMPS
 
-When adding a new package, the package must be added to the list of
-packages in the `Packages_list.rst` file.  If additional build instructions
-need to be followed, a corresponding section should be added to the
-`Build_extras.rst` file and linked from the list at the top of the
-file as well as the equivalent list in the `Build_packages.rst` file.
-
-A detailed description of the package and pointers to configuration,
-included commands and examples, external pages, author information and
-more should be added to the `Packages_details.rst` file.
+TODO

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "8 February 2023" "2023-02-08"
+.TH LAMMPS "1" "23 June 2022" "2022-6-23"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 8 February 2023
+\- Molecular Dynamics Simulator.  Version 23 June 2022
 
 .SH SYNOPSIS
 .B lmp

doc/src/2001/basics.html

@@ -63,7 +63,7 @@ In the src directory, there is one top-level Makefile and several
 low-level machine-specific files named Makefile.xxx where xxx = the
 machine name. If a low-level Makefile exists for your platform, you do
 not need to edit the top-level Makefile.  However you should check the
-system-specific section of the low-level Makefile to ensure the
+system-specific section of the low-level Makefile to insure the
 various paths are correct for your environment. If a low-level
 Makefile does not exist for your platform, you will need to add a
 suitable target to the top-level Makefile. You will also need to

doc/src/2001/input_commands.html

@@ -1206,7 +1206,7 @@ this command is not typically needed if the "nonbond style" and "
 an exception to this is if a short cutoff is used initially,
   but a longer cutoff will be used for a subsequent run (in the same
   input script), in this case the "maximum cutoff" command should be
-  used to ensure enough memory is allocated for the later run
+  used to insure enough memory is allocated for the later run
 note that a restart file contains nonbond cutoffs (so it is not necessary
   to use a "nonbond style" command before "read restart"), but LAMMPS
   still needs to know what the maximum cutoff will be before the

doc/src/Bibliography.rst

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

doc/src/Build.rst

@@ -6,9 +6,9 @@ either traditional makefiles for use with GNU make (which may require
 manual editing), or using a build environment generated by CMake (Unix
 Makefiles, Ninja, Xcode, Visual Studio, KDevelop, CodeBlocks and more).
 
-As an alternative, you can download a package with pre-built executables
-or automated build trees, as described in the :doc:`Install <Install>`
-section of the manual.
+As an alternative you can download a package with pre-built executables
+or automated build trees as described on the :doc:`Install <Install>`
+page.
 
 .. toctree::
    :maxdepth: 1

doc/src/Build_basics.rst

@@ -44,7 +44,7 @@ standard. A more detailed discussion of that is below.
 
       The executable created by CMake (after running make) is named
       ``lmp`` unless the ``LAMMPS_MACHINE`` option is set.  When setting
-      ``LAMMPS_MACHINE=name``, the executable will be called
+      ``LAMMPS_MACHINE=name`` the executable will be called
       ``lmp_name``.  Using ``BUILD_MPI=no`` will enforce building a
       serial executable using the MPI STUBS library.
 
@@ -60,7 +60,7 @@ standard. A more detailed discussion of that is below.
 
       Any ``make machine`` command will look up the make settings from a
       file ``Makefile.machine`` in the folder ``src/MAKE`` or one of its
-      subdirectories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
+      sub-directories ``MINE``, ``MACHINES``, or ``OPTIONS``, create a
       folder ``Obj_machine`` with all objects and generated files and an
       executable called ``lmp_machine``\ .  The standard parallel build
       with ``make mpi`` assumes a standard MPI installation with MPI
@@ -107,9 +107,9 @@ MPI and OpenMP support in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 If you are installing MPI yourself to build a parallel LAMMPS
-executable, we recommend either MPICH or OpenMPI, which are regularly
+executable, we recommend either MPICH or OpenMPI which are regularly
 used and tested with LAMMPS by the LAMMPS developers.  MPICH can be
-downloaded from the `MPICH home page <https://www.mpich.org>`_, and
+downloaded from the `MPICH home page <https://www.mpich.org>`_ and
 OpenMPI can be downloaded correspondingly from the `OpenMPI home page
 <https://www.open-mpi.org>`_.  Other MPI packages should also work.  No
 specific vendor provided and standard compliant MPI library is currently
@@ -130,12 +130,12 @@ package can be compiled to include OpenMP threading.
 
 In addition, there are a few commands in LAMMPS that have native OpenMP
 support included as well.  These are commands in the ``MPIIO``,
-``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  Furthermore,
+``ML-SNAP``, ``DIFFRACTION``, and ``DPD-REACT`` packages.  In addition
 some packages support OpenMP threading indirectly through the libraries
-they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.  See the
-:doc:`Packages details <Packages_details>` page for more info on these
-packages, and the pages for their respective commands for OpenMP
-threading info.
+they interface to: e.g. ``LATTE``, ``KSPACE``, and ``COLVARS``.
+See the :doc:`Packages details <Packages_details>` page for more
+info on these packages and the pages for their respective commands
+for OpenMP threading info.
 
 For CMake, if you use ``BUILD_OMP=yes``, you can use these packages
 and turn on their native OpenMP support and turn on their native OpenMP
@@ -144,9 +144,9 @@ variable before you launch LAMMPS.
 
 For building via conventional make, the ``CCFLAGS`` and ``LINKFLAGS``
 variables in Makefile.machine need to include the compiler flag that
-enables OpenMP. For the GNU compilers or Clang, it is ``-fopenmp``\ .
-For (recent) Intel compilers, it is ``-qopenmp``\ .  If you are using a
-different compiler, please refer to its documentation.
+enables OpenMP. For GNU compilers it is ``-fopenmp``\ .  For (recent) Intel
+compilers it is ``-qopenmp``\ .  If you are using a different compiler,
+please refer to its documentation.
 
 .. _default-none-issues:
 
@@ -174,16 +174,15 @@ Choice of compiler and compile/link options
 The choice of compiler and compiler flags can be important for maximum
 performance.  Vendor provided compilers for a specific hardware can
 produce faster code than open-source compilers like the GNU compilers.
-On the most common x86 hardware, the most popular C++ compilers are
-quite similar in their ability to optimize regular C/C++ source code at
-high optimization levels.  When using the ``INTEL`` package, there is a
-distinct advantage in using the `Intel C++ compiler <intel_>`_ due to
-much improved vectorization through SSE and AVX instructions on
-compatible hardware.  The source code in that package conditionally
-includes compiler specific directives to enable these high degrees of
-vectorization.  This may change over time as equivalent vectorization
-directives are included into the OpenMP standard and other compilers
-adopt them.
+On the most common x86 hardware most popular C++ compilers are quite
+similar in performance of C/C++ code at high optimization levels.  When
+using the ``INTEL`` package, there is a distinct advantage in using
+the `Intel C++ compiler <intel_>`_ due to much improved vectorization
+through SSE and AVX instructions on compatible hardware as the source
+code includes changes and Intel compiler specific directives to enable
+high degrees of vectorization.  This may change over time as equivalent
+vectorization directives are included into OpenMP standard revisions and
+other compilers adopt them.
 
 .. _intel: https://software.intel.com/en-us/intel-compilers
 
@@ -197,7 +196,7 @@ LAMMPS.
    .. tab:: CMake build
 
       By default CMake will use the compiler it finds according to
-      internal preferences, and it will add optimization flags
+      internal preferences and it will add optimization flags
       appropriate to that compiler and any :doc:`accelerator packages
       <Speed_packages>` you have included in the build.  CMake will
       check if the detected or selected compiler is compatible with the
@@ -251,9 +250,9 @@ LAMMPS.
       and `-C ../cmake/presets/pgi.cmake`
       will switch the compiler to the PGI compilers.
 
-      Furthermore, you can set ``CMAKE_TUNE_FLAGS`` to specifically add
-      compiler flags to tune for optimal performance on given hosts.
-      This variable is empty by default.
+      In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
+      compiler flags to tune for optimal performance on given hosts. By
+      default this variable is empty.
 
       .. note::
 
@@ -277,7 +276,7 @@ LAMMPS.
 
       Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-      .. code-block:: make
+      .. code-block:: bash
 
          CC =            mpicxx
          CCFLAGS =       -g -O3
@@ -297,7 +296,7 @@ LAMMPS.
 
          If compilation stops with a message like the following:
 
-         .. code-block:: output
+         .. code-block::
 
             g++ -g -O3  -DLAMMPS_GZIP -DLAMMPS_MEMALIGN=64    -I../STUBS     -c ../main.cpp
             In file included from ../pointers.h:24:0,
@@ -369,10 +368,10 @@ running LAMMPS from Python via its library interface.
                                       # no default value
 
       The compilation will always produce a LAMMPS library and an
-      executable linked to it.  By default, this will be a static
-      library named ``liblammps.a`` and an executable named ``lmp``
-      Setting ``BUILD_SHARED_LIBS=yes`` will instead produce a shared
-      library called ``liblammps.so`` (or ``liblammps.dylib`` or
+      executable linked to it.  By default this will be a static library
+      named ``liblammps.a`` and an executable named ``lmp`` Setting
+      ``BUILD_SHARED_LIBS=yes`` will instead produce a shared library
+      called ``liblammps.so`` (or ``liblammps.dylib`` or
       ``liblammps.dll`` depending on the platform) If
       ``LAMMPS_MACHINE=name`` is set in addition, the name of the
       generated libraries will be changed to either ``liblammps_name.a``
@@ -430,7 +429,7 @@ You may need to use ``sudo make install`` in place of the last line if
 you do not have write privileges for ``/usr/local/lib`` or use the
 ``--prefix`` configuration option to select an installation folder,
 where you do have write access.  The end result should be the file
-``/usr/local/lib/libmpich.so``.  On many Linux installations, the folder
+``/usr/local/lib/libmpich.so``.  On many Linux installations the folder
 ``${HOME}/.local`` is an alternative to using ``/usr/local`` and does
 not require superuser or sudo access.  In that case the configuration
 step becomes:
@@ -439,10 +438,9 @@ step becomes:
 
   ./configure --enable-shared --prefix=${HOME}/.local
 
-Avoiding the use of "sudo" for custom software installation (i.e. from
-source and not through a package manager tool provided by the OS) is
-generally recommended to ensure the integrity of the system software
-installation.
+Avoiding to use "sudo" for custom software installation (i.e. from source
+and not through a package manager tool provided by the OS) is generally
+recommended to ensure the integrity of the system software installation.
 
 ----------
 
@@ -516,11 +514,11 @@ using CMake or Make.
 Install LAMMPS after a build
 ------------------------------------------
 
-After building LAMMPS, you may wish to copy the LAMMPS executable or
-library, along with other LAMMPS files (library header, doc files), to a
-globally visible place on your system, for others to access.  Note that
-you may need super-user privileges (e.g. sudo) if the directory you want
-to copy files to is protected.
+After building LAMMPS, you may wish to copy the LAMMPS executable of
+library, along with other LAMMPS files (library header, doc files) to
+a globally visible place on your system, for others to access.  Note
+that you may need super-user privileges (e.g. sudo) if the directory
+you want to copy files to is protected.
 
 .. tabs::
 
@@ -538,7 +536,7 @@ to copy files to is protected.
       environment variable, if you are installing LAMMPS into a non-system
       location and/or are linking to libraries in a non-system location that
       depend on such runtime path settings.
-      As an alternative, you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
       to ``on`` and then the runtime paths for any linked shared libraries
       and the library installation folder for the LAMMPS library will be
       embedded and thus the requirement to set environment variables is avoided.

doc/src/Build_cmake.rst

@@ -9,10 +9,10 @@ page.
 
 The following text assumes some familiarity with CMake and focuses on
 using the command line tool ``cmake`` and what settings are supported
-for building LAMMPS.  A more detailed tutorial on how to use CMake
-itself, the text mode or graphical user interface, to change the
-generated output files for different build tools and development
-environments is on a :doc:`separate page <Howto_cmake>`.
+for building LAMMPS.  A more detailed tutorial on how to use ``cmake``
+itself, the text mode or graphical user interface, change the generated
+output files for different build tools and development environments is
+on a :doc:`separate page <Howto_cmake>`.
 
 .. note::
 
@@ -22,12 +22,12 @@ environments is on a :doc:`separate page <Howto_cmake>`.
 .. warning::
 
    You must not mix the :doc:`traditional make based <Build_make>`
-   LAMMPS build procedure with using CMake.  No packages may be
+   LAMMPS build procedure with using CMake.  Thus no packages may be
    installed or a build been previously attempted in the LAMMPS source
    directory by using ``make <machine>``.  CMake will detect if this is
    the case and generate an error.  To remove conflicting files from the
    ``src`` you can use the command ``make no-all purge`` which will
-   uninstall all packages and delete all auto-generated files.
+   un-install all packages and delete all auto-generated files.
 
 
 Advantages of using CMake
@@ -44,9 +44,9 @@ software or for people that want to modify or extend LAMMPS.
   and adapt the LAMMPS default build configuration accordingly.
 - CMake can generate files for different build tools and integrated
   development environments (IDE).
-- CMake supports customization of settings with a command line, text
-  mode, or graphical user interface.  No knowledge of file formats or
-  complex command line syntax is required.
+- CMake supports customization of settings with a text mode or graphical
+  user interface. No knowledge of file formats or and complex command
+  line syntax required.
 - All enabled components are compiled in a single build operation.
 - Automated dependency tracking for all files and configuration options.
 - Support for true out-of-source compilation. Multiple configurations
@@ -55,23 +55,23 @@ software or for people that want to modify or extend LAMMPS.
   source tree.
 - Simplified packaging of LAMMPS for Linux distributions, environment
   modules, or automated build tools like `Homebrew <https://brew.sh/>`_.
-- Integration of automated unit and regression testing (the LAMMPS side
-  of this is still under active development).
+- Integration of automated regression testing (the LAMMPS side for that
+  is still under development).
 
 .. _cmake_build:
 
 Getting started
 ^^^^^^^^^^^^^^^
 
-Building LAMMPS with CMake is a two-step process.  In the first step,
-you use CMake to generate a build environment in a new directory.  For
-that purpose you can use either the command-line utility ``cmake`` (or
-``cmake3``), the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the
-graphical utility ``cmake-gui``, or use them interchangeably.  The
-second step is then the compilation and linking of all objects,
-libraries, and executables using the selected build tool.  Here is a
-minimal example using the command line version of CMake to build LAMMPS
-with no add-on packages enabled and no customization:
+Building LAMMPS with CMake is a two-step process.  First you use CMake
+to generate a build environment in a new directory.  For that purpose
+you can use either the command-line utility ``cmake`` (or ``cmake3``),
+the text-mode UI utility ``ccmake`` (or ``ccmake3``) or the graphical
+utility ``cmake-gui``, or use them interchangeably.  The second step is
+then the compilation and linking of all objects, libraries, and
+executables. Here is a minimal example using the command line version of
+CMake to build LAMMPS with no add-on packages enabled and no
+customization:
 
 .. code-block:: bash
 
@@ -96,17 +96,17 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
-Cache) software may speed up repeated compilation even more, e.g. during
-code development, especially when repeatedly switching between branches.
+tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
+Compiler Cache) software may speed up repeated compilation even more,
+e.g. during code development.
 
 After the initial build, whenever you edit LAMMPS source files, enable
 or disable packages, change compiler flags or build options, you must
 re-compile and relink the LAMMPS executable with ``cmake --build .`` (or
 ``make``).  If the compilation fails for some reason, try running
 ``cmake .`` and then compile again. The included dependency tracking
-should make certain that only the necessary subset of files is
-re-compiled.  You can also delete compiled objects, libraries, and
+should make certain that only the necessary subset of files are
+re-compiled.  You can also delete compiled objects, libraries and
 executables with ``cmake --build . --target clean`` (or ``make clean``).
 
 After compilation, you may optionally install the LAMMPS executable into
@@ -132,12 +132,12 @@ file called ``CMakeLists.txt`` (for LAMMPS it is located in the
 ``CMakeCache.txt``, which is generated at the end of the CMake
 configuration step.  The cache file contains all current CMake settings.
 
-To modify settings, enable or disable features, you need to set
-*variables* with either the *-D* command line flag (``-D
-VARIABLE1_NAME=value``) or change them in the text mode of the graphical
-user interface.  The *-D* flag can be used several times in one command.
+To modify settings, enable or disable features, you need to set *variables*
+with either the *-D* command line flag (``-D VARIABLE1_NAME=value``) or
+change them in the text mode of graphical user interface.  The *-D* flag
+can be used several times in one command.
 
-For your convenience, we provide :ref:`CMake presets <cmake_presets>`
+For your convenience we provide :ref:`CMake presets <cmake_presets>`
 that combine multiple settings to enable optional LAMMPS packages or use
 a different compiler tool chain.  Those are loaded with the *-C* flag
 (``-C ../cmake/presets/basic.cmake``).  This step would only be needed
@@ -155,23 +155,22 @@ specific CMake version is given when running ``cmake --help``.
 Multi-configuration build systems
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-Throughout this manual, it is mostly assumed that LAMMPS is being built
+Throughout this manual it is mostly assumed that LAMMPS is being built
 on a Unix-like operating system with "make" as the underlying "builder",
-since this is the most common case.  In this case the build
-"configuration" is chose using ``-D CMAKE_BUILD_TYPE=<configuration>``
-with ``<configuration>`` being one of "Release", "Debug",
-"RelWithDebInfo", or "MinSizeRel".  Some build tools, however, can also
-use or even require having a so-called multi-configuration build system
-setup.  For a multi-configuration build, the built type (or
-configuration) is selected at compile time using the same build
-files. E.g.  with:
+since this is the most common case.  In this case the build "configuration"
+is chose using ``-D CMAKE_BUILD_TYPE=<configuration>`` with ``<configuration>``
+being one of "Release", "Debug", "RelWithDebInfo", or "MinSizeRel".
+Some build tools, however, can also use or even require to have a so-called
+multi-configuration build system setup.  For those the built type (or
+configuration) is chosen at compile time using the same build files. E.g.
+with:
 
 .. code-block:: bash
 
    cmake --build build-multi --config Release
 
 In that case the resulting binaries are not in the build folder directly
-but in subdirectories corresponding to the build type (i.e. Release in
+but in sub-directories corresponding to the build type (i.e. Release in
 the example from above).  Similarly, for running unit tests the
 configuration is selected with the *-C* flag:
 
@@ -185,7 +184,7 @@ particular applicable to compiling packages that require additional libraries
 that would be downloaded and compiled by CMake.  The "windows" preset file
 tries to keep track of which packages can be compiled natively with the
 MSVC compilers out-of-the box.  Not all of those external libraries are
-portable to Windows, either.
+portable to Windows either.
 
 
 Installing CMake

doc/src/Build_development.rst

@@ -46,7 +46,7 @@ It can be enabled for all C++ code with the following CMake flag
 
 With this flag enabled all source files will be processed twice, first to
 be compiled and then to be analyzed. Please note that the analysis can be
-significantly more time-consuming than the compilation itself.
+significantly more time consuming than the compilation itself.
 
 ----------
 
@@ -140,7 +140,7 @@ of the LAMMPS project on GitHub.
 The unit testing facility is integrated into the CMake build process
 of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <https://pyyaml.org/>`_ library and development
+It requires the `YAML <http://pyyaml.org/>`_ library and development
 headers (if those are not found locally a recent version will be
 downloaded and compiled along with LAMMPS and the test program) to
 compile and will download and compile a specific recent version of the
@@ -154,48 +154,32 @@ for implementing the tests.
    framework are more strict than for the main part of LAMMPS.  For
    example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
    (version 4.8.x) are not sufficient.  The CMake configuration will try
-   to detect incompatible versions and either skip incompatible tests or
-   stop with an error.  Also the number of tests will depend on
-   installed LAMMPS packages, development environment, operating system,
-   and configuration settings.
+   to detect compatible versions and either skip incompatible tests or
+   stop with an error.
 
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
-The output of this command will be looking something like this:
+The output of this command will be looking something like this::
 
-.. code-block:: console
+   [...]$ ctest
+   Test project /home/akohlmey/compile/lammps/build-testing
+         Start  1: MolPairStyle:hybrid-overlay
+   1/109 Test  #1: MolPairStyle:hybrid-overlay .........   Passed    0.02 sec
+         Start  2: MolPairStyle:hybrid
+   2/109 Test  #2: MolPairStyle:hybrid .................   Passed    0.01 sec
+         Start  3: MolPairStyle:lj_class2
+    [...]
+         Start 107: PotentialFileReader
+ 107/109 Test #107: PotentialFileReader ................   Passed    0.04 sec
+         Start 108: EIMPotentialFileReader
+ 108/109 Test #108: EIMPotentialFileReader .............   Passed    0.03 sec
+         Start 109: TestSimpleCommands
+ 109/109 Test #109: TestSimpleCommands .................   Passed    0.02 sec
 
-    $ ctest
-    Test project /home/akohlmey/compile/lammps/build-testing
-         Start   1: RunLammps
-   1/563 Test   #1: RunLammps ..........................................   Passed    0.28 sec
-         Start   2: HelpMessage
-   2/563 Test   #2: HelpMessage ........................................   Passed    0.06 sec
-         Start   3: InvalidFlag
-   3/563 Test   #3: InvalidFlag ........................................   Passed    0.06 sec
-         Start   4: Tokenizer
-   4/563 Test   #4: Tokenizer ..........................................   Passed    0.05 sec
-         Start   5: MemPool
-   5/563 Test   #5: MemPool ............................................   Passed    0.05 sec
-         Start   6: ArgUtils
-   6/563 Test   #6: ArgUtils ...........................................   Passed    0.05 sec
-       [...]
-         Start 561: ImproperStyle:zero
- 561/563 Test #561: ImproperStyle:zero .................................   Passed    0.07 sec
-         Start 562: TestMliapPyUnified
- 562/563 Test #562: TestMliapPyUnified .................................   Passed    0.16 sec
-         Start 563: TestPairList
- 563/563 Test #563: TestPairList .......................................   Passed    0.06 sec
+   100% tests passed, 0 tests failed out of 26
 
- 100% tests passed, 0 tests failed out of 563
+   Total Test time (real) =  25.57 sec
 
- Label Time Summary:
- generated    =   0.85 sec*proc (3 tests)
- noWindows    =   4.16 sec*proc (2 tests)
- slow         =  78.33 sec*proc (67 tests)
- unstable     =  28.23 sec*proc (34 tests)
-
- Total Test time (real) = 132.34 sec
 
 The ``ctest`` command has many options, the most important ones are:
 
@@ -226,13 +210,11 @@ Fortran) and testing different aspects of the LAMMPS software and its features.
 The tests will adapt to the compilation settings of LAMMPS, so that tests
 will be skipped if prerequisite features are not available in LAMMPS.
 
-.. admonition:: Work in Progress
-   :class: note
+.. note::
 
    The unit test framework was added in spring 2020 and is under active
    development.  The coverage is not complete and will be expanded over
-   time.  Preference is given to parts of the code base that are easy to
-   test or commonly used.
+   time.
 
 Tests for styles of the same kind of style (e.g. pair styles or bond
 styles) are performed with the same test executable using different
@@ -266,9 +248,9 @@ the CMake option ``-D BUILD_MPI=off`` can significantly speed up testing,
 since this will skip the MPI initialization for each test run.
 Below is an example command and output:
 
-.. code-block:: console
+.. parsed-literal::
 
-   $ test_pair_style mol-pair-lj_cut.yaml
+   [tests]$ test_pair_style mol-pair-lj_cut.yaml
    [==========] Running 6 tests from 1 test suite.
    [----------] Global test environment set-up.
    [----------] 6 tests from PairStyle
@@ -548,7 +530,7 @@ commands like the following:
 
 .. code-block:: bash
 
-   clang-format -i some_file.cpp
+   $ clang-format -i some_file.cpp
 
 
 The following target are available for both, GNU make and CMake:
@@ -557,19 +539,3 @@ The following target are available for both, GNU make and CMake:
 
    make format-src       # apply clang-format to all files in src and the package folders
    make format-tests     # apply clang-format to all files in the unittest tree
-
-----------
-
-.. _gh-cli:
-
-GitHub command line interface
------------------------------
-
-GitHub is developing a `tool for the command line
-<https://cli.github.com>`_ that interacts with the GitHub website via a
-command called ``gh``.  This can be extremely convenient when working
-with a Git repository hosted on GitHub (like LAMMPS).  It is thus highly
-recommended to install it when doing LAMMPS development.
-
-The capabilities of the ``gh`` command is continually expanding, so
-please see the documentation at https://cli.github.com/manual/

doc/src/Build_extras.rst

@@ -12,11 +12,11 @@ in addition to
      - Traditional make
    * - .. code-block:: bash
 
-          cmake -D PKG_NAME=yes
+          $ cmake -D PKG_NAME=yes
 
-     - .. code-block:: console
+     - .. code-block:: bash
 
-          make yes-name
+          $ make yes-name
 
 as described on the :doc:`Build_package <Build_package>` page.
 
@@ -28,29 +28,26 @@ You may need to tell LAMMPS where it is found on your system.
 
 This is the list of packages that may require additional steps.
 
-.. this list must be kept in sync with its counterpart in Build_package.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvar>`
+   * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
-   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
-   * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
    * :ref:`MDI <mdi>`
+   * :ref:`MESONT <mesont>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
    * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
-   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -126,11 +123,10 @@ 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)
-   -D GPU_DEBUG=value           # enable debug code in the GPU package library, mostly useful for developers
-                                # value = yes or no (default)
-   -D HIP_PATH=value            # value = path to HIP installation. Must be set if GPU_API=HIP
+                                # value = sm_XX, see below
+                                # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
                                 # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
@@ -152,9 +148,7 @@ CMake build
 * sm_60 or sm_61 for Pascal (supported since CUDA 8)
 * sm_70 for Volta (supported since CUDA 9)
 * sm_75 for Turing (supported since CUDA 10)
-* sm_80 or sm_86 for Ampere (supported since CUDA 11, sm_86 since CUDA 11.1)
-* sm_89 for Lovelace (supported since CUDA 11.8)
-* sm_90 for Hopper (supported since CUDA 12.0)
+* sm_80 for Ampere (supported since CUDA 11)
 
 A more detailed list can be found, for example,
 at `Wikipedia's CUDA article <https://en.wikipedia.org/wiki/CUDA#GPUs_supported>`_
@@ -186,17 +180,10 @@ 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
@@ -205,7 +192,6 @@ should only use this option in preparations to run on Aurora system at ANL.
 
    # 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
 
@@ -214,20 +200,10 @@ should only use this option in preparations to run on Aurora system at ANL.
    # 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
 ^^^^^^^^^^^^^^^^
 
@@ -245,10 +221,10 @@ script with the specified args:
 
 .. code-block:: bash
 
-  make lib-gpu               # print help message
-  make lib-gpu args="-b"     # build GPU library with default Makefile.linux
-  make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
-  make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
+  $ make lib-gpu               # print help message
+  $ make lib-gpu args="-b"     # build GPU library with default Makefile.linux
+  $ make lib-gpu args="-m xk7 -p single -o xk7.single"  # create new Makefile.xk7.single, altered for single-precision
+  $ make lib-gpu args="-m mpi -a sm_60 -p mixed -b" # build GPU library with mixed precision and P100 using other settings in Makefile.mpi
 
 Note that this procedure starts with a Makefile.machine in lib/gpu, as
 specified by the "-m" switch.  For your convenience, machine makefiles
@@ -288,7 +264,7 @@ your machine are not correct, the LAMMPS build will fail, and
 .. note::
 
    If you re-build the GPU library in ``lib/gpu``, you should always
-   uninstall the GPU package in ``lammps/src``, then re-install it and
+   un-install the GPU package in ``lammps/src``, then re-install it and
    re-build LAMMPS.  This is because the compilation of files in the GPU
    package uses the library settings from the ``lib/gpu/Makefile.machine``
    used to build the GPU library.
@@ -361,13 +337,13 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         make lib-kim              # print help message
-         make lib-kim args="-b "   # (re-)install KIM API lib with only example models
-         make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
-         make lib-kim args="-b -a everything"     # install KIM API lib with all models
-         make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
-         make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
-         make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
+         $ make lib-kim              # print help message
+         $ make lib-kim args="-b "   # (re-)install KIM API lib with only example models
+         $ make lib-kim args="-b -a Glue_Ercolessi_Adams_Al__MO_324507536345_001"  # ditto plus one model
+         $ make lib-kim args="-b -a everything"     # install KIM API lib with all models
+         $ make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_002"       # add one model or model driver
+         $ make lib-kim args="-p /usr/local" # use an existing KIM API installation at the provided location
+         $ make lib-kim args="-p /usr/local -a EAM_Dynamo_Ackland_W__MO_141627196590_002" # ditto but add one model or driver
 
       When using the "-b " option, the KIM library is built using its native
       cmake build system.  The ``lib/kim/Install.py`` script supports a
@@ -379,7 +355,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: bash
 
-         CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
+         $ CMAKE=cmake3 CXX=g++-11 CC=gcc-11 FC=gfortran-11 make lib-kim args="-b "  # (re-)install KIM API lib using cmake3 and gnu v11 compilers with only example models
 
       Settings for debugging OpenKIM web queries discussed below need to
       be applied by adding them to the ``LMP_INC`` variable through
@@ -489,9 +465,6 @@ They must be specified in uppercase.
    *  - **Arch-ID**
       - **HOST or GPU**
       - **Description**
-   *  - NATIVE
-      - HOST
-      - Local machine
    *  - AMDAVX
       - HOST
       - AMD 64-bit x86 CPU (AVX 1)
@@ -531,21 +504,9 @@ They must be specified in uppercase.
    *  - BDW
       - HOST
       - Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
-   *  - SKL
-      - HOST
-      - Intel Skylake Client CPU
    *  - SKX
       - HOST
-      - Intel Skylake Xeon Server CPU (AVX512)
-   *  - ICL
-      - HOST
-      - Intel Ice Lake Client CPU (AVX512)
-   *  - ICX
-      - HOST
-      - Intel Ice Lake Xeon Server CPU (AVX512)
-   *  - SPR
-      - HOST
-      - Intel Sapphire Rapids Xeon Server CPU (AVX512)
+      - Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
    *  - KNC
       - HOST
       - Intel Knights Corner Xeon Phi
@@ -606,12 +567,6 @@ They must be specified in uppercase.
    *  - AMPERE86
       - GPU
       - NVIDIA Ampere generation CC 8.6 GPU
-   *  - ADA89
-      - GPU
-      - NVIDIA Ada Lovelace generation CC 8.9 GPU
-   *  - HOPPER90
-      - GPU
-      - NVIDIA Hopper generation CC 9.0 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -623,10 +578,7 @@ They must be specified in uppercase.
       - AMD GPU MI100 GFX908
    *  - VEGA90A
       - GPU
-      - AMD GPU MI200 GFX90A
-   *  - INTEL_GEN
-      - GPU
-      - SPIR64-based devices, e.g. Intel GPUs, using JIT
+      - AMD GPU
    *  - INTEL_DG1
       - GPU
       - Intel Iris XeMAX GPU
@@ -641,12 +593,9 @@ They must be specified in uppercase.
       - Intel GPU Gen12LP
    *  - INTEL_XEHP
       - GPU
-      - Intel GPU Xe-HP
-   *  - INTEL_PVC
-      - GPU
-      - Intel GPU Ponte Vecchio
+      - Intel GPUs Xe-HP
 
-This list was last updated for version 3.7.1 of the Kokkos library.
+This list was last updated for version 3.5.0 of the Kokkos library.
 
 .. tabs::
 
@@ -840,10 +789,8 @@ 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 USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
-                                      #   value = no (default) or yes
+         -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
+         -D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location)
 
       If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
       and built inside the CMake build directory.  If the LATTE library
@@ -851,13 +798,6 @@ 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
@@ -868,11 +808,11 @@ library.
 
       .. code-block:: bash
 
-         make lib-latte                        # print help message
-         make lib-latte args="-b"              # download and build in lib/latte/LATTE-master
-         make lib-latte args="-p $HOME/latte"  # use existing LATTE installation in $HOME/latte
-         make lib-latte args="-b -m gfortran"  # download and build in lib/latte and
-                                               #   copy Makefile.lammps.gfortran to Makefile.lammps
+         $ make lib-latte                          # print help message
+         $ make lib-latte args="-b"                # download and build in lib/latte/LATTE-master
+         $ make lib-latte args="-p $HOME/latte"    # use existing LATTE installation in $HOME/latte
+         $ make lib-latte args="-b -m gfortran"    # download and build in lib/latte and
+                                                   #   copy Makefile.lammps.gfortran to Makefile.lammps
 
       Note that 3 symbolic (soft) links, ``includelink`` and ``liblink``
       and ``filelink.o``, are created in ``lib/latte`` to point to
@@ -883,55 +823,6 @@ library.
 
 ----------
 
-.. _lepton:
-
-LEPTON package
---------------
-
-To build with this package, you must build the Lepton library which is
-included in the LAMMPS source distribution in the ``lib/lepton`` folder.
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      This is the recommended build procedure for using Lepton in
-      LAMMPS. No additional settings are normally needed besides
-      ``-D PKG_LEPTON=yes``.
-
-      On x86 hardware the Lepton library will also include a just-in-time
-      compiler for faster execution.  This is auto detected but can
-      be explicitly disabled by setting ``-D LEPTON_ENABLE_JIT=no``
-      (or enabled by setting it to yes).
-
-   .. tab:: Traditional make
-
-      Before building LAMMPS, one must build the Lepton library in lib/lepton.
-
-      This can be done manually in the same folder by using or adapting
-      one of the provided Makefiles: for example, ``Makefile.serial`` for
-      the GNU C++ compiler, or ``Makefile.mpi`` for the MPI compiler wrapper.
-      The Lepton library is written in C++-11 and thus the C++ compiler
-      may need to be instructed to enable support for that.
-
-      In general, it is safer to use build setting consistent with the
-      rest of LAMMPS.  This is best carried out from the LAMMPS src
-      directory using a command like these, which simply invokes the
-      ``lib/lepton/Install.py`` script with the specified args:
-
-      .. code-block:: bash
-
-         make lib-lepton                      # print help message
-         make lib-lepton args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         make lib-lepton args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-
-      The "machine" argument of the "-m" flag is used to find a
-      Makefile.machine to use as build recipe.
-
-      The build should produce a ``build`` folder and the library ``lib/lepton/liblmplepton.a``
-
-----------
-
 .. _mliap:
 
 ML-IAP package
@@ -1020,12 +911,12 @@ more details.
 
       .. code-block:: bash
 
-         make lib-mscg             # print help message
-         make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
-                                             # with the settings compatible with "make serial"
-         make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
-                                             # with the settings compatible with "make mpi"
-         make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
+         $ make lib-mscg             # print help message
+         $ make lib-mscg args="-b -m serial"   # download and build in lib/mscg/MSCG-release-master
+                                               # with the settings compatible with "make serial"
+         $ make lib-mscg args="-b -m mpi"      # download and build in lib/mscg/MSCG-release-master
+                                               # with the settings compatible with "make mpi"
+         $ make lib-mscg args="-p /usr/local/mscg-release" # use the existing MS-CG installation in /usr/local/mscg-release
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``,
       will be created in ``lib/mscg`` to point to the MS-CG
@@ -1077,10 +968,10 @@ POEMS package
 
       .. code-block:: bash
 
-         make lib-poems                   # print help message
-         make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
-         make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-poems args="-m icc"     # build with Intel icc compiler
+         $ make lib-poems                   # print help message
+         $ make lib-poems args="-m serial"  # build with GNU g++ compiler (settings as with "make serial")
+         $ make lib-poems args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
+         $ make lib-poems args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/poems/libpoems.a`` and
       ``lib/poems/Makefile.lammps``.  The latter is copied from an
@@ -1166,10 +1057,10 @@ binary package provided by your operating system.
 
       .. code-block:: bash
 
-         make lib-voronoi                          # print help message
-         make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
-         make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
-         make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
+         $ make lib-voronoi                          # print help message
+         $ make lib-voronoi args="-b"                # download and build the default version in lib/voronoi/voro++-<version>
+         $ make lib-voronoi args="-p $HOME/voro++"   # use existing Voro++ installation in $HOME/voro++
+         $ make lib-voronoi args="-b -v voro++0.4.6" # download and build the 0.4.6 version in lib/voronoi/voro++-0.4.6
 
       Note that 2 symbolic (soft) links, ``includelink`` and
       ``liblink``, are created in lib/voronoi to point to the Voro++
@@ -1210,13 +1101,13 @@ systems.
 
       .. code-block:: bash
 
-         make yes-adios
+         $ make yes-adios
 
       otherwise, set ADIOS2_DIR environment variable when turning on the package:
 
       .. code-block:: bash
 
-         ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
+         $ ADIOS2_DIR=path make yes-adios   # path is where ADIOS 2.x is installed
 
 ----------
 
@@ -1245,10 +1136,10 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         make lib-atc                      # print help message
-         make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         make lib-atc args="-m icc"        # build with Intel icc compiler
+         $ make lib-atc                      # print help message
+         $ make lib-atc args="-m serial"     # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-atc args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-atc args="-m icc"        # build with Intel icc compiler
 
       The build should produce two files: ``lib/atc/libatc.a`` and
       ``lib/atc/Makefile.lammps``.  The latter is copied from an
@@ -1267,17 +1158,17 @@ The ATC package requires the MANYBODY package also be installed.
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU Fortran compiler
+         $ make lib-linalg                     # print help message
+         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
 ----------
 
 .. _awpmd:
 
 AWPMD package
--------------
+------------------
 
 .. tabs::
 
@@ -1296,10 +1187,10 @@ AWPMD package
 
       .. code-block:: bash
 
-         make lib-awpmd                   # print help message
-         make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         make lib-awpmd args="-m icc"     # build with Intel icc compiler
+         $ make lib-awpmd                   # print help message
+         $ make lib-awpmd args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-awpmd args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-awpmd args="-m icc"     # build with Intel icc compiler
 
       The build should produce two files: ``lib/awpmd/libawpmd.a`` and
       ``lib/awpmd/Makefile.lammps``.  The latter is copied from an
@@ -1318,20 +1209,21 @@ AWPMD package
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+         $ make lib-linalg                     # print help message
+         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
 ----------
 
-.. _colvar:
+.. _colvars:
 
 COLVARS package
----------------
+---------------------------------------
 
-This package enables the use of the `Colvars <https://colvars.github.io/>`_
-module included in the LAMMPS source distribution.
+This package includes the `Colvars library
+<https://colvars.github.io/>`_ into the LAMMPS distribution, which can
+be built for the most part with all major versions of the C++ language.
 
 
 .. tabs::
@@ -1344,45 +1236,42 @@ module included in the LAMMPS source distribution.
 
    .. tab:: Traditional make
 
-      As with other libraries distributed with LAMMPS, the Colvars library
-      needs to be built before building the LAMMPS program with the COLVARS
-      package enabled.
+      Before building LAMMPS, one must build the Colvars library in lib/colvars.
 
-      From the LAMMPS ``src`` directory, this is most easily and safely done
-      via one of the following commands, which implicitly rely on the
-      ``lib/colvars/Install.py`` script with optional arguments:
+      This can be done manually in the same folder by using or adapting
+      one of the provided Makefiles: for example, ``Makefile.g++`` for
+      the GNU C++ compiler.  C++11 compatibility may need to be enabled
+      for some older compilers (as is done in the example makefile).
+
+      In general, it is safer to use build setting consistent with the
+      rest of LAMMPS.  This is best carried out from the LAMMPS src
+      directory using a command like these, which simply invokes the
+      ``lib/colvars/Install.py`` script with the specified args:
 
       .. code-block:: bash
 
-         make lib-colvars                      # print help message
-         make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
-         make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
-         make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
+         $ make lib-colvars                      # print help message
+         $ make lib-colvars args="-m serial"     # build with GNU g++ compiler (settings as with "make serial")
+         $ make lib-colvars args="-m mpi"        # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-colvars args="-m g++-debug"  # build with GNU g++ compiler and colvars debugging enabled
 
       The "machine" argument of the "-m" flag is used to find a
-      ``Makefile.machine`` file to use as build recipe.  If such recipe does
-      not already exist in ``lib/colvars``, suitable settings will be
-      auto-generated consistent with those used in the core LAMMPS makefiles.
-
-
-      .. versionchanged:: 8Feb2023
-
-      Please note that Colvars uses the Lepton library, which is now
-      included with the LEPTON package; if you use anything other than
-      the ``make lib-colvars`` command, please make sure to :ref:`build
-      Lepton beforehand <lepton>`.
+      Makefile.machine to use as build recipe.  If it does not already
+      exist in ``lib/colvars``, it will be auto-generated by using
+      compiler flags consistent with those parsed from the core LAMMPS
+      makefiles.
 
       Optional flags may be specified as environment variables:
 
       .. code-block:: bash
 
-         COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
-         COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
+         $ COLVARS_DEBUG=yes make lib-colvars args="-m machine"  # Build with debug code (much slower)
+         $ COLVARS_LEPTON=no make lib-colvars args="-m machine"  # Build without Lepton (included otherwise)
 
-      The build should produce two files: the library
-      ``lib/colvars/libcolvars.a`` and the specification file
-      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated,
-      and normally does not need to be edited.
+      The build should produce two files: the library ``lib/colvars/libcolvars.a``
+      (which also includes Lepton objects if enabled) and the specification file
+      ``lib/colvars/Makefile.lammps``.  The latter is auto-generated, and normally does
+      not need to be edited.
 
 ----------
 
@@ -1397,21 +1286,8 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      .. code-block:: bash
-
-         -D PKG_ELECTRODE=yes          # enable the package itself
-         -D PKG_KSPACE=yes             # the ELECTRODE package requires KSPACE
-         -D USE_INTERNAL_LINALG=value  #
-
-      Features in the ELECTRODE package are dependent on code in the
-      KSPACE package so the latter one *must* be enabled.
-
-      The ELECTRODE package also requires LAPACK (and BLAS) and CMake
-      can identify their locations and pass that info to the LATTE build
-      script.  But on some systems this may cause problems when linking
-      or the dependency is not desired.  Try enabling
-      ``USE_INTERNAL_LINALG`` in those cases to use the bundled linear
-      algebra library and work around the limitation.
+      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
+      ``-D PKG_ELECTRODE=yes``.
 
    .. tab:: Traditional make
 
@@ -1424,9 +1300,9 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         make lib-electrode                   # print help message
-         make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
+         $ make lib-electrode                   # print help message
+         $ make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
 
 
       Note that the ``Makefile.lammps`` file has settings for the BLAS
@@ -1437,10 +1313,10 @@ This package depends on the KSPACE package.
 
       .. code-block:: bash
 
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
+         $ make lib-linalg                     # print help message
+         $ make lib-linalg args="-m serial"    # build with GNU Fortran compiler (settings as with "make serial")
+         $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
+         $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
       The package itself is activated with ``make yes-KSPACE`` and
       ``make yes-ELECTRODE``
@@ -1480,56 +1356,13 @@ at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps
 
       .. code-block:: bash
 
-         make lib-pace                          # print help message
-         make lib-pace args="-b"                # download and build the default version in lib/pace
+         $ make lib-pace                          # print help message
+         $ make lib-pace args="-b"                # download and build the default version in lib/pace
 
       You should not need to edit the ``lib/pace/Makefile.lammps`` file.
 
 ----------
 
-.. _ml-pod:
-
-ML-POD package
------------------------------
-
-.. tabs::
-
-   .. tab:: CMake build
-
-      No additional settings are needed besides ``-D PKG_ML-POD=yes``.
-
-   .. tab:: Traditional make
-
-      Before building LAMMPS, you must configure the ML-POD support
-      settings in ``lib/mlpod``.  You can do this manually, if you
-      prefer, or do it in one step from the ``lammps/src`` dir, using a
-      command like the following, which simply invoke the
-      ``lib/mlpod/Install.py`` script with the specified args:
-
-      .. code-block:: bash
-
-         make lib-mlpod                   # print help message
-         make lib-mlpod args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
-         make lib-mlpod args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
-         make lib-mlpod args="-m mpi -e linalg"   # same as above but use the bundled linalg lib
-
-      Note that the ``Makefile.lammps`` file has settings to use the BLAS
-      and LAPACK linear algebra libraries.  These can either exist on
-      your system, or you can use the files provided in ``lib/linalg``.
-      In the latter case you also need to build the library in
-      ``lib/linalg`` with a command like these:
-
-      .. code-block:: bash
-
-         make lib-linalg                   # print help message
-         make lib-linalg args="-m serial"  # build with GNU C++ compiler (settings as with "make serial")
-         make lib-linalg args="-m mpi"     # build with default MPI C++ compiler (settings as with "make mpi")
-         make lib-linalg args="-m g++"     # build with GNU C++ compiler
-
-      The package itself is activated with ``make yes-ML-POD``.
-
-----------
-
 .. _plumed:
 
 PLUMED package
@@ -1623,10 +1456,10 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         make lib-plumed                         # print help message
-         make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
-         make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
-         make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
+         $ make lib-plumed                         # print help message
+         $ make lib-plumed args="-b"               # download and build PLUMED in lib/plumed/plumed2
+         $ make lib-plumed args="-p $HOME/.local"  # use existing PLUMED installation in $HOME/.local
+         $ make lib-plumed args="-p /usr/local -m shared"  # use existing PLUMED installation in
                                                            # /usr/local and use shared linkage mode
 
       Note that 2 symbolic (soft) links, ``includelink`` and ``liblink``
@@ -1639,8 +1472,8 @@ LAMMPS build.
 
       .. code-block:: bash
 
-         make yes-plumed
-         make machine
+         $ make yes-plumed
+         $ make machine
 
       Once this compilation completes you should be able to run LAMMPS
       in the usual way.  For shared linkage mode, libplumed.so must be
@@ -1692,8 +1525,8 @@ the HDF5 library.
 
       .. code-block:: bash
 
-         make lib-h5md                     # print help message
-         make lib-h5md args="-m h5cc"      # build with h5cc compiler
+         $ make lib-h5md                     # print help message
+         $ make lib-h5md args="-m h5cc"      # build with h5cc compiler
 
       The build should produce two files: ``lib/h5md/libch5md.a`` and
       ``lib/h5md/Makefile.lammps``.  The latter is copied from an
@@ -1747,10 +1580,10 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
 
       .. code-block:: bash
 
-         make lib-hdnnp             # print help message
-         make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
-         make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
-         make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
+         $ make lib-hdnnp             # print help message
+         $ make lib-hdnnp args="-b"   # download and build in lib/hdnnp/n2p2-...
+         $ make lib-hdnnp args="-b -v 2.1.4" # download and build specific version
+         $ make lib-hdnnp args="-p /usr/local/n2p2" # use the existing n2p2 installation in /usr/local/n2p2
 
       Note that 3 symbolic (soft) links, ``includelink``, ``liblink`` and
       ``Makefile.lammps``, will be created in ``lib/hdnnp`` to point to
@@ -1850,14 +1683,56 @@ MDI package
 
       .. code-block:: bash
 
-         python Install.py -m gcc       # build using gcc compiler
-         python Install.py -m icc       # build using icc compiler
+         $ python Install.py -m gcc       # build using gcc compiler
+         $ python Install.py -m icc       # build using icc compiler
 
       The build should produce two files: ``lib/mdi/includelink/mdi.h``
       and ``lib/mdi/liblink/libmdi.so``\ .
 
 ----------
 
+.. _mesont:
+
+MESONT package
+-------------------------
+
+This package includes a library written in Fortran 90 in the
+``lib/mesont`` folder, so a working Fortran 90 compiler is required to
+compile it.  Also, the files with the force field data for running the
+bundled examples are not included in the source distribution. Instead
+they will be downloaded the first time this package is installed.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      No additional settings are needed besides ``-D PKG_MESONT=yes``
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must build the *mesont* library in
+      ``lib/mesont``\ .  You can also do it in one step from the
+      ``lammps/src`` dir, using a command like these, which simply
+      invokes the ``lib/mesont/Install.py`` script with the specified
+      args:
+
+      .. code-block:: bash
+
+         $ make lib-mesont                    # print help message
+         $ make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
+         $ make lib-mesont args="-m ifort"    # build with Intel icc compiler
+
+      The build should produce two files: ``lib/mesont/libmesont.a`` and
+      ``lib/mesont/Makefile.lammps``\ .  The latter is copied from an
+      existing ``Makefile.lammps.\*`` and has settings needed to build
+      LAMMPS with the *mesont* library (though typically the settings
+      contain only the Fortran runtime library).  If necessary, you can
+      edit/create a new ``lib/mesont/Makefile.machine`` file for your
+      system, which should define an ``EXTRAMAKE`` variable to specify a
+      corresponding ``Makefile.lammps.machine`` file.
+
+----------
+
 .. _molfile:
 
 MOLFILE package
@@ -1958,22 +1833,6 @@ OPENMP package
       For other platforms and compilers, please consult the
       documentation about OpenMP support for your compiler.
 
-.. admonition:: Adding OpenMP support on macOS
-   :class: note
-
-   Apple offers the `Xcode package and IDE
-   <https://developer.apple.com/xcode/>`_ for compiling software on
-   macOS, so you have likely installed it to compile LAMMPS.  Their
-   compiler is based on `Clang <https://clang.llvm.org/>`, but while it
-   is capable of processing OpenMP directives, the necessary header
-   files and OpenMP runtime library are missing.  The `R developers
-   <https://www.r-project.org/>` have figured out a way to build those
-   in a compatible fashion. One can download them from
-   `https://mac.r-project.org/openmp/
-   <https://mac.r-project.org/openmp/>`_.  Simply adding those files as
-   instructed enables the Xcode C++ compiler to compile LAMMPS with ``-D
-   BUILD_OMP=yes``.
-
 ----------
 
 .. _qmmm:
@@ -2028,10 +1887,10 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
 
       .. code-block:: bash
 
-         make lib-qmmm                      # print help message
-         make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
-         make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
-         make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
+         $ make lib-qmmm                      # print help message
+         $ make lib-qmmm args="-m serial"     # build with GNU Fortran compiler (settings as in "make serial")
+         $ make lib-qmmm args="-m mpi"        # build with default MPI compiler (settings as in "make mpi")
+         $ make lib-qmmm args="-m gfortran"   # build with GNU Fortran compiler
 
       The build should produce two files: ``lib/qmmm/libqmmm.a`` and
       ``lib/qmmm/Makefile.lammps``.  The latter is copied from an
@@ -2070,23 +1929,12 @@ within CMake will download the non-commercial use version.
 
          -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.
-
-      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.
+ 
+      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.
 
    .. tab:: Traditional make
 
@@ -2180,9 +2028,9 @@ Eigen3 is a template library, so you do not need to build it.
 
       .. code-block:: bash
 
-         make lib-smd                         # print help message
-         make lib-smd args="-b"               # download to lib/smd/eigen3
-         make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
+         $ make lib-smd                         # print help message
+         $ make lib-smd args="-b"               # download to lib/smd/eigen3
+         $ make lib-smd args="-p /usr/include/eigen3"    # use existing Eigen installation in /usr/include/eigen3
 
       Note that a symbolic (soft) link named ``includelink`` is created
       in ``lib/smd`` to point to the Eigen dir.  When LAMMPS builds it

doc/src/Build_link.rst

@@ -1,32 +1,33 @@
 Link LAMMPS as a library to another code
 ========================================
 
-LAMMPS is designed as a library of C++ objects that can be integrated
-into other applications, including Python scripts.  The files
-``src/library.cpp`` and ``src/library.h`` define a C-style API for using
-LAMMPS as a library.  See the :doc:`Howto_library` page for a
-description of the interface and how to use it for your needs.
+LAMMPS is designed as a library of C++ objects that can be
+integrated into other applications including Python scripts.
+The files ``src/library.cpp`` and ``src/library.h`` define a
+C-style API for using LAMMPS as a library.  See the
+:doc:`Howto_library` page
+for a description of the interface and how to use it for your needs.
 
-The :doc:`Build_basics` page explains how to build LAMMPS as either a
-shared or static library.  This results in a file in the compilation
-folder called ``liblammps.a`` or ``liblammps_<name>.a`` in case of
-building a static library.  In case of a shared library, the name is the
-same only that the suffix is going to be either ``.so`` or ``.dylib`` or
-``.dll`` instead of ``.a`` depending on the OS.  In some cases, the
-``.so`` file may be a symbolic link to a file with the suffix ``.so.0``
-(or some other number).
+The :doc:`Build_basics` page explains how to build
+LAMMPS as either a shared or static library.  This results in a file
+in the compilation folder called ``liblammps.a`` or ``liblammps_<name>.a``
+in case of building a static library.  In case of a shared library
+the name is the same only that the suffix is going to be either ``.so``
+or ``.dylib`` or ``.dll`` instead of ``.a`` depending on the OS.
+In some cases the ``.so`` file may be a symbolic link to a file with
+the suffix ``.so.0`` (or some other number).
 
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library, unless LAMMPS is to be compiled without (real)
-   MPI support using the included STUBS MPI library.
+   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   MPI support using the include STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
 
 The calling application can link to LAMMPS as a static library with
-compilation and link commands, as in the examples shown below.  These
+compilation and link commands as in the examples shown below.  These
 are examples for a code written in C in the file ``caller.c``.
 The benefit of linking to a static library is, that the resulting
 executable is independent of that library since all required
@@ -141,10 +142,10 @@ Link with LAMMPS as a shared library
 When linking to LAMMPS built as a shared library, the situation becomes
 much simpler, as all dependent libraries and objects are either included
 in the shared library or registered as a dependent library in the shared
-library file.  Thus, those libraries need not be specified when linking
-the calling executable.  Only the *-I* flags are needed.  So the example
-case from above of the serial version static LAMMPS library with the
-POEMS package installed becomes:
+library file.  Thus those libraries need not to be specified when
+linking the calling executable.  Only the *-I* flags are needed.  So the
+example case from above of the serial version static LAMMPS library with
+the POEMS package installed becomes:
 
 .. tabs::
 
@@ -208,7 +209,7 @@ You can verify whether all required shared libraries are found with the
 
 .. code-block:: bash
 
-   LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
+   $ LD_LIBRARY_PATH=/home/user/lammps/src ldd caller
         linux-vdso.so.1 (0x00007ffe729e0000)
         liblammps.so => /home/user/lammps/src/liblammps.so (0x00007fc91bb9e000)
         libstdc++.so.6 => /lib64/libstdc++.so.6 (0x00007fc91b984000)
@@ -221,7 +222,7 @@ If a required library is missing, you would get a 'not found' entry:
 
 .. code-block:: bash
 
-   ldd caller
+   $  ldd caller
         linux-vdso.so.1 (0x00007ffd672fe000)
         liblammps.so => not found
         libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x00007fb7c7e86000)

doc/src/Build_make.rst

@@ -20,22 +20,21 @@ with :doc:`CMake <Build_cmake>`.  The makefiles of the traditional
 make based build process and the scripts they are calling expect a few
 additional tools to be available and functioning.
 
-  * A working C/C++ compiler toolchain supporting the C++11 standard; on
-    Linux, these are often the GNU compilers. Some older compiler versions
+  * a working C/C++ compiler toolchain supporting the C++11 standard; on
+    Linux these are often the GNU compilers. Some older compilers
     require adding flags like ``-std=c++11`` to enable the C++11 mode.
-  * A Bourne shell compatible "Unix" shell program (frequently this is ``bash``)
-  * A few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
-  * Python (optional, required for ``make lib-<pkg>`` in the src
-    folder).  Python scripts are currently tested with python 2.7 and
-    3.6 to 3.11. The procedure for :doc:`building the documentation
-    <Build_manual>` *requires* Python 3.5 or later.
+  * a Bourne shell compatible "Unix" shell program (often this is ``bash``)
+  * a few shell utilities: ``ls``, ``mv``, ``ln``, ``rm``, ``grep``, ``sed``, ``tr``, ``cat``, ``touch``, ``diff``, ``dirname``
+  * python (optional, required for ``make lib-<pkg>`` in the src folder).
+    python scripts are currently tested with python 2.7 and 3.6. The procedure
+    for :doc:`building the documentation <Build_manual>` requires python 3.5 or later.
 
 Getting started
 ^^^^^^^^^^^^^^^
 
 To include LAMMPS packages (i.e. optional commands and styles) you must
 enable (or "install") them first, as discussed on the :doc:`Build
-package <Build_package>` page.  If a package requires (provided or
+package <Build_package>` page.  If a packages requires (provided or
 external) libraries, you must configure and build those libraries
 **before** building LAMMPS itself and especially **before** enabling
 such a package with ``make yes-<package>``.  :doc:`Building LAMMPS with
@@ -57,36 +56,36 @@ Compilation can take a long time, since LAMMPS is a large project with
 many features. If your machine has multiple CPU cores (most do these
 days), you can speed this up by compiling sources in parallel with
 ``make -j N`` (with N being the maximum number of concurrently executed
-tasks).  Installation of the `ccache <https://ccache.dev/>`_ (= Compiler
-Cache) software may speed up repeated compilation even more, e.g. during
-code development, especially when repeatedly switching between branches.
+tasks).  Also installation of the `ccache <https://ccache.dev/>`_ (=
+Compiler Cache) software may speed up repeated compilation even more,
+e.g. during code development.
 
 After the initial build, whenever you edit LAMMPS source files, or add
 or remove new files to the source directory (e.g. by installing or
 uninstalling packages), you must re-compile and relink the LAMMPS
 executable with the same ``make <machine>`` command.  The makefile's
-dependency tracking should ensure that only the necessary subset of
-files is re-compiled.  If you change settings in the makefile, you have
-to recompile *everything*.  To delete all objects, you can use ``make
+dependency tracking should insure that only the necessary subset of
+files are re-compiled.  If you change settings in the makefile, you have
+to recompile *everything*.  To delete all objects you can use ``make
 clean-<machine>``.
 
 .. note::
 
    Before the actual compilation starts, LAMMPS will perform several
-   steps to collect information from the configuration and setup that is
-   then embedded into the executable.  When you build LAMMPS for the
-   first time, it will also compile a tool to quickly determine a list
-   of dependencies.  Those are required for the make program to
-   correctly detect, which files need to be recompiled or relinked
-   after changes were made to the sources.
+   steps to collect information from the configuration and setup that
+   is then embedded into the executable.  When you build LAMMPS for
+   the first time, it will also compile a tool to quickly assemble
+   a list of dependencies, that are required for the make program to
+   correctly detect which parts need to be recompiled after changes
+   were made to the sources.
 
 Customized builds and alternate makefiles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The ``src/MAKE`` directory tree contains the ``Makefile.<machine>``
 files included in the LAMMPS distribution.  Typing ``make example`` uses
-``Makefile.example`` from one of those folders, if available.  The
-``make serial`` and ``make mpi`` lines above, for example, use
+``Makefile.example`` from one of those folders, if available.  Thus the
+``make serial`` and ``make mpi`` lines above use
 ``src/MAKE/Makefile.serial`` and ``src/MAKE/Makefile.mpi``,
 respectively.  Other makefiles are in these directories:
 
@@ -107,13 +106,12 @@ a new name, please edit the first line with the description and machine
 name, so you will not confuse yourself, when looking at the machine
 summary.
 
-Makefiles you may wish to try out, include those listed below (some
-require a package first be installed).  Many of these include specific
-compiler flags for optimized performance.  Please note, however, that
-some of these customized machine Makefile are contributed by users, and
-thus may have modifications specific to the systems of those users.
-Since compilers, OS configurations, and LAMMPS itself keep changing,
-their settings may become outdated, too:
+Makefiles you may wish to try include these (some require a package
+first be installed).  Many of these include specific compiler flags
+for optimized performance.  Please note, however, that some of these
+customized machine Makefile are contributed by users.  Since both
+compilers, OS configurations, and LAMMPS itself keep changing, their
+settings may become outdated:
 
 .. code-block:: bash
 

doc/src/Build_manual.rst

@@ -2,7 +2,7 @@ Build the LAMMPS documentation
 ==============================
 
 Depending on how you obtained LAMMPS and whether you have built the
-manual yourself, this directory has a number of subdirectories and
+manual yourself, this directory has a number of sub-directories and
 files. Here is a list with descriptions:
 
 .. code-block:: bash
@@ -48,15 +48,18 @@ Build using GNU make
 
 The LAMMPS manual is written in `reStructuredText <rst_>`_ format which
 can be translated to different output format using the `Sphinx
-<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``.
+<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
 
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
@@ -125,29 +128,38 @@ common setups:
 
       .. code-block:: bash
 
-         sudo apt-get install git doxygen
+         sudo apt-get install python-virtualenv git doxygen
 
    .. tab:: RHEL or CentOS (Version 7.x)
 
       .. code-block:: bash
 
-         sudo yum install git doxygen
+         sudo yum install python3-virtualenv git doxygen
 
    .. tab:: Fedora or RHEL/CentOS (8.x or later)
 
       .. code-block:: bash
 
-         sudo dnf install git doxygen
+         sudo dnf install python3-virtualenv git doxygen
 
-   .. tab:: macOS
+   .. tab:: MacOS X
 
       *Python 3*
 
-      If Python 3 is not available on your macOS system, you can
-      download the latest Python 3 macOS package from
+      Download the latest Python 3 MacOS X package from
       `https://www.python.org <https://www.python.org>`_ and install it.
       This will install both Python 3 and pip3.
 
+      *virtualenv*
+
+      Once Python 3 is installed, open a Terminal and type
+
+      .. code-block:: bash
+
+         pip3 install virtualenv
+
+      This will install virtualenv from the Python Package Index.
+
 Prerequisites for PDF
 ---------------------
 
@@ -167,7 +179,7 @@ math expressions transparently into embedded images.
 For converting the generated ePUB file to a MOBI format file (for e-book
 readers, like Kindle, that cannot read ePUB), you also need to have the
 ``ebook-convert`` tool from the "calibre" software
-installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
+installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
 Typing ``make mobi`` will first create the ePUB file and then convert
 it.  On the Kindle readers in particular, you also have support for PDF
 files, so you could download and view the PDF version as an alternative.
@@ -207,20 +219,9 @@ be multiple tests run automatically:
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
   thus prints all offending lines with filename and line number
-  prepended to the screen.  Special characters like Greek letters
-  (:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
-  (:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
-  (:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
-  (:math:`\AA`) should be typeset with embedded LaTeX (like this
-  ``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
-  ``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
-
-- Embedded LaTeX is rendered in HTML output with `MathJax
-  <https://www.mathjax.org/>`_ and in PDF output by passing the embedded
-  text to LaTeX.  Some care has to be taken, though, since there are
-  limitations which macros and features can be used in either mode, so
-  it is recommended to always check whether any new or changed
-  documentation does translate and render correctly with either output.
+  prepended to the screen.  Special characters like the Angstrom
+  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
+  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
 
 - A test whether all styles are documented and listed in their
   respective overview pages.  A typical output with warnings looks like this:
@@ -251,5 +252,6 @@ 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

@@ -4,14 +4,13 @@ Include packages in build
 In LAMMPS, a package is a group of files that enable a specific set of
 features.  For example, force fields for molecular systems or
 rigid-body constraints are in packages.  In the src directory, each
-package is a subdirectory with the package name in capital letters.
+package is a sub-directory with the package name in capital letters.
 
 An overview of packages is given on the :doc:`Packages <Packages>` doc
-page.  Brief overviews of each package are on the :doc:`Packages details
-<Packages_details>` page.
+page.  Brief overviews of each package are on the :doc:`Packages details <Packages_details>` page.
 
 When building LAMMPS, you can choose to include or exclude each
-package.  Generally, there is no need to include a package if you
+package.  In general there is no need to include a package if you
 never plan to use its features.
 
 If you get a run-time error that a LAMMPS command or style is
@@ -31,29 +30,23 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-.. this list must be kept in sync with its counterpart in Build_extras.rst
 .. table_from_list::
    :columns: 6
 
    * :ref:`ADIOS <adios>`
    * :ref:`ATC <atc>`
    * :ref:`AWPMD <awpmd>`
-   * :ref:`COLVARS <colvar>`
+   * :ref:`COLVARS <colvars>`
    * :ref:`COMPRESS <compress>`
-   * :ref:`ELECTRODE <electrode>`
    * :ref:`GPU <gpu>`
    * :ref:`H5MD <h5md>`
    * :ref:`INTEL <intel>`
    * :ref:`KIM <kim>`
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
-   * :ref:`LEPTON <lepton>`
    * :ref:`MACHDYN <machdyn>`
-   * :ref:`MDI <mdi>`
    * :ref:`ML-HDNNP <ml-hdnnp>`
-   * :ref:`ML-IAP <mliap>`
    * :ref:`ML-PACE <ml-pace>`
-   * :ref:`ML-POD <ml-pod>`
    * :ref:`ML-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`
    * :ref:`MSCG <mscg>`
@@ -94,7 +87,7 @@ versus make.
          If you switch between building with CMake and make builds, no
          packages in the src directory can be installed when you invoke
          ``cmake``.  CMake will give an error if that is not the case,
-         indicating how you can uninstall all packages in the src dir.
+         indicating how you can un-install all packages in the src dir.
 
    .. tab:: Traditional make
 
@@ -103,7 +96,7 @@ versus make.
          cd lammps/src
          make ps                    # check which packages are currently installed
          make yes-name              # install a package with name
-         make no-name               # uninstall a package with name
+         make no-name               # un-install a package with name
          make mpi                   # build LAMMPS with whatever packages are now installed
 
       Examples:
@@ -119,13 +112,13 @@ versus make.
       .. note::
 
          You must always re-build LAMMPS (via make) after installing or
-         uninstalling a package, for the action to take effect. The
+         un-installing a package, for the action to take effect. The
          included dependency tracking will make certain only files that
          are required to be rebuilt are recompiled.
 
       .. note::
 
-         You cannot install or uninstall packages and build LAMMPS in a
+         You cannot install or un-install packages and build LAMMPS in a
          single make command with multiple targets, e.g. ``make
          yes-colloid mpi``.  This is because the make procedure creates
          a list of source files that will be out-of-date for the build
@@ -150,7 +143,7 @@ other files dependent on that package are also excluded.
    if you downloaded a tarball, 3 packages (KSPACE, MANYBODY, MOLECULE)
    were pre-installed via the traditional make procedure in the ``src``
    directory.  That is no longer the case, so that CMake will build
-   as-is without needing to uninstall those packages.
+   as-is without needing to un-install those packages.
 
 ----------
 
@@ -167,9 +160,9 @@ control flow constructs for more complex operations.
 
 LAMMPS includes several of these files to define configuration
 "presets", similar to the options that exist for the Make based
-system. Using these files, you can enable/disable portions of the
-available packages in LAMMPS. If you need a custom preset, you can
-make a copy of one of them and modify it to suit your needs.
+system. Using these files you can enable/disable portions of the
+available packages in LAMMPS. If you need a custom preset you can take
+one of them as a starting point and customize it to your needs.
 
 .. code-block:: bash
 
@@ -183,7 +176,7 @@ make a copy of one of them and modify it to suit your needs.
     cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     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
+    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
@@ -227,7 +220,7 @@ The following commands are useful for managing package source files
 and their installation when building LAMMPS via traditional make.
 Just type ``make`` in lammps/src to see a one-line summary.
 
-These commands install/uninstall sets of packages:
+These commands install/un-install sets of packages:
 
 .. code-block:: bash
 
@@ -243,40 +236,40 @@ These commands install/uninstall sets of packages:
     make yes-ext                        # install packages that require external libraries
     make no-ext                         # uninstall packages that require external libraries
 
-which install/uninstall various sets of packages.  Typing ``make
+which install/un-install various sets of packages.  Typing ``make
 package`` will list all the these commands.
 
 .. note::
 
-   Installing or uninstalling a package for the make based build process
+   Installing or un-installing a package for the make based build process
    works by simply copying files back and forth between the main source
-   directory src and the subdirectories with the package name (e.g.
+   directory src and the sub-directories with the package name (e.g.
    src/KSPACE, src/ATC), so that the files are included or excluded
    when LAMMPS is built.  Only source files in the src folder will be
    compiled.
 
 The following make commands help manage files that exist in both the
-src directory and in package subdirectories.  You do not normally
+src directory and in package sub-directories.  You do not normally
 need to use these commands unless you are editing LAMMPS files or are
 updating LAMMPS via git.
 
 Type ``make package-status`` or ``make ps`` to show which packages are
 currently installed.  For those that are installed, it will list any
 files that are different in the src directory and package
-subdirectory.
+sub-directory.
 
 Type ``make package-installed`` or ``make pi`` to show which packages are
 currently installed, without listing the status of packages that are
 not installed.
 
 Type ``make package-update`` or ``make pu`` to overwrite src files with
-files from the package subdirectories if the package is installed.  It
+files from the package sub-directories if the package is installed.  It
 should be used after the checkout has been :doc:`updated or changed
-with git <Install_git>`, this will only update the files in the package
-subdirectories, but not the copies in the src folder.
+withy git <Install_git>`, this will only update the files in the package
+sub-directories, but not the copies in the src folder.
 
 Type ``make package-overwrite`` to overwrite files in the package
-subdirectories with src files.
+sub-directories with src files.
 
 Type ``make package-diff`` to list all differences between pairs of
 files in both the source directory and the package directory.

doc/src/Build_settings.rst

@@ -1,8 +1,8 @@
 Optional build settings
 =======================
 
-LAMMPS can be built with several optional settings.  Each subsection
-explains how to do this for building both with CMake and make.
+LAMMPS can be built with several optional settings.  Each sub-section
+explain how to do this for building both with CMake and make.
 
 * `C++11 standard compliance`_ when building all of LAMMPS
 * `FFT library`_ for use with the :doc:`kspace_style pppm <kspace_style>` command
@@ -41,7 +41,7 @@ FFT library
 When the KSPACE package is included in a LAMMPS build, the
 :doc:`kspace_style pppm <kspace_style>` command performs 3d FFTs which
 require use of an FFT library to compute 1d FFTs.  The KISS FFT
-library is included with LAMMPS, but other libraries can be faster.
+library is included with LAMMPS but other libraries can be faster.
 LAMMPS can use them if they are available on your system.
 
 .. tabs::
@@ -63,9 +63,9 @@ LAMMPS can use them if they are available on your system.
       Usually these settings are all that is needed.  If FFTW3 is
       selected, then CMake will try to detect, if threaded FFTW
       libraries are available and enable them by default.  This setting
-      is independent of whether OpenMP threads are enabled and a package
-      like KOKKOS or OPENMP is used.  If CMake cannot detect the FFT
-      library, you can set these variables to assist:
+      is independent of whether OpenMP threads are enabled and a
+      packages like KOKKOS or OPENMP is used.  If CMake cannot detect
+      the FFT library, you can set these variables to assist:
 
       .. code-block:: bash
 
@@ -111,25 +111,26 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
-The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
-included in the LAMMPS distribution.  It is portable across all
-platforms.  Depending on the size of the FFTs and the number of
-processors used, the other libraries listed here can be faster.
+The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+distribution.  It is portable across all platforms.  Depending on the size
+of the FFTs and the number of processors used, the other libraries listed
+here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
-per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
-and 1d FFTs are only a portion of the FFT cost (parallel communication
-can be costly).  A breakdown of these timings is printed to the screen
-at the end of a run when using the :doc:`kspace_style pppm
-<kspace_style>` command. The :doc:`Screen and logfile output
-<Run_output>` page gives more details.  A more detailed (and time
-consuming) report of the FFT performance is generated with the
+per-timestep CPU cost, FFTs are only a portion of long-range
+Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+communication can be costly).  A breakdown of these timings is printed
+to the screen at the end of a run when using the
+:doc:`kspace_style pppm <kspace_style>` command. The
+:doc:`Screen and logfile output <Run_output>`
+page gives more details.  A more detailed (and time consuming)
+report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
-platform and can be faster than the KISS FFT library.  You can download
-it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
-3.X; the legacy version 2.1.X is no longer supported.
+platform and can be faster than the KISS FFT library.  You can
+download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+version 3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges
@@ -141,18 +142,18 @@ The Intel MKL math library is part of the Intel compiler suite.  It
 can be used with the Intel or GNU compiler (see the ``FFT_LIB`` setting
 above).
 
-Performing 3d FFTs in parallel can be time-consuming due to data access
-and required communication.  This cost can be reduced by performing
-single-precision FFTs instead of double precision.  Single precision
-means the real and imaginary parts of a complex datum are 4-byte floats.
-Double precision means they are 8-byte doubles.  Note that Fourier
-transform and related PPPM operations are somewhat less sensitive to
-floating point truncation errors, and thus the resulting error is
-generally less than the difference in precision. Using the
-``-DFFT_SINGLE`` setting trades off a little accuracy for reduced memory
-use and parallel communication costs for transposing 3d FFT data.
+Performing 3d FFTs in parallel can be time consuming due to data
+access and required communication.  This cost can be reduced by
+performing single-precision FFTs instead of double precision.  Single
+precision means the real and imaginary parts of a complex datum are
+4-byte floats.  Double precision means they are 8-byte doubles.  Note
+that Fourier transform and related PPPM operations are somewhat less
+sensitive to floating point truncation errors and thus the resulting
+error is less than the difference in precision. Using the ``-DFFT_SINGLE``
+setting trades off a little accuracy for reduced memory use and
+parallel communication costs for transposing 3d FFT data.
 
-When using ``-DFFT_SINGLE`` with FFTW3, you may need to build the FFTW
+When using ``-DFFT_SINGLE`` with FFTW3 you may need to build the FFTW
 library a second time with support for single-precision.
 
 For FFTW3, do the following, which should produce the additional
@@ -177,11 +178,11 @@ ARRAY mode.
 Size of LAMMPS integer types and size limits
 --------------------------------------------
 
-LAMMPS uses a few custom integer data types, which can be defined as
-either 4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
-This has an impact on the size of a system that can be simulated, or how
-large counters can become before "rolling over".  The default setting of
-"smallbig" is almost always adequate.
+LAMMPS has a few integer data types which can be defined as either
+4-byte (= 32-bit) or 8-byte (= 64-bit) integers at compile time.
+This has an impact on the size of a system that can be simulated
+or how large counters can become before "rolling over".
+The default setting of "smallbig" is almost always adequate.
 
 .. tabs::
 
@@ -254,7 +255,7 @@ topology information, though IDs are enabled by default.  The
 :doc:`atom_modify id no <atom_modify>` command will turn them off.  Atom
 IDs are required for molecular systems with bond topology (bonds,
 angles, dihedrals, etc).  Similarly, some force or compute or fix styles
-require atom IDs.  Thus, if you model a molecular system or use one of
+require atom IDs.  Thus if you model a molecular system or use one of
 those styles with more than 2 billion atoms, you need the "bigbig"
 setting.
 
@@ -264,7 +265,7 @@ systems and 500 million for systems with bonds (the additional
 restriction is due to using the 2 upper bits of the local atom index
 in neighbor lists for storing special bonds info).
 
-Image flags store 3 values per atom in a single integer, which count the
+Image flags store 3 values per atom in a single integer which count the
 number of times an atom has moved through the periodic box in each
 dimension.  See the :doc:`dump <dump>` manual page for a discussion.  If
 an atom moves through the periodic box more than this limit, the value
@@ -285,7 +286,7 @@ 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
+PNG image files.  Likewise the :doc:`dump movie <dump_image>` command
 outputs movie files in a variety of movie formats.  Using these options
 requires the following settings:
 
@@ -354,7 +355,7 @@ Read or write compressed files
 If this option is enabled, large files can be read or written with
 compression by ``gzip`` or similar tools by several LAMMPS commands,
 including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Supported compression tools are currently
+:doc:`dump <dump>`.  Currently supported compression tools are:
 ``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
 
 .. tabs::
@@ -394,7 +395,7 @@ Memory allocation alignment
 ---------------------------------------
 
 This setting enables the use of the "posix_memalign()" call instead of
-"malloc()" when LAMMPS allocates large chunks of memory.  Vector
+"malloc()" when LAMMPS allocates large chunks or memory.  Vector
 instructions on CPUs may become more efficient, if dynamically allocated
 memory is aligned on larger-than-default byte boundaries.  On most
 current operating systems, the "malloc()" implementation returns
@@ -496,7 +497,7 @@ Trigger selected floating-point exceptions
 ------------------------------------------
 
 Many kinds of CPUs have the capability to detect when a calculation
-results in an invalid math operation, like a division by zero or calling
+results in an invalid math operation like a division by zero or calling
 the square root with a negative argument.  The default behavior on
 most operating systems is to continue and have values for ``NaN`` (= not
 a number) or ``Inf`` (= infinity).  This allows software to detect and

doc/src/Commands.rst

@@ -21,7 +21,6 @@ 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

@@ -10,21 +10,17 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================
 
-An alphabetic list of general LAMMPS commands.  Note that style
-commands with many variants, can be more easily accessed via the small
-table above.
+An alphabetic list of general LAMMPS commands.
 
 .. table_from_list::
    :columns: 5
 
    * :doc:`angle_coeff <angle_coeff>`
    * :doc:`angle_style <angle_style>`
-   * :doc:`angle_write <angle_write>`
    * :doc:`atom_modify <atom_modify>`
    * :doc:`atom_style <atom_style>`
    * :doc:`balance <balance>`
@@ -32,6 +28,7 @@ table above.
    * :doc:`bond_style <bond_style>`
    * :doc:`bond_write <bond_write>`
    * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`clear <clear>`
    * :doc:`comm_modify <comm_modify>`
@@ -46,7 +43,6 @@ table above.
    * :doc:`dielectric <dielectric>`
    * :doc:`dihedral_coeff <dihedral_coeff>`
    * :doc:`dihedral_style <dihedral_style>`
-   * :doc:`dihedral_write <dihedral_write>`
    * :doc:`dimension <dimension>`
    * :doc:`displace_atoms <displace_atoms>`
    * :doc:`dump <dump>`
@@ -64,7 +60,6 @@ table above.
    * :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>`
@@ -91,7 +86,8 @@ table above.
    * :doc:`region <region>`
    * :doc:`replicate <replicate>`
    * :doc:`rerun <rerun>`
-   * :doc:`reset_atoms <reset_atoms>`
+   * :doc:`reset_atom_ids <reset_atom_ids>`
+   * :doc:`reset_mol_ids <reset_mol_ids>`
    * :doc:`reset_timestep <reset_timestep>`
    * :doc:`restart <restart>`
    * :doc:`run <run>`
@@ -127,7 +123,6 @@ additional letter in parenthesis: k = KOKKOS.
    * :doc:`group2ndx <group2ndx>`
    * :doc:`hyper <hyper>`
    * :doc:`kim <kim_commands>`
-   * :doc:`fitpod <fitpod_command>`
    * :doc:`mdi <mdi>`
    * :doc:`ndx2group <group2ndx>`
    * :doc:`neb <neb>`

doc/src/Commands_bond.rst

@@ -10,7 +10,6 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
 
 .. _bond:
 
@@ -44,8 +43,6 @@ OPT.
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
-   * :doc:`lepton (o) <bond_lepton>`
-   * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
    * :doc:`nonlinear (o) <bond_nonlinear>`
@@ -77,7 +74,6 @@ OPT.
    *
    *
    *
-   * :doc:`amoeba <angle_amoeba>`
    * :doc:`charmm (iko) <angle_charmm>`
    * :doc:`class2 (ko) <angle_class2>`
    * :doc:`class2/p6 <angle_class2>`
@@ -94,11 +90,9 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
-   * :doc:`lepton (o) <angle_lepton>`
-   * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`spica (o) <angle_spica>`
+   * :doc:`sdk (o) <angle_sdk>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
@@ -129,7 +123,6 @@ OPT.
    * :doc:`fourier (io) <dihedral_fourier>`
    * :doc:`harmonic (iko) <dihedral_harmonic>`
    * :doc:`helix (o) <dihedral_helix>`
-   * :doc:`lepton (o) <dihedral_lepton>`
    * :doc:`multi/harmonic (o) <dihedral_multi_harmonic>`
    * :doc:`nharmonic (o) <dihedral_nharmonic>`
    * :doc:`opls (iko) <dihedral_opls>`
@@ -159,7 +152,6 @@ OPT.
    *
    *
    *
-   * :doc:`amoeba <improper_amoeba>`
    * :doc:`class2 (ko) <improper_class2>`
    * :doc:`cossq (o) <improper_cossq>`
    * :doc:`cvff (io) <improper_cvff>`

doc/src/Commands_category.rst

@@ -25,6 +25,7 @@ Setup simulation box:
    :columns: 4
 
    * :doc:`boundary <boundary>`
+   * :doc:`box <box>`
    * :doc:`change_box <change_box>`
    * :doc:`create_box <create_box>`
    * :doc:`dimension <dimension>`

doc/src/Commands_compute.rst

@@ -10,7 +10,6 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
 
 Compute commands
 ================
@@ -57,7 +56,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`dpd/atom <compute_dpd_atom>`
    * :doc:`edpd/temp/atom <compute_edpd_temp_atom>`
    * :doc:`efield/atom <compute_efield_atom>`
-   * :doc:`efield/wolf/atom <compute_efield_wolf_atom>`
    * :doc:`entropy/atom <compute_entropy_atom>`
    * :doc:`erotate/asphere <compute_erotate_asphere>`
    * :doc:`erotate/rigid <compute_erotate_rigid>`
@@ -88,6 +86,7 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`ke/atom/eff <compute_ke_atom_eff>`
    * :doc:`ke/eff <compute_ke_eff>`
    * :doc:`ke/rigid <compute_ke_rigid>`
+   * :doc:`mesont <compute_mesont>`
    * :doc:`mliap <compute_mliap>`
    * :doc:`momentum <compute_momentum>`
    * :doc:`msd <compute_msd>`
@@ -107,7 +106,6 @@ KOKKOS, o = OPENMP, t = OPT.
    * :doc:`pressure/uef <compute_pressure_uef>`
    * :doc:`property/atom <compute_property_atom>`
    * :doc:`property/chunk <compute_property_chunk>`
-   * :doc:`property/grid <compute_property_grid>`
    * :doc:`property/local <compute_property_local>`
    * :doc:`ptm/atom <compute_ptm_atom>`
    * :doc:`rdf <compute_rdf>`
@@ -140,8 +138,6 @@ 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

@@ -1,57 +0,0 @@
-.. 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:`grid <dump>`
-   * :doc:`grid/vtk <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

@@ -10,7 +10,6 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
 
 Fix commands
 ============
@@ -29,8 +28,6 @@ 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>`
@@ -38,12 +35,14 @@ OPT.
    * :doc:`ave/chunk <fix_ave_chunk>`
    * :doc:`ave/correlate <fix_ave_correlate>`
    * :doc:`ave/correlate/long <fix_ave_correlate_long>`
-   * :doc:`ave/grid <fix_ave_grid>`
    * :doc:`ave/histo <fix_ave_histo>`
    * :doc:`ave/histo/weight <fix_ave_histo>`
    * :doc:`ave/time <fix_ave_time>`
    * :doc:`aveforce <fix_aveforce>`
    * :doc:`balance <fix_balance>`
+   * :doc:`brownian <fix_brownian>`
+   * :doc:`brownian/asphere <fix_brownian>`
+   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`bocs <fix_bocs>`
    * :doc:`bond/break <fix_bond_break>`
    * :doc:`bond/create <fix_bond_create>`
@@ -51,9 +50,6 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
-   * :doc:`brownian <fix_brownian>`
-   * :doc:`brownian/asphere <fix_brownian>`
-   * :doc:`brownian/sphere <fix_brownian>`
    * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -66,13 +62,13 @@ OPT.
    * :doc:`drude <fix_drude>`
    * :doc:`drude/transform/direct <fix_drude_transform>`
    * :doc:`drude/transform/inverse <fix_drude_transform>`
-   * :doc:`dt/reset (k) <fix_dt_reset>`
+   * :doc:`dt/reset <fix_dt_reset>`
    * :doc:`edpd/source <fix_dpd_source>`
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
-   * :doc:`electrode/conp (i) <fix_electrode>`
-   * :doc:`electrode/conq (i) <fix_electrode>`
-   * :doc:`electrode/thermo (i) <fix_electrode>`
+   * :doc:`electrode/conp (i) <fix_electrode_conp>`
+   * :doc:`electrode/conq (i) <fix_electrode_conp>`
+   * :doc:`electrode/thermo (i) <fix_electrode_conp>`
    * :doc:`electron/stopping <fix_electron_stopping>`
    * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
@@ -107,7 +103,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`mdi/qm <fix_mdi_qm>`
+   * :doc:`mdi/aimd <fix_mdi_aimd>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
@@ -166,7 +162,6 @@ 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>`
@@ -214,7 +209,6 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
-   * :doc:`sgcmc <fix_sgcmc>`
    * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
@@ -251,7 +245,7 @@ OPT.
    * :doc:`tune/kspace <fix_tune_kspace>`
    * :doc:`vector <fix_vector>`
    * :doc:`viscosity <fix_viscosity>`
-   * :doc:`viscous (k) <fix_viscous>`
+   * :doc:`viscous <fix_viscous>`
    * :doc:`viscous/sphere <fix_viscous_sphere>`
    * :doc:`wall/body/polygon <fix_wall_body_polygon>`
    * :doc:`wall/body/polyhedron <fix_wall_body_polyhedron>`

doc/src/Commands_kspace.rst

@@ -10,7 +10,6 @@
    * :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

@@ -10,7 +10,6 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
-   * :doc:`Dump styles <Commands_dump>`
 
 Pair_style potentials
 ======================
@@ -39,7 +38,6 @@ OPT.
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
-   * :doc:`amoeba (g) <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -93,8 +91,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (giko) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
-   * :doc:`dpd/ext (ko) <pair_dpd_ext>`
-   * :doc:`dpd/ext/tstat (ko) <pair_dpd_ext>`
+   * :doc:`dpd/ext (k) <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat (k) <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (gko) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -126,7 +124,6 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
-   * :doc:`hippo (g) <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>`
@@ -134,8 +131,6 @@ OPT.
    * :doc:`lcbop <pair_lcbop>`
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
-   * :doc:`lepton (o) <pair_lepton>`
-   * :doc:`lepton/coul (o) <pair_lepton>`
    * :doc:`line/lj <pair_line_lj>`
    * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
@@ -166,7 +161,7 @@ OPT.
    * :doc:`lj/cut/coul/msm (go) <pair_lj_cut_coul>`
    * :doc:`lj/cut/coul/msm/dielectric <pair_dielectric>`
    * :doc:`lj/cut/coul/wolf (o) <pair_lj_cut_coul>`
-   * :doc:`lj/cut/dipole/cut (gko) <pair_dipole>`
+   * :doc:`lj/cut/dipole/cut (go) <pair_dipole>`
    * :doc:`lj/cut/dipole/long (g) <pair_dipole>`
    * :doc:`lj/cut/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/cut/soft (o) <pair_fep_soft>`
@@ -175,7 +170,7 @@ OPT.
    * :doc:`lj/cut/tip4p/long (got) <pair_lj_cut_tip4p>`
    * :doc:`lj/cut/tip4p/long/soft (o) <pair_fep_soft>`
    * :doc:`lj/expand (gko) <pair_lj_expand>`
-   * :doc:`lj/expand/coul/long (gk) <pair_lj_expand>`
+   * :doc:`lj/expand/coul/long (g) <pair_lj_expand>`
    * :doc:`lj/gromacs (gko) <pair_gromacs>`
    * :doc:`lj/gromacs/coul/gromacs (ko) <pair_gromacs>`
    * :doc:`lj/long/coul/long (iot) <pair_lj_long>`
@@ -184,9 +179,9 @@ OPT.
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
-   * :doc:`lj/spica (gko) <pair_spica>`
-   * :doc:`lj/spica/coul/long (go) <pair_spica>`
-   * :doc:`lj/spica/coul/msm (o) <pair_spica>`
+   * :doc:`lj/sdk (gko) <pair_sdk>`
+   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
+   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@@ -199,15 +194,14 @@ OPT.
    * :doc:`lubricateU/poly <pair_lubricateU>`
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
-   * :doc:`meam (k) <pair_meam>`
-   * :doc:`meam/ms (k) <pair_meam>`
+   * :doc:`meam <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>`
-   * :doc:`mliap (k) <pair_mliap>`
+   * :doc:`mliap <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -238,8 +232,6 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
-   * :doc:`pace/extrapolation (k) <pair_pace>`
-   * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`
@@ -276,7 +268,6 @@ 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>`
@@ -298,7 +289,6 @@ OPT.
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`
-   * :doc:`ylz <pair_ylz>`
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_removed.rst

@@ -2,17 +2,14 @@ Removed commands and packages
 =============================
 
 This page lists LAMMPS commands and packages that have been removed from
-the distribution and provides suggestions for alternatives or
-replacements.  LAMMPS has special dummy styles implemented, that will
-stop LAMMPS and print a suitable error message in most cases, when a
-style/command is used that has been removed or will replace the command
-with the direct alternative (if available) and print a warning.
+the distribution and provides suggestions for alternatives or replacements.
+LAMMPS has special dummy styles implemented, that will stop LAMMPS and
+print a suitable error message in most cases, when a style/command is used
+that has been removed.
 
 Fix ave/spatial and fix ave/spatial/sphere
 ------------------------------------------
 
-.. deprecated:: 11Dec2015
-
 The fixes ave/spatial and ave/spatial/sphere have been removed from LAMMPS
 since they were superseded by the more general and extensible "chunk
 infrastructure".  Here the system is partitioned in one of many possible
@@ -20,23 +17,10 @@ ways through the :doc:`compute chunk/atom <compute_chunk_atom>` command
 and then averaging is done using :doc:`fix ave/chunk <fix_ave_chunk>`.
 Please refer to the :doc:`chunk HOWTO <Howto_chunk>` section for an overview.
 
-Box command
------------
+Reset_ids command
+-----------------
 
-.. deprecated:: 22Dec2022
-
-The *box* command has been removed and the LAMMPS code changed so it won't
-be needed.  If present, LAMMPS will ignore the command and print a warning.
-
-Reset_ids, reset_atom_ids, reset_mol_ids commands
--------------------------------------------------
-
-.. deprecated:: 22Dec2022
-
-The *reset_ids*, *reset_atom_ids*, and *reset_mol_ids* commands have
-been folded into the :doc:`reset_atoms <reset_atoms>` command.  If
-present, LAMMPS will replace the commands accordingly and print a
-warning.
+The reset_ids command has been renamed to :doc:`reset_atom_ids <reset_atom_ids>`.
 
 MEAM package
 ------------
@@ -46,42 +30,18 @@ The code in the :ref:`MEAM package <PKG-MEAM>` is a translation of the
 Fortran code of MEAM into C++, which removes several restrictions
 (e.g. there can be multiple instances in hybrid pair styles) and allows
 for some optimizations leading to better performance.  The pair style
-:doc:`meam <pair_meam>` has the exact same syntax.  For a transition
-period the C++ version of MEAM was called USER-MEAMC so it could
-coexist with the Fortran version.
-
-Minimize style fire/old
------------------------
-
-.. deprecated:: 8Feb2023
-
-Minimize style *fire/old* has been removed. Its functionality can be
-reproduced with *fire* with specific options. Please see the
-:doc:`min_modify command <min_modify>` documentation for details.
-
-Pair style mesont/tpm, compute style mesont, atom style mesont
---------------------------------------------------------------
-
-.. deprecated:: 8Feb2023
-
-Pair style *mesont/tpm*, compute style *mesont*, and atom style
-*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
-The same functionality is available through
-:doc:`pair style mesocnt <pair_mesocnt>`,
-:doc:`bond style mesocnt <bond_mesocnt>` and
-:doc:`angle style mesocnt <angle_mesocnt>`.
+:doc:`meam <pair_meam>` has the exact same syntax.
 
 REAX package
 ------------
 
 The REAX package has been removed since it was superseded by the
-:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF package has been tested
-to yield equivalent results to the REAX package, offers better
-performance, supports OpenMP multi-threading via OPENMP, and GPU and
-threading parallelization through KOKKOS.  The new pair styles are not
-syntax compatible with the removed reax pair style, so input files will
-have to be adapted.  The REAXFF package was originally called
-USER-REAXC.
+:ref:`REAXFF package <PKG-REAXFF>`.  The REAXFF
+package has been tested to yield equivalent results to the REAX package,
+offers better performance, supports OpenMP multi-threading via OPENMP,
+and GPU and threading parallelization through KOKKOS.  The new pair styles
+are not syntax compatible with the removed reax pair style, so input
+files will have to be adapted.
 
 USER-CUDA package
 -----------------
@@ -100,6 +60,5 @@ restart2data tool
 The functionality of the restart2data tool has been folded into the
 LAMMPS executable directly instead of having a separate tool.  A
 combination of the commands :doc:`read_restart <read_restart>` and
-:doc:`write_data <write_data>` can be used to the same effect.  For
-added convenience this conversion can also be triggered by
-:doc:`command line flags <Run_options>`
+:doc:`write_data <write_data>` can be used to the same effect.  For added
+convenience this conversion can also be triggered by :doc:`command line flags <Run_options>`

doc/src/Developer.rst

@@ -17,10 +17,8 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
-   Developer_updating
    Developer_plugins
    Developer_unittest
    Classes
    Developer_platform
    Developer_utils
-   Developer_grid

doc/src/Developer_code_design.rst

@@ -1,57 +1,56 @@
 Code design
 -----------
 
-This section explains some code design choices in LAMMPS with the goal
-of helping developers write new code similar to the existing code.
-Please see the section on :doc:`Requirements for contributed code
-<Modify_style>` for more specific recommendations and guidelines.  While
-that section is organized more in the form of a checklist for code
-contributors, the focus here is on overall code design strategy, choices
-made between possible alternatives, and discussing some relevant C++
-programming language constructs.
+This section explains some of the code design choices in LAMMPS with
+the goal of helping developers write new code similar to the existing
+code.  Please see the section on :doc:`Requirements for contributed
+code <Modify_style>` for more specific recommendations and guidelines.
+While that section is organized more in the form of a checklist for
+code contributors, the focus here is on overall code design strategy,
+choices made between possible alternatives, and discussing some
+relevant C++ programming language constructs.
 
 Historically, the basic design philosophy of the LAMMPS C++ code was a
 "C with classes" style.  The motivation was to make it easy to modify
-LAMMPS for people without significant training in C++ programming.  Data
-structures and code constructs were used that resemble the previous
-implementation(s) in Fortran.  A contributing factor to this choice was
-that at the time, C++ compilers were often not mature and some advanced
-features contained bugs or did not function as the standard required.
-There were also disagreements between compiler vendors as to how to
-interpret the C++ standard documents.
+LAMMPS for people without significant training in C++ programming.
+Data structures and code constructs were used that resemble the
+previous implementation(s) in Fortran.  A contributing factor to this
+choice also was that at the time, C++ compilers were often not mature
+and some of the advanced features contained bugs or did not function
+as the standard required.  There were also disagreements between
+compiler vendors as to how to interpret the C++ standard documents.
 
-However, C++ compilers and the C++ programming language have advanced
-significantly.  In 2020, the LAMMPS developers decided to require the
-C++11 standard as the minimum C++ language standard for LAMMPS.  Since
-then, we have begun to replace C-style constructs with equivalent C++
-functionality.  This was taken either from the C++ standard library or
-implemented as custom classes or functions.  The goal is to improve
-readability of the code and to increase code reuse through abstraction
-of commonly used functionality.
+However, C++ compilers have now advanced significantly.  In 2020 we
+decided to to require the C++11 standard as the minimum C++ language
+standard for LAMMPS.  Since then we have begun to also replace some of
+the C-style constructs with equivalent C++ functionality, either from
+the C++ standard library or as custom classes or functions, in order
+to improve readability of the code and to increase code reuse through
+abstraction of commonly used functionality.
 
 .. note::
 
-   Please note that as of spring 2023 there is still a sizable chunk of
-   legacy code in LAMMPS that has not yet been refactored to reflect
-   these style conventions in full.  LAMMPS has a large code base and
-   many contributors.  There is also a hierarchy of precedence in which
-   the code is adapted.  Highest priority has been the code in the
-   ``src`` folder, followed by code in packages in order of their
-   popularity and complexity (simpler code gets adapted sooner), followed
-   by code in the ``lib`` folder.  Source code that is downloaded from
-   external packages or libraries during compilation is not subject to
-   the conventions discussed here.
+   Please note that as of spring 2022 there is still a sizable chunk
+   of legacy code in LAMMPS that has not yet been refactored to
+   reflect these style conventions in full.  LAMMPS has a large code
+   base and many different contributors and there also is a hierarchy
+   of precedence in which the code is adapted.  Highest priority has
+   been the code in the ``src`` folder, followed by code in packages
+   in order of their popularity and complexity (simpler code is
+   adapted sooner), followed by code in the ``lib`` folder.  Source
+   code that is downloaded from external packages or libraries during
+   compilation is not subject to the conventions discussed here.
 
-Object-oriented code
+Object oriented code
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS is designed to be an object-oriented code.  Each simulation is
+LAMMPS is designed to be an object oriented code.  Each simulation is
 represented by an instance of the LAMMPS class.  When running in
-parallel, each MPI process creates such an instance.  This can be seen
+parallel each MPI process creates such an instance.  This can be seen
 in the ``main.cpp`` file where the core steps of running a LAMMPS
 simulation are the following 3 lines of code:
 
-.. code-block:: c++
+.. code-block:: C++
 
     LAMMPS *lammps = new LAMMPS(argc, argv, lammps_comm);
     lammps->input->file();
@@ -68,29 +67,29 @@ other special features.
 The basic LAMMPS class hierarchy which is created by the LAMMPS class
 constructor is shown in :ref:`class-topology`.  When input commands
 are processed, additional class instances are created, or deleted, or
-replaced.  Likewise, specific member functions of specific classes are
+replaced.  Likewise specific member functions of specific classes are
 called to trigger actions such creating atoms, computing forces,
 computing properties, time-propagating the system, or writing output.
 
 Compositing and Inheritance
 ===========================
 
-LAMMPS makes extensive use of the object-oriented programming (OOP)
+LAMMPS makes extensive use of the object oriented programming (OOP)
 principles of *compositing* and *inheritance*. Classes like the
 ``LAMMPS`` class are a **composite** containing pointers to instances
 of other classes like ``Atom``, ``Comm``, ``Force``, ``Neighbor``,
-``Modify``, and so on.  Each of these classes implements certain
+``Modify``, and so on.  Each of these classes implement certain
 functionality by storing and manipulating data related to the
 simulation and providing member functions that trigger certain
 actions.  Some of those classes like ``Force`` are themselves
 composites, containing instances of classes describing different force
-interactions.  Similarly, the ``Modify`` class contains a list of
+interactions.  Similarly the ``Modify`` class contains a list of
 ``Fix`` and ``Compute`` classes.  If the input commands that
 correspond to these classes include the word *style*, then LAMMPS
 stores only a single instance of that class.  E.g. *atom_style*,
-*comm_style*, *pair_style*, *bond_style*.  If the input command does
-**not** include the word *style*, then there may be many instances of
-that class defined, for example *region*, *fix*, *compute*, *dump*.
+*comm_style*, *pair_style*, *bond_style*.  It the input command does
+not include the word *style*, there can be many instances of that
+class defined.  E.g. *region*, *fix*, *compute*, *dump*.
 
 **Inheritance** enables creation of *derived* classes that can share
 common functionality in their base class while providing a consistent
@@ -101,18 +100,19 @@ derived class variant was instantiated.  In LAMMPS these derived
 classes are often referred to as "styles", e.g.  pair styles, fix
 styles, atom styles and so on.
 
-This is the origin of the flexibility of LAMMPS.  For example, pair
+This is the origin of the flexibility of LAMMPS.  For example pair
 styles implement a variety of different non-bonded interatomic
 potentials functions.  All details for the implementation of a
 potential are stored and executed in a single class.
 
 As mentioned above, there can be multiple instances of classes derived
 from the ``Fix`` or ``Compute`` base classes.  They represent a
-different facet of LAMMPS' flexibility, as they provide methods which
-can be called at different points within a timestep, as explained in
-`Developer_flow`.  This allows the input script to tailor how a specific
-simulation is run, what diagnostic computations are performed, and how
-the output of those computations is further processed or output.
+different facet of LAMMPS flexibility as they provide methods which
+can be called at different points in time within a timestep, as
+explained in `Developer_flow`.  This allows the input script to tailor
+how a specific simulation is run, what diagnostic computations are
+performed, and how the output of those computations is further
+processed or output.
 
 Additional code sharing is possible by creating derived classes from the
 derived classes (e.g., to implement an accelerated version of a pair
@@ -164,15 +164,15 @@ The difference in behavior of the ``normal()`` and the ``poly()`` member
 functions is which of the two member functions is called when executing
 `base1->call()` versus `base2->call()`.  Without polymorphism, a
 function within the base class can only call member functions within the
-same scope: that is, ``Base::call()`` will always call
-``Base::normal()``.  But for the `base2->call()` case, the call of the
+same scope, that is ``Base::call()`` will always call
+``Base::normal()``.  But for the `base2->call()` case the call of the
 virtual member function will be dispatched to ``Derived::poly()``
-instead.  This mechanism results in calling functions that are within
-the scope of the class that was used to *create* the instance, even if
-they are assigned to a pointer for their base class.  This is the
-desired behavior, and this way LAMMPS can even use styles that are loaded
-at runtime from a shared object file with the :doc:`plugin command
-<plugin>`.
+instead.  This mechanism means that functions are called within the
+scope of the class type that was used to *create* the class instance are
+invoked; even if they are assigned to a pointer using the type of a base
+class.  This is the desired behavior and this way LAMMPS can even use
+styles that are loaded at runtime from a shared object file with the
+:doc:`plugin command <plugin>`.
 
 A special case of virtual functions are so-called pure functions.  These
 are virtual functions that are initialized to 0 in the class declaration
@@ -189,12 +189,12 @@ This has the effect that an instance of the base class cannot be
 created and that derived classes **must** implement these functions.
 Many of the functions listed with the various class styles in the
 section :doc:`Modify` are pure functions.  The motivation for this is
-to define the interface or API of the functions, but defer their
+to define the interface or API of the functions but defer their
 implementation to the derived classes.
 
 However, there are downsides to this. For example, calls to virtual
-functions from within a constructor, will *not* be in the scope of the
-derived class, and thus it is good practice to either avoid calling them
+functions from within a constructor, will not be in the scope of the
+derived class and thus it is good practice to either avoid calling them
 or to provide an explicit scope such as ``Base::poly()`` or
 ``Derived::poly()``.  Furthermore, any destructors in classes containing
 virtual functions should be declared virtual too, so they will be
@@ -208,8 +208,8 @@ dispatch.
    that are intended to replace a virtual or pure function use the
    ``override`` property keyword.  For the same reason, the use of
    overloads or default arguments for virtual functions should be
-   avoided, as they lead to confusion over which function is supposed to
-   override which, and which arguments need to be declared.
+   avoided as they lead to confusion over which function is supposed to
+   override which and which arguments need to be declared.
 
 Style Factories
 ===============
@@ -219,10 +219,10 @@ uses a programming pattern called `Factory`.  Those are functions that
 create an instance of a specific derived class, say ``PairLJCut`` and
 return a pointer to the type of the common base class of that style,
 ``Pair`` in this case.  To associate the factory function with the
-style keyword, a ``std::map`` class is used with function pointers
+style keyword, an ``std::map`` class is used with function pointers
 indexed by their keyword (for example "lj/cut" for ``PairLJCut`` and
 "morse" for ``PairMorse``).  A couple of typedefs help keep the code
-readable, and a template function is used to implement the actual
+readable and a template function is used to implement the actual
 factory functions for the individual classes.  Below is an example
 of such a factory function from the ``Force`` class as declared in
 ``force.h`` and implemented in ``force.cpp``.  The file ``style_pair.h``
@@ -232,7 +232,7 @@ macro ``PairStyle()`` will associate the style name "lj/cut"
 with a factory function creating an instance of the ``PairLJCut``
 class.
 
-.. code-block:: c++
+.. code-block:: C++
 
    // from force.h
    typedef Pair *(*PairCreator)(LAMMPS *);
@@ -279,26 +279,26 @@ from and writing to files and console instead of C++ "iostreams".
 This is mainly motivated by better performance, better control over
 formatting, and less effort to achieve specific formatting.
 
-Since mixing "stdio" and "iostreams" can lead to unexpected behavior,
-use of the latter is strongly discouraged.  Output to the screen should
-*not* use the predefined ``stdout`` FILE pointer, but rather the
-``screen`` and ``logfile`` FILE pointers managed by the LAMMPS class.
-Furthermore, output should generally only be done by MPI rank 0
-(``comm->me == 0``).  Output that is sent to both ``screen`` and
-``logfile`` should use the :cpp:func:`utils::logmesg() convenience
-function <LAMMPS_NS::utils::logmesg>`.
+Since mixing "stdio" and "iostreams" can lead to unexpected
+behavior. use of the latter is strongly discouraged.  Also output to
+the screen should not use the predefined ``stdout`` FILE pointer, but
+rather the ``screen`` and ``logfile`` FILE pointers managed by the
+LAMMPS class.  Furthermore, output should generally only be done by
+MPI rank 0 (``comm->me == 0``).  Output that is sent to both
+``screen`` and ``logfile`` should use the :cpp:func:`utils::logmesg()
+convenience function <LAMMPS_NS::utils::logmesg>`.
 
-We discourage the use of stringstreams because the bundled {fmt} library
-and the customized tokenizer classes provide the same functionality in a
-cleaner way with better performance.  This also helps maintain a
-consistent programming syntax with code from many different
-contributors.
+We also discourage the use of stringstreams because the bundled {fmt}
+library and the customized tokenizer classes can provide the same
+functionality in a cleaner way with better performance.  This also
+helps maintain a consistent programming syntax with code from many
+different contributors.
 
 Formatting with the {fmt} library
 ===================================
 
 The LAMMPS source code includes a copy of the `{fmt} library
-<https://fmt.dev>`_, which is preferred over formatting with the
+<https://fmt.dev>`_ which is preferred over formatting with the
 "printf()" family of functions.  The primary reason is that it allows
 a typesafe default format for any type of supported data.  This is
 particularly useful for formatting integers of a given size (32-bit or
@@ -313,16 +313,17 @@ been included into the C++20 language standard, so changes to adopt it
 are future-proof.
 
 Formatted strings are frequently created by calling the
-``fmt::format()`` function, which will return a string as a
-``std::string`` class instance.  In contrast to the ``%`` placeholder in
-``printf()``, the {fmt} library uses ``{}`` to embed format descriptors.
-In the simplest case, no additional characters are needed, as {fmt} will
-choose the default format based on the data type of the argument.
-Otherwise, the ``fmt::print()`` function may be used instead of
-``printf()`` or ``fprintf()``.  In addition, several LAMMPS output
-functions, that originally accepted a single string as argument have
-been overloaded to accept a format string with optional arguments as
-well (e.g., ``Error::all()``, ``Error::one()``, ``utils::logmesg()``).
+``fmt::format()`` function which will return a string as a
+``std::string`` class instance.  In contrast to the ``%`` placeholder
+in ``printf()``, the {fmt} library uses ``{}`` to embed format
+descriptors.  In the simplest case, no additional characters are
+needed as {fmt} will choose the default format based on the data type
+of the argument.  Otherwise the ``fmt::print()`` function may be
+used instead of ``printf()`` or ``fprintf()``.  In addition, several
+LAMMPS output functions, that originally accepted a single string as
+argument have been overloaded to accept a format string with optional
+arguments as well (e.g., ``Error::all()``, ``Error::one()``,
+``utils::logmesg()``).
 
 Summary of the {fmt} format syntax
 ==================================
@@ -331,11 +332,10 @@ The syntax of the format string is "{[<argument id>][:<format spec>]}",
 where either the argument id or the format spec (separated by a colon
 ':') is optional.  The argument id is usually a number starting from 0
 that is the index to the arguments following the format string.  By
-default, these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The
-most common case for using argument id would be to use the same argument
-in multiple places in the format string without having to provide it as
-an argument multiple times. The argument id is rarely used in the LAMMPS
-source code.
+default these are assigned in order (i.e. 0, 1, 2, 3, 4 etc.).  The most
+common case for using argument id would be to use the same argument in
+multiple places in the format string without having to provide it as an
+argument multiple times. In LAMMPS the argument id is rarely used.
 
 More common is the use of a format specifier, which starts with a colon.
 This may optionally be followed by a fill character (default is ' '). If
@@ -347,21 +347,20 @@ width, which may be followed by a dot '.' and a precision for floating
 point numbers.  The final character in the format string would be an
 indicator for the "presentation", i.e. 'd' for decimal presentation of
 integers, 'x' for hexadecimal, 'o' for octal, 'c' for character etc.
-This mostly follows the "printf()" scheme, but without requiring an
+This mostly follows the "printf()" scheme but without requiring an
 additional length parameter to distinguish between different integer
 widths.  The {fmt} library will detect those and adapt the formatting
 accordingly.  For floating point numbers there are correspondingly, 'g'
 for generic presentation, 'e' for exponential presentation, and 'f' for
 fixed point presentation.
 
-The format string "{:8}" would thus represent *any* type argument and be
-replaced by at least 8 characters; "{:<8}" would do this as left
-aligned, "{:^8}" as centered, "{:>8}" as right aligned.  If a specific
-presentation is selected, the argument type must be compatible or else
-the {fmt} formatting code will throw an exception.  Some format string
-examples are given below:
+Thus "{:8}" would represent *any* type argument using at least 8
+characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
+"{:>8}" as right aligned.  If a specific presentation is selected, the
+argument type must be compatible or else the {fmt} formatting code will
+throw an exception. Some format string examples are given below:
 
-.. code-block:: c++
+.. code-block:: C
 
    auto mesg = fmt::format("  CPU time: {:4d}:{:02d}:{:02d}\n", cpuh, cpum, cpus);
    mesg = fmt::format("{:<8s}| {:<10.5g} | {:<10.5g} | {:<10.5g} |{:6.1f} |{:6.2f}\n",
@@ -393,12 +392,12 @@ documentation <https://fmt.dev/latest/syntax.html>`_ website.
 Memory management
 ^^^^^^^^^^^^^^^^^
 
-Dynamical allocation of small data and objects can be done with the C++
-commands "new" and "delete/delete[]".  Large data should use the member
-functions of the ``Memory`` class, most commonly, ``Memory::create()``,
-``Memory::grow()``, and ``Memory::destroy()``, which provide variants
-for vectors, 2d arrays, 3d arrays, etc.  These can also be used for
-small data.
+Dynamical allocation of small data and objects can be done with the
+the C++ commands "new" and "delete/delete[].  Large data should use
+the member functions of the ``Memory`` class, most commonly,
+``Memory::create()``, ``Memory::grow()``, and ``Memory::destroy()``,
+which provide variants for vectors, 2d arrays, 3d arrays, etc.
+These can also be used for small data.
 
 The use of ``malloc()``, ``calloc()``, ``realloc()`` and ``free()``
 directly is strongly discouraged.  To simplify adapting legacy code
@@ -409,24 +408,26 @@ perform additional error checks for safety.
 Use of these custom memory allocation functions is motivated by the
 following considerations:
 
-- Memory allocation failures on *any* MPI rank during a parallel run
-  will trigger an immediate abort of the entire parallel calculation.
-- A failing "new" will trigger an exception, which is also captured by
-  LAMMPS and triggers a global abort.
-- Allocation of multidimensional arrays will be done in a C compatible
-  fashion, but such that the storage of the actual data is stored in one
-  large contiguous block.  Thus, when MPI communication is needed,
+- memory allocation failures on *any* MPI rank during a parallel run
+  will trigger an immediate abort of the entire parallel calculation
+  instead of stalling it
+- a failing "new" will trigger an exception which is also captured by
+  LAMMPS and triggers a global abort
+- allocation of multi-dimensional arrays will be done in a C compatible
+  fashion but so that the storage of the actual data is stored in one
+  large contiguous block.  Thus when MPI communication is needed,
   the data can be communicated directly (similar to Fortran arrays).
-- The "destroy()" and "sfree()" functions may safely be called on NULL
-  pointers.
-- The "destroy()" functions will nullify the pointer variables, thus
-  making "use after free" errors easy to detect.
-- It is possible to use a larger than default memory alignment (not on
+- the "destroy()" and "sfree()" functions may safely be called on NULL
+  pointers
+- the "destroy()" functions will nullify the pointer variables making
+  "use after free" errors easy to detect
+- it is possible to use a larger than default memory alignment (not on
   all operating systems, since the allocated storage pointers must be
-  compatible with ``free()`` for technical reasons).
+  compatible with ``free()`` for technical reasons)
 
-In the practical implementation of code this means, that any pointer
-variables, that are class members should be initialized to a ``nullptr``
-value in their respective constructors.  That way, it is safe to call
-``Memory::destroy()`` or ``delete[]`` on them before *any* allocation
-outside the constructor.  This helps prevent memory leaks.
+In the practical implementation of code this means that any pointer
+variables that are class members should be initialized to a
+``nullptr`` value in their respective constructors.  That way it is
+safe to call ``Memory::destroy()`` or ``delete[]`` on them before
+*any* allocation outside the constructor.  This helps prevent memory
+leaks.

doc/src/Developer_comm_ops.rst

@@ -14,8 +14,8 @@ Owned and ghost atoms
 As described on the :doc:`parallel partitioning algorithms
 <Developer_par_part>` page, LAMMPS spatially decomposes the simulation
 domain, either in a *brick* or *tiled* manner.  Each processor (MPI
-task) owns atoms within its subdomain and additionally stores ghost
-atoms within a cutoff distance of its subdomain.
+task) owns atoms within its sub-domain and additionally stores ghost
+atoms within a cutoff distance of its sub-domain.
 
 Forward and reverse communication
 =================================
@@ -28,7 +28,7 @@ The need to do this communication arises when data from the owned atoms
 is updated (e.g. their positions) and this updated information needs to
 be **copied** to the corresponding ghost atoms.
 
-And second, *reverse communication*, which sends ghost atom information
+And second, *reverse communication* which sends ghost atom information
 from each processor to the owning processor to **accumulate** (sum)
 the values with the corresponding owned atoms.  The need for this
 arises when data is computed and also stored with ghost atoms
@@ -58,7 +58,7 @@ embedded-atom method (EAM) which compute intermediate values in the
 first part of the compute() function that need to be stored by both
 owned and ghost atoms for the second part of the force computation.
 The *Comm* class methods perform the MPI communication for buffers of
-per-atom data.  They "call back" to the *Pair* class, so it can *pack*
+per-atom data.  They "call back" to the *Pair* class so it can *pack*
 or *unpack* the buffer with data the *Pair* class owns.  There are 4
 such methods that the *Pair* class must define, assuming it uses both
 forward and reverse communication:
@@ -70,7 +70,7 @@ forward and reverse communication:
 
 The arguments to these methods include the buffer and a list of atoms
 to pack or unpack.  The *Pair* class also must set the *comm_forward*
-and *comm_reverse* variables, which store the number of values stored
+and *comm_reverse* variables which store the number of values stored
 in the communication buffers for each operation.  This means, if
 desired, it can choose to store multiple per-atom values in the
 buffer, and they will be communicated together to minimize
@@ -81,11 +81,11 @@ containing ``double`` values.  To correctly store integers that may be
 
 The *Fix*, *Compute*, and *Dump* classes can also invoke the same kind
 of forward and reverse communication operations using the same *Comm*
-class methods.  Likewise, the same pack/unpack methods and
+class methods.  Likewise the same pack/unpack methods and
 comm_forward/comm_reverse variables must be defined by the calling
 *Fix*, *Compute*, or *Dump* class.
 
-For *Fix* classes, there is an optional second argument to the
+For *Fix* classes there is an optional second argument to the
 *forward_comm()* and *reverse_comm()* call which can be used when the
 fix performs multiple modes of communication, with different numbers
 of values per atom.  The fix should set the *comm_forward* and
@@ -150,7 +150,7 @@ latter case, when the *ring* operation is complete, each processor can
 examine its original buffer to extract modified values.
 
 Note that the *ring* operation is similar to an MPI_Alltoall()
-operation, where every processor effectively sends and receives data to
+operation where every processor effectively sends and receives data to
 every other processor.  The difference is that the *ring* operation
 does it one step at a time, so the total volume of data does not need
 to be stored by every processor.  However, the *ring* operation is
@@ -184,8 +184,8 @@ The *exchange_data()* method triggers the communication to be
 performed.  Each processor provides the vector of *N* datums to send,
 and the size of each datum.  All datums must be the same size.
 
-The *create_atom()* and *exchange_atom()* methods are similar, except
-that the size of each datum can be different.  Typically, this is used
+The *create_atom()* and *exchange_atom()* methods are similar except
+that the size of each datum can be different.  Typically this is used
 to communicate atoms, each with a variable amount of per-atom data, to
 other processors.
 

doc/src/Developer_flow.rst

@@ -45,9 +45,9 @@ other methods in the class.
   zero before each timestep, so that forces (torques, etc) can be
   accumulated.
 
-Now for the ``Verlet::run()`` method.  Its basic structure in hi-level
-pseudocode is shown below.  In the actual code in ``src/verlet.cpp``
-some of these operations are conditionally invoked.
+Now for the ``Verlet::run()`` method.  Its basic structure in hi-level pseudo
+code is shown below.  In the actual code in ``src/verlet.cpp`` some of
+these operations are conditionally invoked.
 
 .. code-block:: python
 
@@ -105,17 +105,17 @@ need it.  These flags are passed to the various methods that compute
 particle interactions, so that they either compute and tally the
 corresponding data or can skip the extra calculations if the energy and
 virial are not needed.  See the comments for the ``Integrate::ev_set()``
-method, which document the flag values.
+method which document the flag values.
 
 At various points of the timestep, fixes are invoked,
 e.g. ``fix->initial_integrate()``.  In the code, this is actually done
-via the Modify class, which stores all the Fix objects and lists of which
+via the Modify class which stores all the Fix objects and lists of which
 should be invoked at what point in the timestep.  Fixes are the LAMMPS
 mechanism for tailoring the operations of a timestep for a particular
 simulation.  As described elsewhere, each fix has one or more methods,
 each of which is invoked at a specific stage of the timestep, as show in
-the timestep pseudocode.  All the active fixes defined in an input
-script, that are flagged to have an ``initial_integrate()`` method, are
+the timestep pseudo-code.  All the active fixes defined in an input
+script, that are flagged to have an ``initial_integrate()`` method are
 invoked at the beginning of each timestep.  Examples are :doc:`fix nve
 <fix_nve>` or :doc:`fix nvt or fix npt <fix_nh>` which perform the
 start-of-timestep velocity-Verlet integration operations to update
@@ -131,15 +131,15 @@ can be changed using the :doc:`neigh_modify every/delay/check
 <neigh_modify>` command.  If not, coordinates of ghost atoms are
 acquired by each processor via the ``forward_comm()`` method of the Comm
 class.  If neighbor lists need to be built, several operations within
-the inner if clause of the pseudocode are first invoked.  The
+the inner if clause of the pseudo-code are first invoked.  The
 ``pre_exchange()`` method of any defined fixes is invoked first.
-Typically, this inserts or deletes particles from the system.
+Typically this inserts or deletes particles from the system.
 
 Periodic boundary conditions are then applied by the Domain class via
 its ``pbc()`` method to remap particles that have moved outside the
 simulation box back into the box.  Note that this is not done every
 timestep, but only when neighbor lists are rebuilt.  This is so that
-each processor's subdomain will have consistent (nearby) atom
+each processor's sub-domain will have consistent (nearby) atom
 coordinates for its owned and ghost atoms.  It is also why dumped atom
 coordinates may be slightly outside the simulation box if not dumped
 on a step where the neighbor lists are rebuilt.
@@ -148,15 +148,15 @@ The box boundaries are then reset (if needed) via the ``reset_box()``
 method of the Domain class, e.g. if box boundaries are shrink-wrapped to
 current particle coordinates.  A change in the box size or shape
 requires internal information for communicating ghost atoms (Comm class)
-and neighbor list bins (Neighbor class) to be updated.  The ``setup()``
+and neighbor list bins (Neighbor class) be updated.  The ``setup()``
 method of the Comm class and ``setup_bins()`` method of the Neighbor
 class perform the update.
 
 The code is now ready to migrate atoms that have left a processor's
-geometric subdomain to new processors.  The ``exchange()`` method of
+geometric sub-domain to new processors.  The ``exchange()`` method of
 the Comm class performs this operation.  The ``borders()`` method of the
 Comm class then identifies ghost atoms surrounding each processor's
-subdomain and communicates ghost atom information to neighboring
+sub-domain and communicates ghost atom information to neighboring
 processors.  It does this by looping over all the atoms owned by a
 processor to make lists of those to send to each neighbor processor.  On
 subsequent timesteps, the lists are used by the ``Comm::forward_comm()``
@@ -217,21 +217,20 @@ file, and restart files.  See the :doc:`thermo_style <thermo_style>`,
 :doc:`dump <dump>`, and :doc:`restart <restart>` commands for more
 details.
 
-The flow of control during energy minimization iterations is similar to
-that of a molecular dynamics timestep.  Forces are computed, neighbor
-lists are built as needed, atoms migrate to new processors, and atom
-coordinates and forces are communicated to neighboring processors.  The
-only difference is what Fix class operations are invoked when.  Only a
-subset of LAMMPS fixes are useful during energy minimization, as
+The the flow of control during energy minimization iterations is
+similar to that of a molecular dynamics timestep.  Forces are computed,
+neighbor lists are built as needed, atoms migrate to new processors, and
+atom coordinates and forces are communicated to neighboring processors.
+The only difference is what Fix class operations are invoked when.  Only
+a subset of LAMMPS fixes are useful during energy minimization, as
 explained in their individual doc pages.  The relevant Fix class methods
-are ``min_pre_exchange()``, ``min_pre_force()``, and
-``min_post_force()``.  Each fix is invoked at the appropriate place
-within the minimization iteration.  For example, the
-``min_post_force()`` method is analogous to the ``post_force()`` method
-for dynamics; it is used to alter or constrain forces on each atom,
-which affects the minimization procedure.
+are ``min_pre_exchange()``, ``min_pre_force()``, and ``min_post_force()``.
+Each fix is invoked at the appropriate place within the minimization
+iteration.  For example, the ``min_post_force()`` method is analogous to
+the ``post_force()`` method for dynamics; it is used to alter or constrain
+forces on each atom, which affects the minimization procedure.
 
-After all iterations are completed, there is a ``cleanup`` step which
+After all iterations are completed there is a ``cleanup`` step which
 calls the ``post_run()`` method of fixes to perform operations only required
-at the end of a calculation (like freeing temporary storage or creating
+at the end of a calculations (like freeing temporary storage or creating
 final outputs).

doc/src/Developer_grid.rst

@@ -1,845 +0,0 @@
-Use of distributed grids within style classes
----------------------------------------------
-
-.. versionadded:: 22Dec2022
-
-The LAMMPS source code includes two classes which facilitate the
-creation and use of distributed grids.  These are the Grid2d and
-Grid3d classes in the src/grid2d.cpp.h and src/grid3d.cpp.h files
-respectively.  As the names imply, they are used for 2d or 3d
-simulations, as defined by the :doc:`dimension <dimension>` command.
-
-The :doc:`Howto_grid <Howto_grid>` page gives an overview of how
-distributed grids are defined from a user perspective, lists LAMMPS
-commands which use them, and explains how grid cell data is referenced
-from an input script.  Please read that page first as it motivates the
-coding details discussed here.
-
-This doc page is for users who wish to write new styles (input script
-commands) which use distributed grids.  There are a variety of
-material models and analysis methods which use atoms (or
-coarse-grained particles) and grids in tandem.
-
-A *distributed* grid means each processor owns a subset of the grid
-cells.  In LAMMPS, the subset for each processor will be a sub-block
-of grid cells with low and high index bounds in each dimension of the
-grid.  The union of the sub-blocks across all processors is the global
-grid.
-
-More specifically, a grid point is defined for each cell (by default
-the center point), and a processor owns a grid cell if its point is
-within the processor's spatial subdomain.  The union of processor
-subdomains is the global simulation box.  If a grid point is on the
-boundary of two subdomains, the lower processor owns the grid cell.  A
-processor may also store copies of ghost cells which surround its
-owned cells.
-
-----------
-
-Style commands
-^^^^^^^^^^^^^^
-
-Style commands which can define and use distributed grids include the
-:doc:`compute <compute>`, :doc:`fix <fix>`, :doc:`pair <pair_style>`,
-and :doc:`kspace <kspace_style>` styles.  If you wish grid cell data
-to persist across timesteps, then use a fix.  If you wish grid cell
-data to be accessible by other commands, then use a fix or compute.
-Currently in LAMMPS, the :doc:`pair_style amoeba <pair_amoeba>`,
-:doc:`kspace_style pppm <kspace_style>`, and :doc:`kspace_style msm
-<kspace_style>` commands use distributed grids but do not require
-either of these capabilities; they thus create and use distributed
-grids internally.  Note that a pair style which needs grid cell data
-to persist could be coded to work in tandem with a fix style which
-provides that capability.
-
-The *size* of a grid is specified by the number of grid cells in each
-dimension of the simulation domain.  In any dimension the size can be
-any value >= 1.  Thus a 10x10x1 grid for a 3d simulation is
-effectively a 2d grid, where each grid cell spans the entire
-z-dimension.  A 1x100x1 grid for a 3d simulation is effectively a 1d
-grid, where grid cells are a series of thin xz slabs in the
-y-dimension.  It is even possible to define a 1x1x1 3d grid, though it
-may be inefficient to use it in a computational sense.
-
-Note that the choice of grid size is independent of the number of
-processors or their layout in a grid of processor subdomains which
-overlays the simulations domain.  Depending on the distributed grid
-size, a single processor may own many 1000s or no grid cells.
-
-A command can define multiple grids, each of a different size.  Each
-grid is an instantiation of the Grid2d or Grid3d class.
-
-The command also defines what data it will store for each grid it
-creates and it allocates the multidimensional array(s) needed to
-store the data.  No grid cell data is stored within the Grid2d or
-Grid3d classes.
-
-If a single value per grid cell is needed, the data array will have
-the same dimension as the grid, i.e. a 2d array for a 2d grid,
-likewise for 3d.  If multiple values per grid cell are needed, the
-data array will have one more dimension than the grid, i.e. a 3d array
-for a 2d grid, or 4d array for a 3d grid.  A command can choose to
-define multiple data arrays for each grid it defines.
-
-----------
-
-Grid data allocation and access
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The simplest way for a command to allocate and access grid cell data
-is to use the *create_offset()* methods provided by the Memory class.
-Arguments for these methods can be values returned by the
-*setup_grid()* method (described below), which define the extent of
-the grid cells (owned+ghost) the processor owns.  These 4 methods
-allocate memory for 2d (first two) and 3d (second two) grid data.  The
-two methods that end in "_one" allocate an array which stores a single
-value per grid cell.  The two that end in "_multi" allocate an array
-which stores *Nvalues* per grid cell.
-
-.. code-block:: c++
-
-   // single value per cell for a 2d grid = 2d array
-   memory->create2d_offset(data2d_one, nylo_out, nyhi_out,
-                           nxlo_out, nxhi_out, "data2d_one");
-
-   // nvalues per cell for a 2d grid = 3d array
-   memory->create3d_offset_last(data2d_multi, nylo_out, nyhi_out,
-                                nxlo_out, nxhi_out, nvalues, "data2d_multi");
-
-   // single value per cell for a 3d grid = 3d array
-   memory->create3d_offset(data3d_one, nzlo_out, nzhi_out, nylo_out,
-                           nyhi_out, nxlo_out, nxhi_out, "data3d_one");
-
-   // nvalues per cell for a 3d grid = 4d array
-   memory->create4d_offset_last(data3d_multi, nzlo_out, nzhi_out, nylo_out,
-                                nyhi_out, nxlo_out, nxhi_out, nvalues,
-                                "data3d_multi");
-
-Note that these multidimensional arrays are allocated as contiguous
-chunks of memory where the x-index of the grid varies fastest, then y,
-and the z-index slowest.  For multiple values per grid cell, the
-Nvalues are contiguous, so their index varies even faster than the
-x-index.
-
-The key point is that the "offset" methods create arrays which are
-indexed by the range of indices which are the bounds of the sub-block
-of the global grid owned by this processor.  This means loops like
-these can be written in the caller code to loop over owned grid cells,
-where the "i" loop bounds are the range of owned grid cells for the
-processor.  These are the bounds returned by the *setup_grid()*
-method:
-
-.. code-block:: c++
-
-    for (int iy = iylo; iy <= iyhi; iy++)
-      for (int ix = ixlo; ix <= ixhi; ix++)
-        data2d_one[iy][ix] = 0.0;
-
-    for (int iy = iylo; iy <= iyhi; iy++)
-      for (int ix = ixlo; ix <= ixhi; ix++)
-        for (int m = 0; m < nvalues; m++)
-          data2d_multi[iy][ix][m] = 0.0;
-
-    for (int iz = izlo; iz <= izhi; iz++)
-      for (int iy = iylo; iy <= iyhi; iy++)
-        for (int ix = ixlo; ix <= ixhi; ix++)
-          data3d_one[iz][iy][ix] = 0.0;
-
-    for (int iz = izlo; iz <= izhi; iz++)
-      for (int iy = iylo; iy <= iyhi; iy++)
-        for (int ix = ixlo; ix <= ixhi; ix++)
-           for (int m = 0; m < nvalues; m++)
-              data3d_multi[iz][iy][ix][m] = 0.0;
-
-Simply replacing the "i" bounds with "o" bounds, also returned by the
-*setup_grid()* method, would alter this code to loop over owned+ghost
-cells (the entire allocated grid).
-
-----------
-
-Grid class constructors
-^^^^^^^^^^^^^^^^^^^^^^^
-
-The following subsections describe the public methods of the Grid3d
-class which a style command can invoke.  The Grid2d methods are
-similar; simply remove arguments which refer to the z-dimension.
-
-There are 2 constructors which can be used.  They differ in the extra
-i/o xyz lo/hi arguments:
-
-.. code-block:: c++
-
-   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz)
-   Grid3d(class LAMMPS *lmp, MPI_Comm gcomm, int gnx, int gny, int gnz,
-          int ixlo, int ixhi, int iylo, int iyhi, int izlo, int izhi,
-          int oxlo, int oxhi, int oylo, int oyhi, int ozlo, int ozhi)
-
-Both constructors take the LAMMPS instance pointer and a communicator
-over which the grid will be distributed.  Typically this is the
-*world* communicator the LAMMPS instance is using.  The
-:doc:`kspace_style msm <kspace_style>` command creates a series of
-grids, each of different size, which are partitioned across different
-sub-communicators of processors.  Both constructors are also passed
-the global grid size: *gnx* by *gny* by *gnz*.
-
-The first constructor is used when the caller wants the Grid class to
-partition the global grid across processors; the Grid class defines
-which grid cells each processor owns and also which it stores as ghost
-cells.  A subsequent call to *setup_grid()*, discussed below, returns
-this info to the caller.
-
-The second constructor allows the caller to define the extent of owned
-and ghost cells, and pass them to the Grid class.  The 6 arguments
-which start with "i" are the inclusive lower and upper index bounds of
-the owned (inner) grid cells this processor owns in each of the 3
-dimensions within the global grid.  Owned grid cells are indexed from
-0 to N-1 in each dimension.
-
-The 6 arguments which start with "o" are the inclusive bounds of the
-owned+ghost (outer) grid cells it stores.  If the ghost cells are on
-the other side of a periodic boundary, then these indices may be < 0
-or >= N in any dimension, so that oxlo <= ixlo and ixhi >= ixhi is
-always the case.
-
-For example, if Nx = 100, then a processor might pass ixlo=50,
-ixhi=60, oxlo=48, oxhi=62 to the Grid class.  Or ixlo=0, ixhi=10,
-oxlo=-2, oxhi=13.  If a processor owns no grid cells in a dimension,
-then the ihi value should be specified as one less than the ilo value.
-
-Note that the only reason to use the second constructor is if the
-logic for assigning ghost cells is too complex for the Grid class to
-compute, using the various set() methods described next.  Currently
-only the kspace_style pppm/electrode and kspace_style msm commands use
-the second constructor.
-
-----------
-
-Grid class set methods
-^^^^^^^^^^^^^^^^^^^^^^
-
-The following methods affect how the Grid class computes which owned
-and ghost cells are assigned to each processor.  *Set_shift_grid()* is
-the only method which influences owned cell assignment; all the rest
-influence ghost cell assignment.  These methods are only used with the
-first constructor; they are ignored if the second constructor is used.
-These methods must be called before the *setup_grid()* method is
-invoked, because they influence its operation.
-
-.. code-block:: c++
-
-   void set_shift_grid(double shift);
-   void set_distance(double distance);
-   void set_stencil_atom(int lo, int hi);
-   void set_shift_atom(double shift_lo, double shift_hi);
-   void set_stencil_grid(int lo, int hi);
-   void set_zfactor(double factor);
-
-Processors own a grid cell if a point within the grid cell is inside
-the processor's subdomain.  By default this is the center point of the
-grid cell.  The *set_shift_grid()* method can change this.  The *shift*
-argument is a value from 0.0 to 1.0 (inclusive) which is the offset of
-the point within the grid cell in each dimension.  The default is 0.5
-for the center of the cell.  A value of 0.0 is the lower left corner
-point; a value of 1.0 is the upper right corner point.  There is
-typically no need to change the default as it is optimal for
-minimizing the number of ghost cells needed.
-
-If a processor maps its particles to grid cells, it needs to allow for
-its particles being outside its subdomain between reneighboring.  The
-*distance* argument of the *set_distance()* method sets the furthest
-distance outside a processor's subdomain which a particle can move.
-Typically this is half the neighbor skin distance, assuming
-reneighboring is done appropriately.  This distance is used in
-determining how many ghost cells a processor needs to store to enable
-its particles to be mapped to grid cells.  The default value is 0.0.
-
-Some commands, like the :doc:`kspace_style pppm <kspace_style>`
-command, map values (charge in the case of PPPM) to a stencil of grid
-cells beyond the grid cell the particle is in.  The stencil extent may
-be different in the low and high directions.  The *set_stencil_atom()*
-method defines the maximum values of those 2 extents, assumed to be
-the same in each of the 3 dimensions.  Both the lo and hi values are
-specified as positive integers.  The default values are both 0.
-
-Some commands, like the :doc:`kspace_style pppm <kspace_style>`
-command, shift the position of an atom when mapping it to a grid cell,
-based on the size of the stencil used to map values to the grid
-(charge in the case of PPPM).  The lo and hi arguments of the
-*set_shift_atom()* method are the minimum shift in the low direction
-and the maximum shift in the high direction, assumed to be the same in
-each of the 3 dimensions.  The shifts should be fractions of a grid
-cell size with values between 0.0 and 1.0 inclusive.  The default
-values are both 0.0.  See the src/pppm.cpp file for examples of these
-lo/hi values for regular and staggered grids.
-
-Some methods like the :doc:`fix ttm/grid <fix_ttm>` command, perform
-finite difference kinds of operations on the grid, to diffuse electron
-heat in the case of the two-temperature model (TTM).  This operation
-uses ghost grid values beyond the owned grid values the processor
-updates.  The *set_stencil_grid()* method defines the extent of this
-stencil in both directions, assumed to be the same in each of the 3
-dimensions.  Both the lo and hi values are specified as positive
-integers.  The default values are both 0.
-
-The kspace_style pppm commands allow a grid to be defined which
-overlays a volume which extends beyond the simulation box in the z
-dimension.  This is for the purpose of modeling a 2d-periodic slab
-(non-periodic in z) as if it were a larger 3d periodic system,
-extended (with empty space) in the z dimension.  The
-:doc:`kspace_modify slab <kspace_modify>` command is used to specify
-the ratio of the larger volume to the simulation volume; a volume
-ratio of ~3 is typical.  For this kind of model, the PPPM caller sets
-the global grid size *gnz* ~3x larger than it would be otherwise.
-This same ratio is passed by the PPPM caller as the *factor* argument
-to the Grid class via the *set_zfactor()* method (*set_yfactor()* for
-2d grids).  The Grid class will then assign ownership of the 1/3 of
-grid cells that overlay the simulation box to the processors which
-also overlay the simulation box.  The remaining 2/3 of the grid cells
-are assigned to processors whose subdomains are adjacent to the upper
-z boundary of the simulation box.
-
-----------
-
-Grid class setup_grid method
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The *setup_grid()* method is called after the first constructor
-(above) to partition the grid across processors, which determines
-which grid cells each processor owns.  It also calculates how many
-ghost grid cells in each dimension and each direction each processor
-needs to store.
-
-Note that this method is NOT called if the second constructor above is
-used.  In that case, the caller assigns owned and ghost cells to each
-processor.
-
-Also note that this method must be invoked after any *set_*()* methods have
-been used, since they can influence the assignment of owned and ghost
-cells.
-
-.. code-block:: c++
-
-   void setup_grid(int &ixlo, int &ixhi, int &iylo, int &iyhi, int &izlo, int &izhi,
-                   int &oxlo, int &oxhi, int &oylo, int &oyhi, int &ozlo, int &ozhi)
-
-The 6 return arguments which start with "i" are the inclusive lower
-and upper index bounds of the owned (inner) grid cells this processor
-owns in each of the 3 dimensions within the global grid.  Owned grid
-cells are indexed from 0 to N-1 in each dimension.
-
-The 6 return arguments which start with "o" are the inclusive bounds of
-the owned+ghost cells it owns.  If the ghost cells are on the other
-side of a periodic boundary, then these indices may be < 0 or >= N in
-any dimension, so that oxlo <= ixlo and ixhi >= ixhi is always the
-case.
-
-----------
-
-More grid class set methods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The following 2 methods can be used to override settings made by the
-constructors above.  If used, they must be called called before the
-*setup_comm()* method is invoked, since it uses the settings that
-these methods override.  In LAMMPS these methods are called by by the
-:doc:`kspace_style msm <kspace_style>` command for the grids it
-instantiates using the 2nd constructor above.
-
-.. code-block:: c++
-
-   void set_proc_neighs(int pxlo, int pxhi, int pylo, int pyhi, int pzlo, int pzhi)
-   void set_caller_grid(int fxlo, int fxhi, int fylo, int fyhi, int fzlo, int fzhi)
-
-The *set_proc_neighs()* method sets the processor IDs of the 6
-neighboring processors for each processor.  Normally these would match
-the processor grid neighbors which LAMMPS creates to overlay the
-simulation box (the default).  However, MSM excludes non-participating
-processors from coarse grid communication when less processors are
-used.  This method allows MSM to override the default values.
-
-The *set_caller_grid()* method species the size of the data arrays the
-caller allocates.  Normally these would match the extent of the ghost
-grid cells (the default).  However the MSM caller allocates a larger
-data array (more ghost cells) for its finest-level grid, for use in
-other operations besides owned/ghost cell communication.  This method
-allows MSM to override the default values.
-
-
-----------
-
-Grid class get methods
-^^^^^^^^^^^^^^^^^^^^^^
-
-The following methods allow the caller to query the settings for a
-specific grid, whether it created the grid or another command created
-it.
-
-.. code-block:: c++
-
-   void get_size(int &nxgrid, int &nygrid, int &nzgrid);
-   void get_bounds_owned(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
-   void get_bounds_ghost(int &xlo, int &xhi, int &ylo, int &yhi, int &zlo, int &zhi)
-
-The *get_size()* method returns the size of the global grid in each dimension.
-
-The *get_bounds_owned()* method return the inclusive index bounds of
-the grid cells this processor owns.  The values range from 0 to N-1 in
-each dimension.  These values are the same as the "i" values returned
-by *setup_grid()*.
-
-The *get_bounds_ghost()* method return the inclusive index bounds of
-the owned+ghost grid cells this processor stores.  The owned cell
-indices range from 0 to N-1, so these indices may be less than 0 or
-greater than or equal to N in each dimension.  These values are the
-same as the "o" values returned by *setup_grid()*.
-
-----------
-
-Grid class owned/ghost communication
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-If needed by the command, the following methods setup and perform
-communication of grid data to/from neighboring processors.  The
-*forward_comm()* method sends owned grid cell data to the
-corresponding ghost grid cells on other processors.  The
-*reverse_comm()* method sends ghost grid cell data to the
-corresponding owned grid cells on another processor.  The caller can
-choose to sum ghost grid cell data to the owned grid cell or simply
-copy it.
-
-.. code-block:: c++
-
-   void setup_comm(int &nbuf1, int &nbuf2)
-   void forward_comm(int caller, void *ptr, int which, int nper, int nbyte,
-                     void *buf1, void *buf2, MPI_Datatype datatype);
-   void reverse_comm(int caller, void *ptr, int which, int nper, int nbyte,
-                     void *buf1, void *buf2, MPI_Datatype datatype)
-   int ghost_adjacent();
-
-The *setup_comm()* method must be called one time before performing
-*forward* or *reverse* communication (multiple times if needed).  It
-returns two integers, which should be used to allocate two buffers.
-The *nbuf1* and *nbuf2* values are the number of grid cells whose data
-will be stored in two buffers by the Grid class when *forward* or
-*reverse* communication is performed.  The caller should thus allocate
-them to a size large enough to hold all the data used in any single
-forward or reverse communication operation it performs.  Note that the
-caller may allocate and communicate multiple data arrays for a grid it
-instantiates.  This size includes the bytes needed for the data type
-of the grid data it stores, e.g. double precision values.
-
-The *forward_comm()* and *reverse_comm()* methods send grid cell data
-from owned to ghost cells, or ghost to owned cells, respectively, as
-described above.  The *caller* argument should be one of these values
--- Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
-depending on the style of the caller class.  The *ptr* argument is the
-"this" pointer to the caller class.  These 2 arguments are used to
-call back to pack()/unpack() functions in the caller class, as
-explained below.
-
-The *which* argument is a flag the caller can set which is passed to
-the caller's pack()/unpack() methods.  This allows a single callback
-method to pack/unpack data for several different flavors of
-forward/reverse communication, e.g. operating on different grids or
-grid data.
-
-The *nper* argument is the number of values per grid cell to be
-communicated.  The *nbyte* argument is the number of bytes per value,
-e.g. 8 for double-precision values.  The *buf1* and *buf2* arguments
-are the two allocated buffers described above.  So long as they are
-allocated for the maximum size communication, they can be re-used for
-any *forward_comm()/reverse_comm()* call.  The *datatype* argument is
-the MPI_Datatype setting, which should match the buffer allocation and
-the *nbyte* argument.  E.g. MPI_DOUBLE for buffers storing double
-precision values.
-
-To use the *forward_grid()* method, the caller must provide two
-callback functions; likewise for use of the *reverse_grid()* methods.
-These are the 4 functions, their arguments are all the same.
-
-.. code-block:: c++
-
-   void pack_forward_grid(int which, void *vbuf, int nlist, int *list);
-   void unpack_forward_grid(int which, void *vbuf, int nlist, int *list);
-   void pack_reverse_grid(int which, void *vbuf, int nlist, int *list);
-   void unpack_reverse_grid(int which, void *vbuf, int nlist, int *list);
-
-The *which* argument is set to the *which* value of the
-*forward_comm()* or *reverse_comm()* calls.  It allows the pack/unpack
-function to select what data values to pack/unpack.  *Vbuf* is the
-buffer to pack/unpack the data to/from.  It is a void pointer so that
-the caller can cast it to whatever data type it chooses, e.g. double
-precision values.  *Nlist* is the number of grid cells to pack/unpack
-and *list* is a vector (nlist in length) of offsets to where the data
-for each grid cell resides in the caller's data arrays, which is best
-illustrated with an example from the src/EXTRA-FIX/fix_ttm_grid.cpp
-class which stores the scalar electron temperature for 3d system in a
-3d grid (one value per grid cell):
-
-.. code-block:: c++
-
-   void FixTTMGrid::pack_forward_grid(int /*which*/, void *vbuf, int nlist, int *list)
-   {
-     auto buf = (double *) vbuf;
-     double *src = &T_electron[nzlo_out][nylo_out][nxlo_out];
-     for (int i = 0; i < nlist; i++) buf[i] = src[list[i]];
-   }
-
-In this case, the *which* argument is not used, *vbuf* points to a
-buffer of doubles, and the electron temperature is stored by the
-FixTTMGrid class in a 3d array of owned+ghost cells called T_electron.
-That array is allocated by the *memory->create_3d_offset()* method
-described above so that the first grid cell it stores is indexed as
-T_electron[nzlo_out][nylo_out][nxlo_out].  The *nlist* values in
-*list* are integer offsets from that first grid cell.  Setting *src*
-to the address of the first cell allows those offsets to be used to
-access the temperatures to pack into the buffer.
-
-Here is a similar portion of code from the src/fix_ave_grid.cpp class
-which can store two kinds of data, a scalar count of atoms in a grid
-cell, and one or more grid-cell-averaged atom properties.  The code
-from its *unpack_reverse_grid()* function for 2d grids and multiple
-per-atom properties per grid cell (*nvalues*) is shown here:
-
-.. code-block:: c++
-
-   void FixAveGrid::unpack_reverse_grid(int /*which*/, void *vbuf, int nlist, int *list)
-   {
-     auto buf = (double *) vbuf;
-     double *count,*data,*values;
-     count = &count2d[nylo_out][nxlo_out];
-     data = &array2d[nylo_out][nxlo_out][0];
-     m = 0;
-     for (i = 0; i < nlist; i++) {
-       count[list[i]] += buf[m++];
-       values = &data[nvalues*list[i]];
-       for (j = 0; j < nvalues; j++)
-        values[j] += buf[m++];
-     }
-   }
-
-Both the count and the multiple values per grid cell are communicated
-in *vbuf*.  Note that *data* is now a pointer to the first value in
-the first grid cell.  And *values* points to where the first value in
-*data* is for an offset of grid cells, calculated by multiplying
-*nvalues* by *list[i]*.  Finally, because this is reverse
-communication, the communicated buffer values are summed to the caller
-values.
-
-The *ghost_adjacent()* method returns a 1 if every processor can
-perform the necessary owned/ghost communication with only its nearest
-neighbor processors (4 in 2d, 6 in 3d).  It returns a 0 if any
-processor's ghost cells extend further than nearest neighbor
-processors.
-
-This can be checked by callers who have the option to change the
-global grid size to ensure more efficient nearest-neighbor-only
-communication if they wish.  In this case, they instantiate a grid of
-a given size (resolution), then invoke *setup_comm()* followed by
-*ghost_adjacent()*.  If the ghost cells are not adjacent, they destroy
-the grid instance and start over with a higher-resolution grid.
-Several of the :doc:`kspace_style pppm <kspace_style>` command
-variants have this option.
-
-----------
-
-Grid class remap methods for load balancing
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-The following methods are used when a load-balancing operation,
-triggered by the :doc:`balance <balance>` or :doc:`fix balance
-<fix_balance>` commands, changes the partitioning of the simulation
-domain into processor subdomains.
-
-In order to work with load-balancing, any style command (compute, fix,
-pair, or kspace style) which allocates a grid and stores per-grid data
-should define a *reset_grid()* method; it takes no arguments.  It will
-be called by the two balance commands after they have reset processor
-subdomains and migrated atoms (particles) to new owning processors.
-The *reset_grid()* method will typically perform some or all of the
-following operations.  See the src/fix_ave_grid.cpp and
-src/EXTRA_FIX/fix_ttm_grid.cpp files for examples of *reset_grid()*
-methods, as well as the *pack_remap_grid()* and *unpack_remap_grid()*
-functions.
-
-First, the *reset_grid()* method can instantiate new grid(s) of the
-same global size, then call *setup_grid()* to partition them via the
-new processor subdomains.  At this point, it can invoke the
-*identical()* method which compares the owned and ghost grid cell
-index bounds between two grids, the old grid passed as a pointer
-argument, and the new grid whose *identical()* method is being called.
-It returns 1 if the indices match on all processors, otherwise 0.  If
-they all match, then the new grids can be deleted; the command can
-continue to use the old grids.
-
-If not, then the command should allocate new grid data array(s) which
-depend on the new partitioning.  If the command does not need to
-persist its grid data from the old partitioning to the new one, then
-the command can simply delete the old data array(s) and grid
-instance(s).  It can then return.
-
-If the grid data does need to persist, then the data for each grid
-needs to be "remapped" from the old grid partitioning to the new grid
-partitioning.  The *setup_remap()* and *remap()* methods are used for
-that purpose.
-
-.. code-block:: c++
-
-   int identical(Grid3d *old);
-   void setup_remap(Grid3d *old, int &nremap_buf1, int &nremap_buf2)
-   void remap(int caller, void *ptr, int which, int nper, int nbyte,
-              void *buf1, void *buf2, MPI_Datatype datatype)
-
-The arguments to these methods are identical to those for
-the *setup_comm()* and *forward_comm()* or *reverse_comm()* methods.
-However the returned *nremap_buf1* and *nremap2_buf* values will be
-different than the *nbuf1* and *nbuf2* values.  They should be used to
-allocate two different remap buffers, separate from the owned/ghost
-communication buffers.
-
-To use the *remap()* method, the caller must provide two
-callback functions:
-
-.. code-block:: c++
-
-   void pack_remap_grid(int which, void *vbuf, int nlist, int *list);
-   void unpack_remap_grid(int which, void *vbuf, int list, int *list);
-
-Their arguments are identical to those for the *pack_forward_grid()*
-and *unpack_forward_grid()* callback functions (or the reverse
-variants) discussed above.  Normally, both these methods pack/unpack
-all the data arrays for a given grid.  The *which* argument of the
-*remap()* method sets the *which* value for the pack/unpack functions.
-If the command instantiates multiple grids (of different sizes), it
-can be used within the pack/unpack methods to select which grid's data
-is being remapped.
-
-Note that the *pack_remap_grid()* function must copy values from the
-OLD grid data arrays into the *vbuf* buffer. The *unpack_remap_grid()*
-function must copy values from the *vbuf* buffer into the NEW grid
-data arrays.
-
-After the remap operation for grid cell data has been performed, the
-*reset_grid()* method can deallocate the two remap buffers it created,
-and can then exit.
-
-----------
-
-Grid class I/O methods
-^^^^^^^^^^^^^^^^^^^^^^
-
-There are two I/O methods in the Grid classes which can be used to
-read and write grid cell data to files.  The caller can decide on the
-precise format of each file, e.g. whether header lines are prepended
-or comment lines are allowed.  Fundamentally, the file should contain
-one line per grid cell for the entire global grid.  Each line should
-contain identifying info as to which grid cell it is, e.g. a unique
-grid cell ID or the ix,iy,iz indices of the cell within a 3d grid.
-The line should also contain one or more data values which are stored
-within the grid data arrays created by the command
-
-For grid cell IDs, the LAMMPS convention is that the IDs run from 1 to
-N, where N = Nx * Ny for 2d grids and N = Nx * Ny * Nz for 3d grids.
-The x-index of the grid cell varies fastest, then y, and the z-index
-varies slowest.  So for a 10x10x10 grid the cell IDs from 901-1000
-would be in the top xy layer of the z dimension.
-
-The *read_file()* method does something simple.  It reads a chunk of
-consecutive lines from the file and passes them back to the caller to
-process.  The caller provides a *unpack_read_grid()* function for this
-purpose.  The function checks the grid cell ID or indices and only
-stores grid cell data for the grid cells it owns.
-
-The *write_file()* method does something slightly more complex.  Each
-processor packs the data for its owned grid cells into a buffer.  The
-caller provides a *pack_write_grid()* function for this purpose.  The
-*write_file()* method then loops over all processors and each sends
-its buffer one at a time to processor 0, along with the 3d (or 2d)
-index bounds of its grid cell data within the global grid.  Processor
-0 calls back to the *unpack_write_grid()* function provided by the
-caller with the buffer.  The function writes one line per grid cell to
-the file.
-
-See the src/EXTRA_FIX/fix_ttm_grid.cpp file for examples of now both
-these methods are used to read/write electron temperature values
-from/to a file, as well as for implementations of the the pack/unpack
-functions described below.
-
-Here are the details of the two I/O methods and the 3 callback
-functions.  See the src/fix_ave_grid.cpp file for examples of all of
-them.
-
-.. code-block:: c++
-
-   void read_file(int caller, void *ptr, FILE *fp, int nchunk, int maxline)
-   void write_file(int caller, void *ptr, int which,
-                   int nper, int nbyte, MPI_Datatype datatype
-
-The *caller* argument in both methods should be one of these values --
-Grid3d::COMPUTE, Grid3d::FIX, Grid3d::KSPACE, Grid3d::PAIR --
-depending on the style of the caller class.  The *ptr* argument in
-both methods is the "this" pointer to the caller class.  These 2
-arguments are used to call back to pack()/unpack() functions in the
-caller class, as explained below.
-
-For the *read_file()* method, the *fp* argument is a file pointer to
-the file to be read from, opened on processor 0 by the caller.
-*Nchunk* is the number of lines to read per chunk, and *maxline* is
-the maximum number of characters per line.  The Grid class will
-allocate a buffer for storing chunks of lines based on these values.
-
-For the *write_file()* method, the *which* argument is a flag the
-caller can set which is passed back to the caller's pack()/unpack()
-methods.  If the command instantiates multiple grids (of different
-sizes), this flag can be used within the pack/unpack methods to select
-which grid's data is being written out (presumably to different
-files).  the *nper* argument is the number of values per grid cell to
-be written out.  The *nbyte* argument is the number of bytes per
-value, e.g. 8 for double-precision values.  The *datatype* argument is
-the MPI_Datatype setting, which should match the *nbyte* argument.
-E.g. MPI_DOUBLE for double precision values.
-
-To use the *read_grid()* method, the caller must provide one callback
-function.  To use the *write_grid()* method, it provides two callback
-functions:
-
-.. code-block:: c++
-
-   int unpack_read_grid(int nlines, char *buffer)
-   void pack_write_grid(int which, void *vbuf)
-   void unpack_write_grid(int which, void *vbuf, int *bounds)
-
-For *unpack_read_grid()* the *nlines* argument is the number of lines
-of character data read from the file and contained in *buffer*.  The
-lines each include a newline character at the end.  When the function
-processes the lines, it may choose to skip some of them (header or
-comment lines).  It returns an integer count of the number of grid
-cell lines it processed.  This enables the Grid class *read_file()*
-method to know when it has read the correct number of lines.
-
-For *pack_write_grid()* and *unpack_write_grid()*, the *vbuf* argument
-is the buffer to pack/unpack data to/from.  It is a void pointer so
-that the caller can cast it to whatever data type it chooses,
-e.g. double precision values.  the *which* argument is set to the
-*which* value of the *write_file()* method.  It allows the caller to
-choose which grid data to operate on.
-
-For *unpack_write_grid()*, the *bounds* argument is a vector of 4 or 6
-integer grid indices (4 for 2d, 6 for 3d).  They are the
-xlo,xhi,ylo,yhi,zlo,zhi index bounds of the portion of the global grid
-which the *vbuf* holds owned grid cell data values for.  The caller
-should loop over the values in *vbuf* with a double loop (2d) or
-triple loop (3d), similar to the code snippets listed above.  The
-x-index varies fastest, then y, and the z-index slowest.  If there are
-multiple values per grid cell, the index for those values varies
-fastest of all.  The caller can add the x,y,z indices of the grid cell
-(or the corresponding grid cell ID) to the data value(s) written as
-one line to the output file.
-
-----------
-
-Style class grid access methods
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-A style command can enable its grid cell data to be accessible from
-other commands.  For example :doc:`fix ave/grid <fix_ave_grid>` or
-:doc:`dump grid <dump>` or :doc:`dump grid/vtk <dump>`.  Those
-commands access the grid cell data by using a *grid reference* in
-their input script syntax, as described on the :doc:`Howto_grid
-<Howto_grid>` doc page.  They look like this:
-
-* c_ID:gname:dname
-* c_ID:gname:dname[I]
-* f_ID:gname:dname
-* f_ID:gname:dname[I]
-
-Each grid command instantiates has a unique *gname*, defined by the
-command.  Likewise each grid cell data structure (scalar or vector)
-associated with a grid has a unique *dname*, also defined by the
-command.
-
-To provide access to its grid cell data, a style command needs to
-implement the following 4 methods:
-
-.. code-block:: c++
-
-   int get_grid_by_name(const std::string &name, int &dim);
-   void *get_grid_by_index(int index);
-   int get_griddata_by_name(int igrid, const std::string &name, int &ncol);
-   void *get_griddata_by_index(int index);
-
-Currently only computes and fixes can implement these methods.  If it
-does so, the compute of fix should also set the variable
-*pergrid_flag* to 1.  See any of the compute or fix commands which set
-"pergrid_flag = 1" for examples of how these 4 functions can be
-implemented.
-
-The *get_grid_by_name()* method takes a grid name as input and returns
-two values.  The *dim* argument is returned as 2 or 3 for the
-dimensionality of the grid.  The function return is a grid index from
-0 to G-1 where *G* is the number of grids the command instantiates.  A
-value of -1 is returned if the grid name is not recognized.
-
-The *get_grid_by_index()* method is called after the
-*get_grid_by_name()* method, using the grid index it returned as its
-argument.  This method will return a pointer to the Grid2d or Grid3d
-class.  The caller can use this to query grid attributes, such as the
-global size of the grid, to ensure it is of the expected size.
-
-The *get_griddata_by_name()* method takes a grid index *igrid* and a
-data name as input.  It returns two values.  The *ncol* argument is
-returned as a 0 if the grid data is a single value (scalar) per grid
-cell, or an integer M > 0 if there are M values (vector) per grid
-cell.  Note that even if M = 1, it is still a 1-length vector, not a
-scalar.  The function return is a data index from 0 to D-1 where *D*
-is the number of data sets associated with that grid by the command.
-A value of -1 is returned if the data name is not recognized.
-
-The *get_griddata_by_index()* method is called after the
-*get_griddata_by_name()* method, using the data index it returned as
-its argument.  This method will return a pointer to the
-multidimensional array which stores the requested data.
-
-As in the discussion above of the Memory class *create_offset()*
-methods, the dimensionality of the array associated with the returned
-pointer depends on whether it is a 2d or 3d grid and whether there is
-a single or multiple values stored for each grid cell:
-
-* single value per cell for a 2d grid = 2d array pointer
-* multiple values per cell for a 2d grid = 3d array pointer
-* single value per cell for a 3d grid = 3d array pointer
-* multiple values per cell for a 3d grid = 4d array pointer
-
-The caller will typically access the data by casting the void pointer
-to the corresponding array pointer and using nested loops in x,y,z
-between owned or ghost index bounds returned by the
-*get_bounds_owned()* or *get_bounds_ghost()* methods to index into the
-array.  Example code snippets with this logic were listed above,
-
-----------
-
-Final notes
-^^^^^^^^^^^
-
-Finally, here are some additional issues to pay attention to for
-writing any style command which uses distributed grids via the Grid2d
-or Grid3d class.
-
-The command destructor should delete all instances of the Grid class,
-any buffers it allocated for forward/reverse or remap communication,
-and any data arrays it allocated to store grid cell data.
-
-If a command is intended to work for either 2d or 3d simulations, then
-it should have logic to instantiate either 2d or 3d grids and their
-associated data arrays, depending on the dimension of the simulation
-box.  The :doc:`fix ave/grid <fix_ave_grid>` command is an example of
-such a command.
-
-When a command maps its particles to the grid and updates grid cell
-values, it should check that it is not updating or accessing a grid
-cell value outside the range of its owned+ghost cells, and generate an
-error message if that is the case.  This could happen, for example, if
-a particle has moved further than half the neighbor skin distance,
-because the neighbor list update criterion are not adequate to prevent
-it from happening.  See the src/KSPACE/pppm.cpp file and its
-*particle_map()* method for an example of this kind of error check.

doc/src/Developer_notes.rst

@@ -102,10 +102,10 @@ build is then :doc:`processed in parallel <Developer_par_neigh>`.
 The most commonly required neighbor list is a so-called "half" neighbor
 list, where each pair of atoms is listed only once (except when the
 :doc:`newton command setting <newton>` for pair is off; in that case
-pairs straddling subdomains or periodic boundaries will be listed twice).
+pairs straddling sub-domains or periodic boundaries will be listed twice).
 Thus these are the default settings when a neighbor list request is created in:
 
-.. code-block:: c++
+.. code-block:: C++
 
    void Pair::init_style()
    {
@@ -129,7 +129,7 @@ neighbor list request to the specific needs of a style an additional
 request flag is needed.  The :doc:`tersoff <pair_tersoff>` pair style,
 for example, needs a "full" neighbor list:
 
-.. code-block:: c++
+.. code-block:: C++
 
    void PairTersoff::init_style()
    {
@@ -141,7 +141,7 @@ When a pair style supports r-RESPA time integration with different cutoff region
 the request flag may depend on the corresponding r-RESPA settings. Here an example
 from pair style lj/cut:
 
-.. code-block:: c++
+.. code-block:: C++
 
    void PairLJCut::init_style()
    {
@@ -160,7 +160,7 @@ Granular pair styles need neighbor lists based on particle sizes and not cutoff
 and also may require to have the list of previous neighbors available ("history").
 For example with:
 
-.. code-block:: c++
+.. code-block:: C++
 
    if (use_history) neighbor->add_request(this, NeighConst::REQ_SIZE | NeighConst::REQ_HISTORY);
    else neighbor->add_request(this, NeighConst::REQ_SIZE);
@@ -170,7 +170,7 @@ settings each request can set an id which is then used in the corresponding
 ``init_list()`` function to assign it to the suitable pointer variable. This is
 done for example by the :doc:`pair style meam <pair_meam>`:
 
-.. code-block:: c++
+.. code-block:: C++
 
    void PairMEAM::init_style()
    {
@@ -189,7 +189,7 @@ just once) and this can also be indicated by a flag.  As an example here
 is the request from the ``FixPeriNeigh`` class which is created
 internally by :doc:`Peridynamics pair styles <pair_peri>`:
 
-.. code-block:: c++
+.. code-block:: C++
 
    neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_OCCASIONAL);
 
@@ -198,7 +198,7 @@ than what is usually inferred from the pair style settings (largest cutoff of
 all pair styles plus neighbor list skin).  The following is used in the
 :doc:`compute rdf <compute_rdf>` command implementation:
 
-.. code-block:: c++
+.. code-block:: C++
 
   if (cutflag)
     neighbor->add_request(this, NeighConst::REQ_OCCASIONAL)->set_cutoff(mycutneigh);
@@ -212,7 +212,7 @@ for printing the neighbor list summary the name of the requesting command
 should be set.  Below is the request from the :doc:`delete atoms <delete_atoms>`
 command:
 
-.. code-block:: c++
+.. code-block:: C++
 
    neighbor->add_request(this, "delete_atoms", NeighConst::REQ_FULL);
 
@@ -361,7 +361,7 @@ allocated as a 1d vector or 3d array.  Either way, the ordering of
 values within contiguous memory x fastest, then y, z slowest.
 
 For the ``3d decomposition`` of the grid, the global grid is
-partitioned into bricks that correspond to the subdomains of the
+partitioned into bricks that correspond to the sub-domains of the
 simulation box that each processor owns.  Often, this is a regular 3d
 array (Px by Py by Pz) of bricks, where P = number of processors =
 Px * Py * Pz.  More generally it can be a tiled decomposition, where

doc/src/Developer_org.rst

@@ -7,7 +7,7 @@ but there are small a number of files in several other languages like C,
 Fortran, Shell script, or Python.
 
 The core of the code is located in the ``src`` folder and its
-subdirectories.  A sizable number of these files are in the ``src``
+sub-directories.  A sizable number of these files are in the ``src``
 directory itself, but there are plenty of :doc:`packages <Packages>`,
 which can be included or excluded when LAMMPS is built.  See the
 :doc:`Include packages in build <Build_package>` section of the manual
@@ -15,42 +15,42 @@ for more information about that part of the build process.  LAMMPS
 currently supports building with :doc:`conventional makefiles
 <Build_make>` and through :doc:`CMake <Build_cmake>`.  Those procedures
 differ in how packages are enabled or disabled for inclusion into a
-LAMMPS binary, so they cannot be mixed.  The source files for each
-package are in all-uppercase subdirectories of the ``src`` folder, for
+LAMMPS binary so they cannot be mixed.  The source files for each
+package are in all-uppercase sub-directories of the ``src`` folder, for
 example ``src/MOLECULE`` or ``src/EXTRA-MOLECULE``.  The ``src/STUBS``
-subdirectory is not a package but contains a dummy MPI library, that is
+sub-directory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
-directory and its subdirectories contain makefiles with settings and
+directory and its sub-directories contain makefiles with settings and
 flags for a variety of configuration and machines for the build process
 with traditional makefiles.
 
 The ``lib`` directory contains the source code for several supporting
 libraries or files with configuration settings to use globally installed
-libraries, that are required by some optional packages.  They may
+libraries, that are required by some of the optional packages.  They may
 include python scripts that can transparently download additional source
-code on request.  Each subdirectory, like ``lib/poems`` or ``lib/gpu``,
+code on request.  Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
 contains the source files, some of which are in different languages such
-as Fortran or CUDA. These libraries included in the LAMMPS build, if the
-corresponding package is installed.
+as Fortran or CUDA. These libraries included in the LAMMPS build,
+if the corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as
 ``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
 Each pair of files defines a C++ class, for example the
-:cpp:class:`LAMMPS_NS::Run` class, which contains the code invoked by
-the :doc:`run <run>` command in a LAMMPS input script.  As this example
+:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
+:doc:`run <run>` command in a LAMMPS input script.  As this example
 illustrates, source file and class names often have a one-to-one
 correspondence with a command used in a LAMMPS input script.  Some
 source files and classes do not have a corresponding input script
-command, for example ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
+command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
 class.  They are discussed in the next section.
 
 The names of all source files are in lower case and may use the
-underscore character '_' to separate words. Apart from bundled,
-externally maintained libraries, which may have different conventions,
-all C and C++ header files have a ``.h`` extension, all C++ files have a
-``.cpp`` extension, and C files a ``.c`` extension.  A few C++ classes
-and utility functions are implemented with only a ``.h`` file. Examples
-are the Pointers and Commands classes or the MathVec functions.
+underscore character '_' to separate words. Outside of bundled libraries
+which may have different conventions, all C and C++ header files have a
+``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
+``.c`` extension. A small number of C++ classes and utility functions
+are implemented with only a ``.h`` file. Examples are the Pointers and
+Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -62,36 +62,35 @@ associated source files in the ``src`` folder, for example the class
 :cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
 and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
 corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``.  Full
-lines in the figure represent compositing: that is, the class at the
-base of the arrow holds a pointer to an instance of the class at the
-tip.  Dashed lines instead represent inheritance: the class at the tip
-of the arrow is derived from the class at the base.  Classes with a red
-boundary are not instantiated directly, but they represent the base
-classes for "styles".  Those "styles" make up the bulk of the LAMMPS
-code and only a few representative examples are included in the figure,
-so it remains readable.
+lines in the figure represent compositing: that is the class at the base
+of the arrow holds a pointer to an instance of the class at the tip.
+Dashed lines instead represent inheritance: the class to the tip of the
+arrow is derived from the class at the base.  Classes with a red boundary
+are not instantiated directly, but they represent the base classes for
+"styles".  Those "styles" make up the bulk of the LAMMPS code and only
+a few representative examples are included in the figure so it remains
+readable.
 
 .. _class-topology:
 .. figure:: JPG/lammps-classes.png
 
    LAMMPS class topology
 
-      This figure shows relations of base classes of the LAMMPS
-      simulation package.  Full lines indicate that a class holds an
-      instance of the class it is pointing to; dashed lines point to
-      derived classes that are given as examples of what classes may be
-      instantiated during a LAMMPS run based on the input commands and
-      accessed through the API define by their respective base classes.
-      At the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class,
-      which holds pointers to class instances with specific purposes.
-      Those may hold instances of other classes, sometimes directly, or
-      only temporarily, sometimes as derived classes or derived classes
-      of derived classes, which may also hold instances of other
-      classes.
+   This figure shows some of the relations of the base classes of the
+   LAMMPS simulation package.  Full lines indicate that a class holds an
+   instance of the class it is pointing to; dashed lines point to
+   derived classes that are given as examples of what classes may be
+   instantiated during a LAMMPS run based on the input commands and
+   accessed through the API define by their respective base classes.  At
+   the core is the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class, which
+   holds pointers to class instances with specific purposes.  Those may
+   hold instances of other classes, sometimes directly, or only
+   temporarily, sometimes as derived classes or derived classes of
+   derived classes, which may also hold instances of other classes.
 
 The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
-represents what is generally referred to as an "instance of LAMMPS".  It
-is a composite holding pointers to instances of other core classes
+represents what is generally referred to an "instance" of LAMMPS.  It is
+a composite holding pointers to instances of other core classes
 providing the core functionality of the MD engine in LAMMPS and through
 them abstractions of the required operations.  The constructor of the
 LAMMPS class will instantiate those instances, process the command line
@@ -103,44 +102,42 @@ LAMMPS while passing it the command line flags and input script. It
 deletes the LAMMPS instance after the method reading the input returns
 and shuts down the MPI environment before it exits the executable.
 
-The :cpp:class:`LAMMPS_NS::Pointers` class is not shown in the
+The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
 :ref:`class-topology` figure for clarity.  It holds references to many
 of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
 from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
-references.  From the class topology all classes with blue boundary are
+reference.  From the class topology all classes with blue boundary are
 referenced in the Pointers class and all classes in the second and third
-columns, that are not listed as derived classes, are instead derived
-from :cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer
-references in Pointers, a pointer to the LAMMPS class instance needs to
-be passed to the constructor. All constructors for classes derived from
-it, must do so and thus pass that pointer to the constructor for
-:cpp:class:`LAMMPS_NS::Pointers`.  The default constructor for
-:cpp:class:`LAMMPS_NS::Pointers` is disabled to enforce this.
+columns, that are not listed as derived classes are instead derived from
+:cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer references
+in Pointers, a pointer to the LAMMPS class instance needs to be passed
+to the constructor and thus all constructors for classes derived from it
+must do so and pass this pointer to the constructor for Pointers.
 
 Since all storage is supposed to be encapsulated (there are a few
 exceptions), the LAMMPS class can also be instantiated multiple times by
-a calling code.  Outside the aforementioned exceptions, those LAMMPS
+a calling code.  Outside of the aforementioned exceptions, those LAMMPS
 instances can be used alternately.  As of the time of this writing
-(early 2023) LAMMPS is not yet sufficiently thread-safe for concurrent
+(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
 execution.  When running in parallel with MPI, care has to be taken,
 that suitable copies of communicators are used to not create conflicts
 between different instances.
 
-The LAMMPS class currently holds instances of 19 classes representing
-the core functionality.  There are a handful of virtual parent classes
-in LAMMPS that define what LAMMPS calls ``styles``.  These are shaded
-red in the :ref:`class-topology` figure.  Each of these are parents of a
-number of child classes that implement the interface defined by the
-parent class.  There are two main categories of these ``styles``: some
-may only have one instance active at a time (e.g. atom, pair, bond,
-angle, dihedral, improper, kspace, comm) and there is a dedicated
-pointer variable for each of them in the corresponding composite class.
+The LAMMPS class currently (early 2021) holds instances of 19 classes
+representing the core functionality.  There are a handful of virtual
+parent classes in LAMMPS that define what LAMMPS calls ``styles``.  They
+are shaded red in the :ref:`class-topology` figure.  Each of these are
+parents of a number of child classes that implement the interface
+defined by the parent class.  There are two main categories of these
+``styles``: some may only have one instance active at a time (e.g. atom,
+pair, bond, angle, dihedral, improper, kspace, comm) and there is a
+dedicated pointer variable for each of them in the composite class.
 Setups that require a mix of different such styles have to use a
-*hybrid* class instance that acts as a proxy, and manages and forwards
-calls to the corresponding sub-style class instances for the designated
-subset of atoms or data.  The composite class may also have lists of
-class instances, e.g. ``Modify`` handles lists of compute and fix
-styles, while ``Output`` handles a list of dump class instances.
+*hybrid* class that takes the place of the one allowed instance and then
+manages and forwards calls to the corresponding sub-styles for the
+designated subset of atoms or data.  The composite class may also have
+lists of class instances, e.g. Modify handles lists of compute and fix
+styles, while Output handles a list of dump class instances.
 
 The exception to this scheme are the ``command`` style classes.  These
 implement specific commands that can be invoked before, after, or in
@@ -149,19 +146,19 @@ command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
 run, set, or velocity command styles.
 
-For all those ``styles``, certain naming conventions are employed: for
+For all those ``styles`` certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
-``fix_nve.h`` and ``fix_nve.cpp``. Similarly, for fix ave/time we have
+``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
 FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``.  Style names
 are lower case and without spaces or special characters. A suffix or
 words are appended with a forward slash '/' which denotes a variant of
 the corresponding class without the suffix.  To connect the style name
 and the class name, LAMMPS uses macros like: ``AtomStyle()``,
 ``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
-corresponding header file.  During configuration or compilation, files
+corresponding header file.  During configuration or compilation files
 with the pattern ``style_<name>.h`` are created that consist of a list
 of include statements including all headers of all styles of a given
-type that are currently enabled (or "installed").
+type that are currently active (or "installed).
 
 
 More details on individual classes in the :ref:`class-topology` are as
@@ -175,8 +172,8 @@ follows:
   that one or multiple simulations can be run, on the processors
   allocated for a run, e.g. by the mpirun command.
 
-- The Input class reads and processes input (strings and files), stores
-  variables, and invokes :doc:`commands <Commands_all>`.
+- The Input class reads and processes input input strings and files,
+  stores variables, and invokes :doc:`commands <Commands_all>`.
 
 - Command style classes are derived from the Command class. They provide
   input script commands that perform one-time operations
@@ -195,7 +192,7 @@ follows:
 - The Atom class stores per-atom properties associated with atom styles.
   More precisely, they are allocated and managed by a class derived from
   the AtomVec class, and the Atom class simply stores pointers to them.
-  The classes derived from AtomVec represent the different atom styles,
+  The classes derived from AtomVec represent the different atom styles
   and they are instantiated through the :doc:`atom_style <atom_style>`
   command.
 
@@ -209,22 +206,18 @@ follows:
   class stores a single list (for all atoms).  A NeighRequest class
   instance is created by pair, fix, or compute styles when they need a
   particular kind of neighbor list and use the NeighRequest properties
-  to select the neighbor list settings for the given request.  There can
-  be multiple instances of the NeighRequest class. The Neighbor class
-  will try to optimize how the requests are processed.  Depending on the
-  NeighRequest properties, neighbor lists are constructed from scratch,
-  aliased, or constructed by post-processing an existing list into
-  sub-lists.
+  to select the neighbor list settings for the given request. There can
+  be multiple instances of the NeighRequest class and the Neighbor class
+  will try to optimize how they are computed by creating copies or
+  sub-lists where possible.
 
 - The Comm class performs inter-processor communication, typically of
   ghost atom information.  This usually involves MPI message exchanges
   with 6 neighboring processors in the 3d logical grid of processors
   mapped to the simulation box. There are two :doc:`communication styles
-  <comm_style>`, enabling different ways to perform the domain
-  decomposition.
-
-- The Irregular class is used, when atoms may migrate to arbitrary
-  processors.
+  <comm_style>` enabling different ways to do the domain decomposition.
+  Sometimes the Irregular class is used, when atoms may migrate to
+  arbitrary processors.
 
 - The Domain class stores the simulation box geometry, as well as
   geometric Regions and any user definition of a Lattice.  The latter
@@ -253,7 +246,7 @@ follows:
   file, dump file snapshots, and restart files.  These correspond to the
   :doc:`Thermo <thermo_style>`, :doc:`Dump <dump>`, and
   :doc:`WriteRestart <write_restart>` classes respectively.  The Dump
-  class is a base class, with several derived classes implementing
+  class is a base class with several derived classes implementing
   various dump style variants.
 
 - The Timer class logs timing information, output at the end

doc/src/Developer_par_comm.rst

@@ -1,22 +1,22 @@
 Communication
 ^^^^^^^^^^^^^
 
-Following the selected partitioning scheme, all per-atom data is
+Following the partitioning scheme in use all per-atom data is
 distributed across the MPI processes, which allows LAMMPS to handle very
 large systems provided it uses a correspondingly large number of MPI
 processes.  Since The per-atom data (atom IDs, positions, velocities,
-types, etc.)  To be able to compute the short-range interactions, MPI
-processes need not only access to the data of atoms they "own" but also
-information about atoms from neighboring subdomains, in LAMMPS referred
+types, etc.)  To be able to compute the short-range interactions MPI
+processes need not only access to data of atoms they "own" but also
+information about atoms from neighboring sub-domains, in LAMMPS referred
 to as "ghost" atoms.  These are copies of atoms storing required
 per-atom data for up to the communication cutoff distance. The green
 dashed-line boxes in the :ref:`domain-decomposition` figure illustrate
-the extended ghost-atom subdomain for one processor.
+the extended ghost-atom sub-domain for one processor.
 
 This approach is also used to implement periodic boundary
 conditions: atoms that lie within the cutoff distance across a periodic
 boundary are also stored as ghost atoms and taken from the periodic
-replication of the subdomain, which may be the same subdomain, e.g. if
+replication of the sub-domain, which may be the same sub-domain, e.g. if
 running in serial.  As a consequence of this, force computation in
 LAMMPS is not subject to minimum image conventions and thus cutoffs may
 be larger than half the simulation domain.
@@ -28,10 +28,10 @@ be larger than half the simulation domain.
    ghost atom communication
 
    This figure shows the ghost atom communication patterns between
-   subdomains for "brick" (left) and "tiled" communication styles for
+   sub-domains for "brick" (left) and "tiled" communication styles for
    2d simulations.  The numbers indicate MPI process ranks.  Here the
-   subdomains are drawn spatially separated for clarity.  The
-   dashed-line box is the extended subdomain of processor 0 which
+   sub-domains are drawn spatially separated for clarity.  The
+   dashed-line box is the extended sub-domain of processor 0 which
    includes its ghost atoms.  The red- and blue-shaded boxes are the
    regions of communicated ghost atoms.
 
@@ -42,7 +42,7 @@ atom communication is performed in two stages for a 2d simulation (three
 in 3d) for both a regular and irregular partitioning of the simulation
 box.  For the regular case (left) atoms are exchanged first in the
 *x*-direction, then in *y*, with four neighbors in the grid of processor
-subdomains.
+sub-domains.
 
 In the *x* stage, processor ranks 1 and 2 send owned atoms in their
 red-shaded regions to rank 0 (and vice versa).  Then in the *y* stage,
@@ -55,11 +55,11 @@ For the irregular case (right) the two stages are similar, but a
 processor can have more than one neighbor in each direction.  In the
 *x* stage, MPI ranks 1,2,3 send owned atoms in their red-shaded regions to
 rank 0 (and vice versa).  These include only atoms between the lower
-and upper *y*-boundary of rank 0's subdomain.  In the *y* stage, ranks
+and upper *y*-boundary of rank 0's sub-domain.  In the *y* stage, ranks
 4,5,6 send atoms in their blue-shaded regions to rank 0.  This may
 include ghost atoms they received in the *x* stage, but only if they
 are needed by rank 0 to fill its extended ghost atom regions in the
-+/-*y* directions (blue rectangles).  Thus, in this case, ranks 5 and
++/-*y* directions (blue rectangles).  Thus in this case, ranks 5 and
 6 do not include ghost atoms they received from each other (in the *x*
 stage) in the atoms they send to rank 0.  The key point is that while
 the pattern of communication is more complex in the irregular
@@ -78,14 +78,14 @@ A "reverse" communication is when computed ghost atom attributes are
 sent back to the processor who owns the atom.  This is used (for
 example) to sum partial forces on ghost atoms to the complete force on
 owned atoms.  The order of the two stages described in the
-:ref:`ghost-atom-comm` figure is inverted, and the same lists of atoms
+:ref:`ghost-atom-comm` figure is inverted and the same lists of atoms
 are used to pack and unpack message buffers with per-atom forces.  When
 a received buffer is unpacked, the ghost forces are summed to owned atom
 forces.  As in forward communication, forces on atoms in the four blue
 corners of the diagrams are sent, received, and summed twice (once at
 each stage) before owning processors have the full force.
 
-These two operations are used in many places within LAMMPS aside from
+These two operations are used many places within LAMMPS aside from
 exchange of coordinates and forces, for example by manybody potentials
 to share intermediate per-atom values, or by rigid-body integrators to
 enable each atom in a body to access body properties.  Here are
@@ -105,16 +105,16 @@ performed in LAMMPS:
   atom pairs when building neighbor lists or computing forces.
 
 - The cutoff distance for exchanging ghost atoms is typically equal to
-  the neighbor cutoff.  But it can also set to a larger value if needed,
+  the neighbor cutoff.  But it can also chosen to be longer if needed,
   e.g. half the diameter of a rigid body composed of multiple atoms or
   over 3x the length of a stretched bond for dihedral interactions.  It
   can also exceed the periodic box size.  For the regular communication
   pattern (left), if the cutoff distance extends beyond a neighbor
-  processor's subdomain, then multiple exchanges are performed in the
+  processor's sub-domain, then multiple exchanges are performed in the
   same direction.  Each exchange is with the same neighbor processor,
   but buffers are packed/unpacked using a different list of atoms. For
-  forward communication, in the first exchange, a processor sends only
+  forward communication, in the first exchange a processor sends only
   owned atoms.  In subsequent exchanges, it sends ghost atoms received
   in previous exchanges.  For the irregular pattern (right) overlaps of
-  a processor's extended ghost-atom subdomain with all other processors
+  a processor's extended ghost-atom sub-domain with all other processors
   in each dimension are detected.

doc/src/Developer_par_long.rst

@@ -20,7 +20,7 @@ e) electric field values from grid points near each atom are interpolated to com
 
 For any of the spatial-decomposition partitioning schemes each processor
 owns the brick-shaped portion of FFT grid points contained within its
-subdomain.  The two interpolation operations use a stencil of grid
+sub-domain.  The two interpolation operations use a stencil of grid
 points surrounding each atom.  To accommodate the stencil size, each
 processor also stores a few layers of ghost grid points surrounding its
 brick.  Forward and reverse communication of grid point values is
@@ -40,31 +40,31 @@ orthogonal boxes.
 
 .. _fft-parallel:
 .. figure:: img/fft-decomp-parallel.png
+   :align: center
 
-   Parallel FFT in PPPM
+   parallel FFT in PPPM
 
-      Stages of a parallel FFT for a simulation domain overlaid with an
-      8x8x8 3d FFT grid, partitioned across 64 processors.  Within each
-      of the 4 diagrams, grid cells of the same color are owned by a
-      single processor; for simplicity, only cells owned by 4 or 8 of
-      the 64 processors are colored.  The two images on the left
-      illustrate brick-to-pencil communication.  The two images on the
-      right illustrate pencil-to-pencil communication, which in this
-      case transposes the *y* and *z* dimensions of the grid.
+   Stages of a parallel FFT for a simulation domain overlaid
+   with an 8x8x8 3d FFT grid, partitioned across 64 processors.
+   Within each of the 4 diagrams, grid cells of the same color are
+   owned by a single processor; for simplicity only cells owned by 4
+   or 8 of the 64 processors are colored.  The two images on the left
+   illustrate brick-to-pencil communication.  The two images on the
+   right illustrate pencil-to-pencil communication, which in this
+   case transposes the *y* and *z* dimensions of the grid.
 
 Parallel 3d FFTs require substantial communication relative to their
 computational cost.  A 3d FFT is implemented by a series of 1d FFTs
-along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus, the
-FFT grid cannot be decomposed like atoms into 3 dimensions for parallel
+along the *x-*, *y-*, and *z-*\ direction of the FFT grid.  Thus the FFT
+grid cannot be decomposed like atoms into 3 dimensions for parallel
 processing of the FFTs but only in 1 (as planes) or 2 (as pencils)
 dimensions and in between the steps the grid needs to be transposed to
 have the FFT grid portion "owned" by each MPI process complete in the
 direction of the 1d FFTs it has to perform. LAMMPS uses the
-pencil-decomposition algorithm as shown in the :ref:`fft-parallel`
-figure.
+pencil-decomposition algorithm as shown in the :ref:`fft-parallel` figure.
 
 Initially (far left), each processor owns a brick of same-color grid
-cells (actually grid points) contained within in its subdomain.  A
+cells (actually grid points) contained within in its sub-domain.  A
 brick-to-pencil communication operation converts this layout to 1d
 pencils in the *x*-dimension (center left).  Again, cells of the same
 color are owned by the same processor.  Each processor can then compute
@@ -97,7 +97,7 @@ across all $P$ processors with a single call to ``MPI_Alltoall()``, but
 this is typically much slower.  However, for the specialized brick and
 pencil tiling illustrated in :ref:`fft-parallel` figure, collective
 communication across the entire MPI communicator is not required.  In
-the example, an :math:`8^3` grid with 512 grid cells is partitioned
+the example an :math:`8^3` grid with 512 grid cells is partitioned
 across 64 processors; each processor owns a 2x2x2 3d brick of grid
 cells.  The initial brick-to-pencil communication (upper left to upper
 right) only requires collective communication within subgroups of 4
@@ -132,7 +132,7 @@ grid/particle operations that LAMMPS supports:
 - The fftMPI library allows each grid dimension to be a multiple of
   small prime factors (2,3,5), and allows any number of processors to
   perform the FFT.  The resulting brick and pencil decompositions are
-  thus not always as well-aligned, but the size of subgroups of
+  thus not always as well-aligned but the size of subgroups of
   processors for the two modes of communication (brick/pencil and
   pencil/pencil) still scale as :math:`O(P^{\frac{1}{3}})` and
   :math:`O(P^{\frac{1}{2}})`.
@@ -143,28 +143,26 @@ grid/particle operations that LAMMPS supports:
   in memory.  This reordering can be done during the packing or
   unpacking of buffers for MPI communication.
 
-- For large systems and particularly many MPI processes, the dominant
-  cost for parallel FFTs is often the communication, not the computation
-  of 1d FFTs, even though the latter scales as :math:`N \log(N)` in the
-  number of grid points *N* per grid direction.  This is due to the fact
-  that only a 2d decomposition into pencils is possible while atom data
-  (and their corresponding short-range force and energy computations)
-  can be decomposed efficiently in 3d.
+- For large systems and particularly a large number of MPI processes,
+  the dominant cost for parallel FFTs is often the communication, not
+  the computation of 1d FFTs, even though the latter scales as :math:`N
+  \log(N)` in the number of grid points *N* per grid direction.  This is
+  due to the fact that only a 2d decomposition into pencils is possible
+  while atom data (and their corresponding short-range force and energy
+  computations) can be decomposed efficiently in 3d.
 
-  Reducing the number of MPI processes involved in the MPI communication
-  will reduce this kind of overhead.  By using a :doc:`hybrid MPI +
-  OpenMP parallelization <Speed_omp>` it is still possible to use all
-  processes for parallel computation.  It will use OpenMP
-  parallelization inside the MPI domains. While that may have a lower
-  parallel efficiency for some part of the computation, that can be less
-  than the communication overhead in the 3d FFTs.
+  This can be addressed by reducing the number of MPI processes involved
+  in the MPI communication by using :doc:`hybrid MPI + OpenMP
+  parallelization <Speed_omp>`.  This will use OpenMP parallelization
+  inside the MPI domains and while that may have a lower parallel
+  efficiency, it reduces the communication overhead.
 
-  As an alternative, it is also possible to start a :ref:`multi-partition
+  As an alternative it is also possible to start a :ref:`multi-partition
   <partition>` calculation and then use the :doc:`verlet/split
   integrator <run_style>` to perform the PPPM computation on a
   dedicated, separate partition of MPI processes.  This uses an integer
-  "1:*p*" mapping of *p* subdomains of the atom decomposition to one
-  subdomain of the FFT grid decomposition and where pairwise non-bonded
+  "1:*p*" mapping of *p* sub-domains of the atom decomposition to one
+  sub-domain of the FFT grid decomposition and where pairwise non-bonded
   and bonded forces and energies are computed on the larger partition
   and the PPPM kspace computation concurrently on the smaller partition.
 
@@ -174,10 +172,10 @@ grid/particle operations that LAMMPS supports:
 
 - LAMMPS implements a ``GridComm`` class which overlays the simulation
   domain with a regular grid, partitions it across processors in a
-  manner consistent with processor subdomains, and provides methods for
+  manner consistent with processor sub-domains, and provides methods for
   forward and reverse communication of owned and ghost grid point
   values.  It is used for PPPM as an FFT grid (as outlined above) and
-  also for the MSM algorithm, which uses a cascade of grid sizes from
+  also for the MSM algorithm which uses a cascade of grid sizes from
   fine to coarse to compute long-range Coulombic forces.  The GridComm
   class is also useful for models where continuum fields interact with
   particles.  For example, the two-temperature model (TTM) defines heat

doc/src/Developer_par_neigh.rst

@@ -3,12 +3,12 @@ Neighbor lists
 
 To compute forces efficiently, each processor creates a Verlet-style
 neighbor list which enumerates all pairs of atoms *i,j* (*i* = owned,
-*j* = owned or ghost) with separation less than the applicable neighbor
-list cutoff distance.  In LAMMPS, the neighbor lists are stored in a
-multiple-page data structure; each page is a contiguous chunk of memory
-which stores vectors of neighbor atoms *j* for many *i* atoms.  This
-allows pages to be incrementally allocated or deallocated in blocks as
-needed.  Neighbor lists typically consume the most memory of any data
+*j* = owned or ghost) with separation less than the applicable
+neighbor list cutoff distance.  In LAMMPS the neighbor lists are stored
+in a multiple-page data structure; each page is a contiguous chunk of
+memory which stores vectors of neighbor atoms *j* for many *i* atoms.
+This allows pages to be incrementally allocated or deallocated in blocks
+as needed.  Neighbor lists typically consume the most memory of any data
 structure in LAMMPS.  The neighbor list is rebuilt (from scratch) once
 every few timesteps, then used repeatedly each step for force or other
 computations.  The neighbor cutoff distance is :math:`R_n = R_f +
@@ -16,20 +16,20 @@ computations.  The neighbor cutoff distance is :math:`R_n = R_f +
 the interatomic potential for computing short-range pairwise or manybody
 forces and :math:`\Delta_s` is a "skin" distance that allows the list to
 be used for multiple steps assuming that atoms do not move very far
-between consecutive time steps.  Typically, the code triggers
+between consecutive time steps.  Typically the code triggers
 reneighboring when any atom has moved half the skin distance since the
 last reneighboring; this and other options of the neighbor list rebuild
 can be adjusted with the :doc:`neigh_modify <neigh_modify>` command.
 
 On steps when reneighboring is performed, atoms which have moved outside
-their owning processor's subdomain are first migrated to new processors
+their owning processor's sub-domain are first migrated to new processors
 via communication.  Periodic boundary conditions are also (only)
 enforced on these steps to ensure each atom is re-assigned to the
 correct processor.  After migration, the atoms owned by each processor
-are stored in a contiguous vector.  Periodically, each processor
+are stored in a contiguous vector.  Periodically each processor
 spatially sorts owned atoms within its vector to reorder it for improved
 cache efficiency in force computations and neighbor list building.  For
-that, atoms are spatially binned and then reordered so that atoms in the
+that atoms are spatially binned and then reordered so that atoms in the
 same bin are adjacent in the vector.  Atom sorting can be disabled or
 its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
@@ -39,12 +39,12 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 
    neighbor list stencils
 
-   A 2d simulation subdomain (thick black line) and the corresponding
+   A 2d simulation sub-domain (thick black line) and the corresponding
    ghost atom cutoff region (dashed blue line) for both orthogonal
    (left) and triclinic (right) domains.  A regular grid of neighbor
    bins (thin lines) overlays the entire simulation domain and need not
-   align with subdomain boundaries; only the portion overlapping the
-   augmented subdomain is shown.  In the triclinic case, it overlaps the
+   align with sub-domain boundaries; only the portion overlapping the
+   augmented sub-domain is shown.  In the triclinic case it overlaps the
    bounding box of the tilted rectangle.  The blue- and red-shaded bins
    represent a stencil of bins searched to find neighbors of a particular
    atom (black dot).
@@ -52,13 +52,13 @@ its settings modified with the :doc:`atom_modify <atom_modify>` command.
 To build a local neighbor list in linear time, the simulation domain is
 overlaid (conceptually) with a regular 3d (or 2d) grid of neighbor bins,
 as shown in the :ref:`neighbor-stencil` figure for 2d models and a
-single MPI processor's subdomain.  Each processor stores a set of
-neighbor bins which overlap its subdomain, extended by the neighbor
+single MPI processor's sub-domain.  Each processor stores a set of
+neighbor bins which overlap its sub-domain extended by the neighbor
 cutoff distance :math:`R_n`.  As illustrated, the bins need not align
 with processor boundaries; an integer number in each dimension is fit to
 the size of the entire simulation box.
 
-Most often, LAMMPS builds what is called a "half" neighbor list where
+Most often LAMMPS builds what it calls a "half" neighbor list where
 each *i,j* neighbor pair is stored only once, with either atom *i* or
 *j* as the central atom.  The build can be done efficiently by using a
 pre-computed "stencil" of bins around a central origin bin which
@@ -67,18 +67,18 @@ is simply a list of integer offsets in *x,y,z* of nearby bins
 surrounding the origin bin which are close enough to contain any
 neighbor atom *j* within a distance :math:`R_n` from any atom *i* in the
 origin bin.  Note that for a half neighbor list, the stencil can be
-asymmetric, since each atom only need store half its nearby neighbors.
+asymmetric since each atom only need store half its nearby neighbors.
 
 These stencils are illustrated in the figure for a half list and a bin
 size of :math:`\frac{1}{2} R_n`.  There are 13 red+blue stencil bins in
 2d (for the orthogonal case, 15 for triclinic).  In 3d there would be
 63, 13 in the plane of bins that contain the origin bin and 25 in each
 of the two planes above it in the *z* direction (75 for triclinic).  The
-triclinic stencil has extra bins because the bins tile the bounding box
-of the entire triclinic domain, and thus are not periodic with respect
-to the simulation box itself.  The stencil and logic for determining
-which *i,j* pairs to include in the neighbor list are altered slightly
-to account for this.
+reason the triclinic stencil has extra bins is because the bins tile the
+bounding box of the entire triclinic domain and thus are not periodic
+with respect to the simulation box itself.  The stencil and logic for
+determining which *i,j* pairs to include in the neighbor list are
+altered slightly to account for this.
 
 To build a neighbor list, a processor first loops over its "owned" plus
 "ghost" atoms and assigns each to a neighbor bin.  This uses an integer
@@ -95,7 +95,7 @@ supports:
   been found to be optimal for many typical cases.  Smaller bins incur
   additional overhead to loop over; larger bins require more distance
   calculations.  Note that for smaller bin sizes, the 2d stencil in the
-  figure would be of a more semicircular shape (hemispherical in 3d),
+  figure would be more semi-circular in shape (hemispherical in 3d),
   with bins near the corners of the square eliminated due to their
   distance from the origin bin.
 
@@ -111,8 +111,8 @@ supports:
   symmetric stencil.  It also includes lists with partial enumeration of
   ghost atom neighbors.  The full and ghost-atom lists are used by
   various manybody interatomic potentials.  Lists may also use different
-  criteria for inclusion of a pairwise interaction.  Typically, this
-  simply depends only on the distance between two atoms and the cutoff
+  criteria for inclusion of a pair interaction.  Typically this simply
+  depends only on the distance between two atoms and the cutoff
   distance.  But for finite-size coarse-grained particles with
   individual diameters (e.g. polydisperse granular particles), it can
   also depend on the diameters of the two particles.
@@ -121,11 +121,11 @@ supports:
   of the master neighbor list for the full system need to be generated,
   one for each sub-style, which contains only the *i,j* pairs needed to
   compute interactions between subsets of atoms for the corresponding
-  potential.  This means, not all *i* or *j* atoms owned by a processor
+  potential.  This means not all *i* or *j* atoms owned by a processor
   are included in a particular sub-list.
 
 - Some models use different cutoff lengths for pairwise interactions
-  between different kinds of particles, which are stored in a single
+  between different kinds of particles which are stored in a single
   neighbor list.  One example is a solvated colloidal system with large
   colloidal particles where colloid/colloid, colloid/solvent, and
   solvent/solvent interaction cutoffs can be dramatically different.
@@ -144,7 +144,7 @@ supports:
 
 - For small and sparse systems and as a fallback method, LAMMPS also
   supports neighbor list construction without binning by using a full
-  :math:`O(N^2)` loop over all *i,j* atom pairs in a subdomain when
+  :math:`O(N^2)` loop over all *i,j* atom pairs in a sub-domain when
   using the :doc:`neighbor nsq <neighbor>` command.
 
 - Dependent on the "pair" setting of the :doc:`newton <newton>` command,
@@ -153,7 +153,7 @@ supports:
   For the newton pair *on* setting the atom *j* is only added to the
   list if its *z* coordinate is larger, or if equal the *y* coordinate
   is larger, and that is equal, too, the *x* coordinate is larger.  For
-  homogeneously dense systems, that will result in picking neighbors from
+  homogeneously dense systems that will result in picking neighbors from
   a same size sector in always the same direction relative to the
-  "owned" atom, and thus it should lead to similar length neighbor lists
-  and reduce the chance of a load imbalance.
+  "owned" atom and thus it should lead to similar length neighbor lists
+  and thus reduce the chance of a load imbalance.

doc/src/Developer_par_openmp.rst

@@ -6,7 +6,7 @@ thread parallelism to predominantly distribute loops over local data
 and thus follow an orthogonal parallelization strategy to the
 decomposition into spatial domains used by the :doc:`MPI partitioning
 <Developer_par_part>`.  For clarity, this section discusses only the
-implementation in the OPENMP package, as it is the simplest. The INTEL
+implementation in the OPENMP package as it is the simplest. The INTEL
 and KOKKOS package offer additional options and are more complex since
 they support more features and different hardware like co-processors
 or GPUs.
@@ -14,7 +14,7 @@ or GPUs.
 One of the key decisions when implementing the OPENMP package was to
 keep the changes to the source code small, so that it would be easier to
 maintain the code and keep it in sync with the non-threaded standard
-implementation.  This is achieved by a) making the OPENMP version a
+implementation.  this is achieved by a) making the OPENMP version a
 derived class from the regular version (e.g. ``PairLJCutOMP`` from
 ``PairLJCut``) and overriding only methods that are multi-threaded or
 need to be modified to support multi-threading (similar to what was done
@@ -26,13 +26,13 @@ into three separate classes ``ThrOMP``, ``ThrData``, and ``FixOMP``.
 available in the corresponding base class (e.g. ``Pair`` for
 ``PairLJCutOMP``) like multi-thread aware variants of the "tally"
 functions. Those functions are made available through multiple
-inheritance, so those new functions have to have unique names to avoid
+inheritance so those new functions have to have unique names to avoid
 ambiguities; typically ``_thr`` is appended to the name of the function.
-``ThrData`` is a class that manages per-thread data structures.  It is
-used instead of extending the corresponding storage to per-thread arrays
-to avoid slowdowns due to "false sharing" when multiple threads update
-adjacent elements in an array and thus force the CPU cache lines to be
-reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
+``ThrData`` is a classes that manages per-thread data structures.
+It is used instead of extending the corresponding storage to per-thread
+arrays to avoid slowdowns due to "false sharing" when multiple threads
+update adjacent elements in an array and thus force the CPU cache lines
+to be reset and re-fetched.  ``FixOMP`` finally manages the "multi-thread
 state" like settings and access to per-thread storage, it is activated
 by the :doc:`package omp <package>` command.
 
@@ -46,24 +46,24 @@ involve multiple atoms and thus there are race conditions when multiple
 threads want to update per-atom data of the same atoms.  Five possible
 strategies have been considered to avoid this:
 
-1. Restructure the code so that there is no overlapping access possible
+1) restructure the code so that there is no overlapping access possible
    when computing in parallel, e.g. by breaking lists into multiple
    parts and synchronizing threads in between.
-2. Have each thread be "responsible" for a specific group of atoms and
+2) have each thread be "responsible" for a specific group of atoms and
    compute these interactions multiple times, once on each thread that
-   is responsible for a given atom, and then have each thread only update
+   is responsible for a given atom and then have each thread only update
    the properties of this atom.
-3. Use mutexes around functions and regions of code where the data race
-   could happen.
-4. Use atomic operations when updating per-atom properties.
-5. Use replicated per-thread data structures to accumulate data without
+3) use mutexes around functions and regions of code where the data race
+   could happen
+4) use atomic operations when updating per-atom properties
+5) use replicated per-thread data structures to accumulate data without
    conflicts and then use a reduction to combine those results into the
    data structures used by the regular style.
 
 Option 5 was chosen for the OPENMP package because it would retain the
-performance for the case of a single thread and the code would be more
+performance for the case of 1 thread and the code would be more
 maintainable.  Option 1 would require extensive code changes,
-particularly to the neighbor list code; option 2 would have incurred a
+particularly to the neighbor list code; options 2 would have incurred a
 2x or more performance penalty for the serial case; option 3 causes
 significant overhead and would enforce serialization of operations in
 inner loops and thus defeat the purpose of multi-threading; option 4
@@ -80,7 +80,7 @@ equivalent to the number of CPU cores per CPU socket on high-end
 supercomputers.
 
 Thus arrays like the force array are dimensioned to the number of atoms
-times the number of threads when enabling OpenMP support, and inside the
+times the number of threads when enabling OpenMP support and inside the
 compute functions a pointer to a different chunk is obtained by each thread.
 Similarly, accumulators like potential energy or virial are kept in
 per-thread instances of the ``ThrData`` class and then only reduced and
@@ -91,7 +91,7 @@ Loop scheduling
 """""""""""""""
 
 Multi-thread parallelization is applied by distributing (outer) loops
-statically across threads.  Typically, this would be the loop over local
+statically across threads.  Typically this would be the loop over local
 atoms *i* when processing *i,j* pairs of atoms from a neighbor list.
 The design of the neighbor list code results in atoms having a similar
 number of neighbors for homogeneous systems and thus load imbalances

doc/src/Developer_par_part.rst

@@ -7,39 +7,39 @@ distributed-memory parallelism is set with the :doc:`comm_style command
 
 .. _domain-decomposition:
 .. figure:: img/domain-decomp.png
+   :align: center
 
-   Domain decomposition schemes
+   domain decomposition
 
-      This figure shows the different kinds of domain decomposition used
-      for MPI parallelization: "brick" on the left with an orthogonal
-      (left) and a triclinic (middle) simulation domain, and a "tiled"
-      decomposition (right).  The black lines show the division into
-      subdomains, and the contained atoms are "owned" by the
-      corresponding MPI process. The green dashed lines indicate how
-      subdomains are extended with "ghost" atoms up to the communication
-      cutoff distance.
+   This figure shows the different kinds of domain decomposition used
+   for MPI parallelization: "brick" on the left with an orthogonal
+   (left) and a triclinic (middle) simulation domain, and a "tiled"
+   decomposition (right).  The black lines show the division into
+   sub-domains and the contained atoms are "owned" by the corresponding
+   MPI process. The green dashed lines indicate how sub-domains are
+   extended with "ghost" atoms up to the communication cutoff distance.
 
-The LAMMPS simulation box is a 3d or 2d volume, which can be of
-orthogonal or triclinic shape, as illustrated in the
-:ref:`domain-decomposition` figure for the 2d case.  Orthogonal means
-the box edges are aligned with the *x*, *y*, *z* Cartesian axes, and the
-box faces are thus all rectangular.  Triclinic allows for a more general
-parallelepiped shape in which edges are aligned with three arbitrary
-vectors and the box faces are parallelograms.  In each dimension, box
-faces can be periodic, or non-periodic with fixed or shrink-wrapped
-boundaries.  In the fixed case, atoms which move outside the face are
-deleted; shrink-wrapped means the position of the box face adjusts
-continuously to enclose all the atoms.
+The LAMMPS simulation box is a 3d or 2d volume, which can be orthogonal
+or triclinic in shape, as illustrated in the :ref:`domain-decomposition`
+figure for the 2d case.  Orthogonal means the box edges are aligned with
+the *x*, *y*, *z* Cartesian axes, and the box faces are thus all
+rectangular.  Triclinic allows for a more general parallelepiped shape
+in which edges are aligned with three arbitrary vectors and the box
+faces are parallelograms.  In each dimension box faces can be periodic,
+or non-periodic with fixed or shrink-wrapped boundaries.  In the fixed
+case, atoms which move outside the face are deleted; shrink-wrapped
+means the position of the box face adjusts continuously to enclose all
+the atoms.
 
 For distributed-memory MPI parallelism, the simulation box is spatially
-decomposed (partitioned) into non-overlapping subdomains which fill the
+decomposed (partitioned) into non-overlapping sub-domains which fill the
 box. The default partitioning, "brick", is most suitable when atom
 density is roughly uniform, as shown in the left-side images of the
-:ref:`domain-decomposition` figure.  The subdomains comprise a regular
-grid, and all subdomains are identical in size and shape.  Both the
+:ref:`domain-decomposition` figure.  The sub-domains comprise a regular
+grid and all sub-domains are identical in size and shape.  Both the
 orthogonal and triclinic boxes can deform continuously during a
 simulation, e.g. to compress a solid or shear a liquid, in which case
-the processor subdomains likewise deform.
+the processor sub-domains likewise deform.
 
 
 For models with non-uniform density, the number of particles per
@@ -50,14 +50,14 @@ load.  For such models, LAMMPS supports multiple strategies to reduce
 the load imbalance:
 
 - The processor grid decomposition is by default based on the simulation
-  cell volume and tries to optimize the volume to surface ratio for the subdomains.
+  cell volume and tries to optimize the volume to surface ratio for the sub-domains.
   This can be changed with the :doc:`processors command <processors>`.
-- The parallel planes defining the size of the subdomains can be shifted
+- The parallel planes defining the size of the sub-domains can be shifted
   with the :doc:`balance command <balance>`. Which can be done in addition
   to choosing a more optimal processor grid.
 - The recursive bisectioning algorithm in combination with the "tiled"
   communication style can produce a partitioning with equal numbers of
-  particles in each subdomain.
+  particles in each sub-domain.
 
 
 .. |decomp1| image:: img/decomp-regular.png
@@ -76,14 +76,14 @@ the load imbalance:
 
 The pictures above demonstrate different decompositions for a 2d system
 with 12 MPI ranks.  The atom colors indicate the load imbalance of each
-subdomain, with green being optimal and red the least optimal.
+sub-domain with green being optimal and red the least optimal.
 
-Due to the vacuum in the system, the default decomposition is
-unbalanced, with several MPI ranks without atoms (left). By forcing a
-1x12x1 processor grid, every MPI rank does computations now, but the
-number of atoms per subdomain is still uneven, and the thin slice shape
-increases the amount of communication between subdomains (center
-left). With a 2x6x1 processor grid and shifting the subdomain divisions,
-the load imbalance is further reduced and the amount of communication
-required between subdomains is less (center right).  And using the
-recursive bisectioning leads to further improved decomposition (right).
+Due to the vacuum in the system, the default decomposition is unbalanced
+with several MPI ranks without atoms (left). By forcing a 1x12x1
+processor grid, every MPI rank does computations now, but number of
+atoms per sub-domain is still uneven and the thin slice shape increases
+the amount of communication between sub-domains (center left). With a
+2x6x1 processor grid and shifting the sub-domain divisions, the load
+imbalance is further reduced and the amount of communication required
+between sub-domains is less (center right).  And using the recursive
+bisectioning leads to further improved decomposition (right).

doc/src/Developer_parallel.rst

@@ -3,11 +3,11 @@ Parallel algorithms
 
 LAMMPS is designed to enable running simulations in parallel using the
 MPI parallel communication standard with distributed data via domain
-decomposition.  The parallelization aims to be efficient, and resulting
-in good strong scaling (= good speedup for the same system) and good
-weak scaling (= the computational cost of enlarging the system is
+decomposition.  The parallelization aims to be efficient result in good
+strong scaling (= good speedup for the same system) and good weak
+scaling (= the computational cost of enlarging the system is
 proportional to the system size).  Additional parallelization using GPUs
-or OpenMP can also be applied within the subdomain assigned to an MPI
+or OpenMP can also be applied within the sub-domain assigned to an MPI
 process.  For clarity, most of the following illustrations show the 2d
 simulation case. The underlying algorithms in those cases, however,
 apply to both 2d and 3d cases equally well.

doc/src/Developer_plugins.rst

@@ -95,7 +95,7 @@ a class ``PairMorse2`` in the files ``pair_morse2.h`` and
 ``pair_morse2.cpp`` with the factory function and initialization
 function would look like this:
 
-.. code-block:: c++
+.. code-block:: C++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -141,7 +141,7 @@ list of argument strings), then the pointer type is ``lammpsplugin_factory2``
 and it must be assigned to the *creator.v2* member of the plugin struct.
 Below is an example for that:
 
-.. code-block:: c++
+.. code-block:: C++
 
   #include "lammpsplugin.h"
   #include "version.h"
@@ -176,7 +176,7 @@ demonstrated in the following example, which also shows that the
 implementation of the plugin class may be within the same source
 file as the plugin interface code:
 
-.. code-block:: c++
+.. code-block:: C++
 
    #include "lammpsplugin.h"
 

doc/src/Developer_unittest.rst

@@ -194,7 +194,7 @@ macro. These tests operate by capturing the screen output when executing
 the failing command and then comparing that with a provided regular
 expression string pattern.  Example:
 
-.. code-block:: c++
+.. code-block:: C++
 
    TEST_F(SimpleCommandsTest, UnknownCommand)
    {
@@ -226,9 +226,9 @@ The following test programs are currently available:
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`
-   * - ``test_reset_atoms.cpp``
-     - ResetAtoms
-     - Tests to validate the :doc:`reset_atoms <reset_atoms>` sub-commands
+   * - ``test_reset_ids.cpp``
+     - ResetIDs
+     - Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
 
 
 Tests for the C-style library interface
@@ -249,7 +249,7 @@ MPI support.  These include tests where LAMMPS is run in multi-partition
 mode or only on a subset of the MPI world communicator.  The CMake
 script code for adding this kind of test looks like this:
 
-.. code-block:: cmake
+.. code-block:: CMake
 
    if (BUILD_MPI)
      add_executable(test_library_mpi test_library_mpi.cpp)
@@ -489,7 +489,7 @@ to update the YAML files. Running a command like
 
 .. code-block:: bash
 
-   test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
+   $ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
 
 will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
 the reference data and write a new file with to ``new.yaml``.  If this step fails,
@@ -500,13 +500,13 @@ It is also possible to do an update in place with:
 
 .. code-block:: bash
 
-   test_pair_style mol-pair-lennard_mdf.yaml -u
+   $ test_pair_style mol-pair-lennard_mdf.yaml -u
 
 And one can finally run the full set of tests with:
 
 .. code-block:: bash
 
-   test_pair_style mol-pair-lennard_mdf.yaml
+   $ test_pair_style mol-pair-lennard_mdf.yaml
 
 This will just print a summary of the groups of tests.  When using the "-v" flag
 the test will also keep any LAMMPS output and when using the "-s" flag, there

doc/src/Developer_updating.rst

@@ -1,479 +0,0 @@
-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 developers@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()`_
-- `Refactored grid communication using Grid3d/Grid2d classes instead of GridComm`_
-
-----
-
-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.
-
-Refactored grid communication using Grid3d/Grid2d classes instead of GridComm
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. versionchanged:: 22Dec2022
-
-The ``GridComm`` class was for creating and communicating distributed
-grids was replaced by the ``Grid3d`` class with added functionality.
-A ``Grid2d`` class was also added for additional flexibility.
-
-The new functionality and commands using the two grid classes are
-discussed on the following documentation pages:
-
-- :doc:`Howto_grid`
-- :doc:`Developer_grid`
-
-If you have custom LAMMPS code, which uses the GridComm class, here are some notes
-on how to adapt it for using the Grid3d class.
-
-(1) The constructor has changed to allow the ``Grid3d`` / ``Grid2d``
-    classes to partition the global grid across processors, both for
-    owned and ghost grid cells.  Previously any class which called
-    ``GridComm`` performed the partitioning itself and that information
-    was passed in the ``GridComm::GridComm()`` constructor.  There are
-    several "set" functions which can be called to alter how ``Grid3d``
-    / ``Grid2d`` perform the partitioning.  They should be sufficient
-    for most use cases of the grid classes.
-
-(2) The partitioning is triggered by the ``setup_grid()`` method.
-
-(3) The ``setup()`` method of the ``GridComm`` class has been replaced
-    by the ``setup_comm()`` method in the new grid classes.  The syntax
-    for the ``forward_comm()`` and ``reverse_comm()`` methods is
-    slightly altered as is the syntax of the associated pack/unpack
-    callback methods.  But the functionality of these operations is the
-    same as before.
-
-(4) The new ``Grid3d`` / ``Grid2d`` classes have additional
-    functionality for dynamic load-balancing of grids and their
-    associated data across processors.  This did not exist in the
-    ``GridComm`` class.
-
-This and more is explained in detail on the :doc:`Developer_grid` page.
-The following LAMMPS source files can be used as illustrative examples
-for how the new grid classes are used by computes, fixes, and various
-KSpace solvers which use distributed FFT grids:
-
-- ``src/fix_ave_grid.cpp``
-- ``src/compute_property_grid.cpp``
-- ``src/EXTRA-FIX/fix_ttm_grid.cpp``
-- ``src/KSPACE/pppm.cpp``
-
-This change is **required** or else the code will not compile.

doc/src/Developer_utils.rst

@@ -133,9 +133,6 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_comment
    :project: progguide
 
-.. doxygenfunction:: strip_style_suffix
-   :project: progguide
-
 .. doxygenfunction:: star_subst
    :project: progguide
 
@@ -157,9 +154,6 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_and_count_words
    :project: progguide
 
-.. doxygenfunction:: join_words
-   :project: progguide
-
 .. doxygenfunction:: split_words
    :project: progguide
 
@@ -178,12 +172,6 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
-.. doxygenfunction:: is_id
-   :project: progguide
-
-.. doxygenfunction:: is_type
-   :project: progguide
-
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -214,16 +202,10 @@ Argument processing
 .. doxygenfunction:: expand_args
    :project: progguide
 
-.. doxygenfunction:: parse_grid_id
-   :project: progguide
-
-.. doxygenfunction:: expand_type
-   :project: progguide
-
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &format, Args&&... args)
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
    :project: progguide
 
 .. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
@@ -323,7 +305,7 @@ are all "whitespace" characters, i.e. the space character, the tabulator
 character, the carriage return character, the linefeed character, and
 the form feed character.
 
-.. code-block:: c++
+.. code-block:: C++
    :caption: Tokenizer class example listing entries of the PATH environment variable
 
    #include "tokenizer.h"
@@ -355,7 +337,7 @@ tokenizer into a ``try`` / ``catch`` block to handle errors.  The
 when a (type of) number is requested as next token that is not
 compatible with the string representing the next word.
 
-.. code-block:: c++
+.. code-block:: C++
    :caption: ValueTokenizer class example with exception handling
 
    #include "tokenizer.h"
@@ -433,7 +415,7 @@ one or two array indices "[<number>]" with numbers > 0.
 
 A typical code segment would look like this:
 
-.. code-block:: c++
+.. code-block:: C++
    :caption: Usage example for ArgInfo class
 
    int nvalues = 0;
@@ -482,7 +464,7 @@ open the file, and will call the :cpp:class:`LAMMPS_NS::Error` class in
 case of failures to read or to convert numbers, so that LAMMPS will be
 aborted.
 
-.. code-block:: c++
+.. code-block:: C++
    :caption: Use of PotentialFileReader class in pair style coul/streitz
 
     PotentialFileReader reader(lmp, file, "coul/streitz");
@@ -561,7 +543,7 @@ chunk size needs to be known in advance, 2) with :cpp:func:`MyPage::vget()
 its size is registered later with :cpp:func:`MyPage::vgot()
 <LAMMPS_NS::MyPage::vgot>`.
 
-.. code-block:: c++
+.. code-block:: C++
    :caption: Example of using :cpp:class:`MyPage <LAMMPS_NS::MyPage>`
 
       #include "my_page.h"
@@ -647,7 +629,7 @@ Communication buffer coding with *ubuf*
 ---------------------------------------
 
 LAMMPS uses communication buffers where it collects data from various
-class instances and then exchanges the data with neighboring subdomains.
+class instances and then exchanges the data with neighboring sub-domains.
 For simplicity those buffers are defined as ``double`` buffers and
 used for doubles and integer numbers. This presents a unique problem
 when 64-bit integers are used.  While the storage needed for a ``double``

doc/src/Developer_write.rst

@@ -26,7 +26,7 @@ constructor with the signature: ``FixPrintVel(class LAMMPS *, int, char **)``.
 Every fix must be registered in LAMMPS by writing the following lines
 of code in the header before include guards:
 
-.. code-block:: c++
+.. code-block:: c
 
    #ifdef FIX_CLASS
    // clang-format off
@@ -47,7 +47,7 @@ keyword when it parses the input script.
 Let's write a simple fix which will print the average velocity at the end
 of each timestep. First of all, implement a constructor:
 
-.. code-block:: c++
+.. code-block:: C++
 
    FixPrintVel::FixPrintVel(LAMMPS *lmp, int narg, char **arg)
    : Fix(lmp, narg, arg)
@@ -72,7 +72,7 @@ in the Fix class called ``nevery`` which specifies how often the method
 
 The next method we need to implement is ``setmask()``:
 
-.. code-block:: c++
+.. code-block:: C++
 
    int FixPrintVel::setmask()
    {
@@ -87,7 +87,7 @@ during execution. The constant ``END_OF_STEP`` corresponds to the
 are called during a timestep and the order in which they are called
 are shown in the previous section.
 
-.. code-block:: c++
+.. code-block:: C++
 
    void FixPrintVel::end_of_step()
    {
@@ -143,7 +143,7 @@ The group membership information of an atom is contained in the *mask*
 property of and atom and the bit corresponding to a given group is
 stored in the groupbit variable which is defined in Fix base class:
 
-.. code-block:: c++
+.. code-block:: C++
 
    for (int i = 0; i < nlocal; ++i) {
      if (atom->mask[i] & groupbit) {
@@ -174,7 +174,7 @@ to store positions of atoms from previous timestep, we need to add
 ``double** xold`` to the header file. Than add allocation code
 to the constructor:
 
-.. code-block:: c++
+.. code-block:: C++
 
    FixSavePos::FixSavePos(LAMMPS *lmp, int narg, char **arg), xold(nullptr)
    {
@@ -190,7 +190,7 @@ to the constructor:
 
 Implement the aforementioned methods:
 
-.. code-block:: c++
+.. code-block:: C++
 
    double FixSavePos::memory_usage()
    {

doc/src/Errors_common.rst

@@ -113,7 +113,7 @@ LAMMPS output, something is wrong with your simulation.  If you
 suspect this is happening, it is a good idea to print out
 thermodynamic info frequently (e.g. every timestep) via the
 :doc:`thermo <thermo>` so you can monitor what is happening.
-Visualizing the atom movement is also a good idea to ensure your model
+Visualizing the atom movement is also a good idea to insure your model
 is behaving as you expect.
 
 In parallel, one way LAMMPS can hang is due to how different MPI

doc/src/Errors_debug.rst

@@ -40,7 +40,7 @@ We use it to show how to identify the origin of a segmentation fault.
 
 After recompiling LAMMPS and running the input you should get something like this:
 
-.. code-block:: console
+.. code-block::
 
    $ ./lmp -in in.melt
    LAMMPS (19 Mar 2020)
@@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
 There are two options to use the GDB debugger for identifying the origin
 of the segmentation fault or similar crash. The GDB debugger has many
 more features and options, as can be seen for example its `online
-documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -90,9 +90,8 @@ it.  When it reaches the code causing the segmentation fault, it will
 stop with a message why it stopped, print the current line of code, and
 drop back to the GDB prompt.
 
-.. code-block:: console
+.. code-block::
 
-   (gdb) run
    [...]
    Setting up Verlet run ...
      Unit style    : lj
@@ -107,7 +106,7 @@ drop back to the GDB prompt.
 Now typing the command "where" will show the stack of functions starting from
 the current function back to "main()".
 
-.. code-block:: console
+.. code-block::
 
    (gdb) where
    #0  0x00000000006653ab in LAMMPS_NS::PairLJCut::compute (this=0x829740, eflag=1, vflag=<optimized out>) at /home/akohlmey/compile/lammps/src/pair_lj_cut.cpp:139
@@ -125,7 +124,7 @@ You can also print the value of variables and see if there is anything
 unexpected.  Segmentation faults, for example, commonly happen when a
 pointer variable is not assigned and still initialized to NULL.
 
-.. code-block:: console
+.. code-block::
 
    (gdb) print x
    $1 = (double **) 0x7ffff7ca1010
@@ -154,7 +153,7 @@ utility to the current folder. Example: ``coredumpctl -o core dump lmp``.
 Now you can launch the debugger to load the executable, its debug info
 and the core dump and drop you to a prompt like before.
 
-.. code-block:: console
+.. code-block::
 
    $ gdb lmp core
    Reading symbols from lmp...
@@ -187,7 +186,7 @@ recommended to redirect the valgrind output to a file (e.g. with
 process ID) so that the messages of the multiple valgrind instances to
 the console are not mixed.
 
-.. code-block:: console
+.. code-block::
 
    $ valgrind ./lmp -in in.melt
    ==1933642== Memcheck, a memory error detector

doc/src/Errors_messages.rst

@@ -1232,7 +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/spica/kk*
+*Cannot use chosen neighbor list style with lj/sdk/kk*
    That style is not supported by Kokkos.
 
 *Cannot use chosen neighbor list style with pair eam/kk*
@@ -1600,10 +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/spica/coul/long/gpu pair style*
+*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/spica/gpu pair style*
+*Cannot use newton pair with lj/sdk/gpu pair style*
    Self-explanatory.
 
 *Cannot use newton pair with lj96/cut/gpu pair style*
@@ -5453,11 +5453,6 @@ 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.
@@ -5590,18 +5585,9 @@ 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.
@@ -5635,7 +5621,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's subdomain away before
+   box, or moved further than one processor's sub-domain away before
    reneighboring.
 
 *MEAM library error %d*
@@ -5877,12 +5863,6 @@ 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.
 
@@ -5913,15 +5893,6 @@ 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.
@@ -6092,7 +6063,7 @@ keyword to allow for additional bonds to be formed
    after a read_data, read_restart, or create_box command.
 
 *Next command must list all universe and uloop variables*
-   This is to ensure they stay in sync.
+   This is to insure they stay in sync.
 
 *No Kspace style defined for compute group/group*
    Self-explanatory.
@@ -6266,14 +6237,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a MSM grid point
    that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's subdomain has moved more than 1/2 the
+   boundary of a processor's sub-domain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's subdomain or even the entire
+   moved far outside a processor's sub-domain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6281,14 +6252,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's subdomain has moved more than 1/2 the
+   boundary of a processor's sub-domain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's subdomain or even the entire
+   moved far outside a processor's sub-domain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6296,14 +6267,14 @@ keyword to allow for additional bonds to be formed
    One or more atoms are attempting to map their charge to a PPPM grid
    point that is not owned by a processor.  This is likely for one of two
    reasons, both of them bad.  First, it may mean that an atom near the
-   boundary of a processor's subdomain has moved more than 1/2 the
+   boundary of a processor's sub-domain has moved more than 1/2 the
    :doc:`neighbor skin distance <neighbor>` without neighbor lists being
    rebuilt and atoms being migrated to new processors.  This also means
    you may be missing pairwise interactions that need to be computed.
    The solution is to change the re-neighboring criteria via the
    :doc:`neigh_modify <neigh_modify>` command.  The safest settings are
    "delay 0 every 1 check yes".  Second, it may mean that an atom has
-   moved far outside a processor's subdomain or even the entire
+   moved far outside a processor's sub-domain or even the entire
    simulation box. This indicates bad physics, e.g. due to highly
    overlapping atoms, too large a timestep, etc.
 
@@ -6811,7 +6782,7 @@ 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/spica/coul/long/gpu requires atom attribute q*
+*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
    The atom style defined does not have this attribute.
 
 *Pair style nb3b/harmonic requires atom IDs*
@@ -7231,7 +7202,7 @@ keyword to allow for additional bonds to be formed
 
 *Replacing a fix, but new style != old style*
    A fix ID can be used a second time, but only if the style matches the
-   previous fix.  In this case it is assumed you want to reset a fix's
+   previous fix.  In this case it is assumed you with to reset a fix's
    parameters.  This error may mean you are mistakenly re-using a fix ID
    when you do not intend to.
 
@@ -7337,7 +7308,7 @@ keyword to allow for additional bonds to be formed
 *Rigid body atoms %d %d missing on proc %d at step %ld*
    This means that an atom cannot find the atom that owns the rigid body
    it is part of, or vice versa.  The solution is to use the communicate
-   cutoff command to ensure ghost atoms are acquired from far enough away
+   cutoff command to insure ghost atoms are acquired from far enough away
    to encompass the max distance printed when the fix rigid/small command
    was invoked.
 
@@ -7878,10 +7849,6 @@ 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.
@@ -7906,13 +7873,6 @@ 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

@@ -109,9 +109,9 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
 *Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
    Since LAMMPS stores topology data with individual atoms, all atoms
    comprising a bond, angle, dihedral or improper must be present on any
-   subdomain that "owns" the atom with the information, either as a
+   sub-domain that "owns" the atom with the information, either as a
    local or a ghost atom. The communication cutoff is what determines up
-   to what distance from a subdomain boundary ghost atoms are created.
+   to what distance from a sub-domain boundary ghost atoms are created.
    The communication cutoff is by default the largest non-bonded cutoff
    plus the neighbor skin distance, but for short or non-bonded cutoffs
    and/or long bonds, this may not be sufficient. This warning indicates
@@ -351,7 +351,7 @@ This will most likely cause errors in kinetic fluctuations.
    Self-explanatory.
 
 *Kspace_modify slab param < 2.0 may cause unphysical behavior*
-   The kspace_modify slab parameter should be larger to ensure periodic
+   The kspace_modify slab parameter should be larger to insure periodic
    grids padded with empty space do not overlap.
 
 *Less insertions than requested*
@@ -398,7 +398,7 @@ This will most likely cause errors in kinetic fluctuations.
    Lost atoms are checked for each time thermo output is done.  See the
    thermo_modify lost command for options.  Lost atoms usually indicate
    bad dynamics, e.g. atoms have been blown far out of the simulation
-   box, or moved further than one processor's subdomain away before
+   box, or moved further than one processor's sub-domain away before
    reneighboring.
 
 *MSM mesh too small, increasing to 2 points in each direction*
@@ -470,12 +470,6 @@ 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.
 
@@ -491,7 +485,7 @@ This will most likely cause errors in kinetic fluctuations.
 *Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies*
    This is because excluding specific pair interactions also excludes
    them from long-range interactions which may not be the desired effect.
-   The special_bonds command handles this consistently by ensuring
+   The special_bonds command handles this consistently by insuring
    excluded (or weighted) 1-2, 1-3, 1-4 interactions are treated
    consistently by both the short-range pair style and the long-range
    solver.  This is not done for exclusions of charged atom pairs via the
@@ -545,7 +539,7 @@ This will most likely cause errors in kinetic fluctuations.
    If there are other fixes that act immediately after the initial stage
    of time integration within a timestep (i.e. after atoms move), then
    the command that sets up the dynamic group should appear after those
-   fixes.  This will ensure that dynamic group assignments are made
+   fixes.  This will insure that dynamic group assignments are made
    after all atoms have moved.
 
 *One or more respa levels compute no forces*
@@ -582,13 +576,13 @@ This will most likely cause errors in kinetic fluctuations.
    needed.  The requested volume fraction may be too high, or other atoms
    may be in the insertion region.
 
-*Proc subdomain size < neighbor skin, could lead to lost atoms*
+*Proc sub-domain size < neighbor skin, could lead to lost atoms*
    The decomposition of the physical domain (likely due to load
-   balancing) has led to a processor's subdomain being smaller than the
+   balancing) has led to a processor's sub-domain being smaller than the
    neighbor skin in one or more dimensions.  Since reneighboring is
    triggered by atoms moving the skin distance, this may lead to lost
    atoms, if an atom moves all the way across a neighboring processor's
-   subdomain before reneighboring is triggered.
+   sub-domain before reneighboring is triggered.
 
 *Reducing PPPM order b/c stencil extends beyond nearest neighbor processor*
    This may lead to a larger grid than desired.  See the kspace_modify overlap

doc/src/Examples.rst

@@ -1,7 +1,7 @@
 Example scripts
 ===============
 
-The LAMMPS distribution includes an examples subdirectory with many
+The LAMMPS distribution includes an examples sub-directory with many
 sample problems.  Many are 2d models that run quickly and are
 straightforward to visualize, requiring at most a couple of minutes to
 run on a desktop machine.  Each problem has an input script (in.\*) and
@@ -29,7 +29,7 @@ be quickly post-processed into a movie using commands described on the
 Animations of many of the examples can be viewed on the Movies section
 of the `LAMMPS website <https://www.lammps.org/movies.html>`_.
 
-There are two kinds of subdirectories in the examples folder.  Lower
+There are two kinds of sub-directories in the examples folder.  Lower
 case named directories contain one or a few simple, quick-to-run
 problems.  Upper case named directories contain up to several complex
 scripts that illustrate a particular kind of simulation method or
@@ -221,10 +221,10 @@ Uppercase directories
 Nearly all of these directories have README files which give more
 details on how to understand and use their contents.
 
-The PACKAGES directory has a large number of subdirectories which
+The PACKAGES directory has a large number of sub-directories which
 correspond by name to specific packages.  They contain scripts that
 illustrate how to use the command(s) provided in those packages.  Many
-of the subdirectories have their own README files which give further
+of the sub-directories have their own README files which give further
 instructions.  See the :doc:`Packages_details <Packages_details>` doc
 page for more info on specific packages.