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

Update versions strings for the next patch release

.github/CODEOWNERS

@@ -13,44 +13,40 @@ 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/MLIAP/*           @athomps
+src/SNAP/*            @athomps
+src/SPIN/*            @julient31
 src/BROWNIAN/*        @samueljmcameron
 src/CG-DNA/*          @ohenrich
-src/CG-SDK/*        @yskmiyazaki
+src/CG-SPICA/*        @yskmiyazaki
 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/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
@@ -124,32 +120,27 @@ 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/swig/*          @akohlmey
+tools/offline/*       @rbberger
 tools/vim/*           @hammondkd
 
 # 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
@@ -158,12 +149,13 @@ 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/workflows/compile-msvc.yml

@@ -26,19 +26,15 @@ 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 PKG_PYTHON=on \
-              -D WITH_PNG=off \
-              -D WITH_JPEG=off \
               -S cmake -B build \
               -D BUILD_SHARED_LIBS=on \
               -D LAMMPS_EXCEPTIONS=on \
@@ -54,4 +50,4 @@ 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

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

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

@@ -3,31 +3,15 @@
 # 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)
 endif()
-# set policy to silence warnings about ignoring  ${CMAKE_REQUIRED_LIBRARIES} but use it
-if(POLICY CMP0075)
-  cmake_policy(SET CMP0075 NEW)
-endif()
 # set policy to silence warnings about missing executable permissions in
 # pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
 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 +100,7 @@ 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()
@@ -168,8 +152,8 @@ 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
+# set path to python interpreter and thus enforcing python version if
+# when in a virtual environment and PYTHON_EXECUTABLE is not set on command line
 if(DEFINED ENV{VIRTUAL_ENV} AND NOT PYTHON_EXECUTABLE)
   if(CMAKE_HOST_SYSTEM_NAME STREQUAL "Windows")
     set(PYTHON_EXECUTABLE "$ENV{VIRTUAL_ENV}/Scripts/python.exe")
@@ -202,8 +186,8 @@ 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})
 
@@ -221,6 +205,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES
   ADIOS
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -229,7 +214,7 @@ set(STANDARD_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS
@@ -322,15 +307,6 @@ 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()
 
@@ -394,6 +370,7 @@ 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)
@@ -403,9 +380,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
-find_package(OpenMP COMPONENTS CXX QUIET)
-if(OpenMP_CXX_FOUND)
-  check_omp_h_include()
+find_package(OpenMP QUIET)
+if(OpenMP_FOUND)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
   if(HAVE_OMP_H_INCLUDE)
     set(BUILD_OMP_DEFAULT ON)
   endif()
@@ -414,8 +391,8 @@ endif()
 option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
 
 if(BUILD_OMP)
-  find_package(OpenMP COMPONENTS CXX REQUIRED)
-  check_omp_h_include()
+  find_package(OpenMP REQUIRED)
+  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
   if(NOT HAVE_OMP_H_INCLUDE)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
@@ -439,16 +416,18 @@ endif()
 
 if(PKG_MSCG OR PKG_ATC OR PKG_AWPMD OR PKG_ML-QUIP OR PKG_LATTE OR PKG_ELECTRODE)
   enable_language(C)
-  find_package(LAPACK)
-  find_package(BLAS)
-  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND)
+  if (NOT USE_INTERNAL_LINALG)
+    find_package(LAPACK)
+    find_package(BLAS)
+  endif()
+  if(NOT LAPACK_FOUND OR NOT BLAS_FOUND OR USE_INTERNAL_LINALG)
     include(CheckGeneratorSupport)
     if(NOT CMAKE_GENERATOR_SUPPORT_FORTRAN)
       status(FATAL_ERROR "Cannot build internal linear algebra library as CMake build tool lacks Fortran support")
     endif()
     enable_language(Fortran)
-    file(GLOB LINALG_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/linalg/[^.]*.[fF])
-    add_library(linalg STATIC ${LINALG_SOURCES})
+    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>")
@@ -576,8 +555,8 @@ 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})
@@ -604,8 +583,8 @@ 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})
@@ -621,10 +600,10 @@ foreach(PKG_LIB POEMS ATC AWPMD H5MD MESONT)
     string(TOLOWER "${PKG_LIB}" PKG_LIB)
     if(PKG_LIB STREQUAL "mesont")
       enable_language(Fortran)
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
         ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)
     else()
-      file(GLOB_RECURSE ${PKG_LIB}_SOURCES ${CONFIGURE_DEPENDS}
+      file(GLOB_RECURSE ${PKG_LIB}_SOURCES
         ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.c
         ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.cpp)
     endif()
@@ -670,7 +649,7 @@ endif()
 # packages which selectively include variants based on enabled styles
 # e.g. accelerator packages
 ######################################################################
-foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
+foreach(PKG_WITH_INCL CORESHELL DPD-SMOOTH MISC PHONON QEQ OPENMP KOKKOS OPT INTEL GPU)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
   endif()
@@ -743,17 +722,18 @@ 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})
@@ -762,14 +742,6 @@ 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)
@@ -877,11 +849,8 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     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()
 
@@ -896,23 +865,6 @@ 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")
@@ -924,7 +876,6 @@ 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}")
@@ -1011,10 +962,7 @@ 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/FindCythonize.cmake

@@ -22,7 +22,7 @@ endif()
 if(Python_EXECUTABLE)
   get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
   find_program(Cythonize_EXECUTABLE
-    NAMES cythonize-${Python_VERSION_MAJOR}.${Python_VERSION_MINOR} cythonize3 cythonize cythonize.bat
+    NAMES cythonize3 cythonize cythonize.bat
     HINTS ${_python_path})
 endif()
 

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 ${_dirs})
@@ -88,18 +88,6 @@ function(get_lammps_version version_header variable)
     set(${variable} "${date}" PARENT_SCOPE)
 endfunction()
 
-# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
-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} ${newurl} PARENT_SCOPE)
-  endif()
-endfunction(GetFallbackURL)
-
 #################################################################################
 # LAMMPS C++ interface. We only need the header related parts except on windows.
 add_library(lammps INTERFACE)
@@ -124,76 +112,45 @@ if(BUILD_MPI)
   set(MPI_CXX_SKIP_MPICXX TRUE)
   # We use a non-standard procedure to cross-compile with MPI on Windows
   if((CMAKE_SYSTEM_NAME STREQUAL "Windows") AND CMAKE_CROSSCOMPILING)
-    # Download and configure MinGW compatible MPICH development files for Windows
-    option(USE_MSMPI "Use Microsoft's MS-MPI SDK instead of MPICH2-1.4.1" OFF)
-    if(USE_MSMPI)
-      message(STATUS "Downloading and configuring MS-MPI 10.1 for Windows cross-compilation")
-      set(MPICH2_WIN64_DEVEL_URL "${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

@@ -24,24 +24,9 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
-# helper function to check for usable omp.h header
-function(check_omp_h_include)
-  find_package(OpenMP COMPONENTS CXX QUIET)
-  if(OpenMP_CXX_FOUND)
-    set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
-    set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
-    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
-    set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
-    check_include_file_cxx(omp.h _have_omp_h)
-  else()
-    set(_have_omp_h FALSE)
-  endif()
-  set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
-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 +65,8 @@ 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})
@@ -100,7 +85,7 @@ endfunction()
 
 macro(pkg_depends PKG1 PKG2)
   if(PKG_${PKG1} AND NOT (PKG_${PKG2} OR BUILD_${PKG2}))
-    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be built with the ${PKG2} package")
+    message(FATAL_ERROR "The ${PKG1} package needs LAMMPS to be build with the ${PKG2} package")
   endif()
 endmacro()
 
@@ -149,15 +134,3 @@ if((CMAKE_SYSTEM_NAME STREQUAL "Linux") AND (EXISTS /etc/os-release))
   set(CMAKE_LINUX_DISTRO ${distro})
   set(CMAKE_DISTRO_VERSION ${disversion})
 endif()
-
-# determine canonical URL for downloading backup copy from download.lammps.org/thirdparty
-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

@@ -1,6 +1,6 @@
 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 "Debugging messages for Colvars (quite verbose)" OFF)
 
@@ -9,7 +9,7 @@ option(COLVARS_LEPTON "Build and link the Lepton library" ON)
 
 if(COLVARS_LEPTON)
   set(LEPTON_DIR ${LAMMPS_LIB_SOURCE_DIR}/colvars/lepton)
-  file(GLOB LEPTON_SOURCES ${CONFIGURE_DEPENDS} ${LEPTON_DIR}/src/[^.]*.cpp)
+  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)

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

@@ -26,7 +26,7 @@ elseif(GPU_PREC STREQUAL "SINGLE")
   set(GPU_PREC_SETTING "SINGLE_SINGLE")
 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")
@@ -55,7 +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"
@@ -65,15 +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
@@ -82,7 +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")
@@ -121,14 +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}
@@ -183,7 +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
     ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_gayberne_lj.cu
@@ -277,7 +276,6 @@ elseif(GPU_API STREQUAL "HIP")
     else()
       # build arch/gencode commands for nvcc based on CUDA toolkit version and use choice
       # --arch translates directly instead of JIT, so this should be for the preferred or most common architecture
-      # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
       set(HIP_CUDA_GENCODE "-arch=${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"))
@@ -307,22 +305,14 @@ 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 "")
@@ -400,17 +390,15 @@ 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/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)
@@ -16,9 +15,8 @@ if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   else()
-    # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
-      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
+    if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
+      message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
     endif()
   endif()
 endif()
@@ -53,10 +51,8 @@ if(DOWNLOAD_KOKKOS)
   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

cmake/Modules/Packages/LATTE.cmake

@@ -19,7 +19,6 @@ 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)
@@ -31,7 +30,7 @@ if(DOWNLOAD_LATTE)
 
   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/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/v1.3.2.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "836f5da400d8cff0f0e4435640f9454f" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
-  GetFallbackURL(MDI_URL MDI_FALLBACK)
   enable_language(C)
 
   # only ON/OFF are allowed for "mpi" flag when building MDI library
@@ -27,8 +26,21 @@ if(DOWNLOAD_MDI)
   # detect if we have python development support and thus can enable python plugins
   set(MDI_USE_PYTHON_PLUGINS OFF)
   if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(NOT PYTHON_VERSION_STRING)
+      set(Python_ADDITIONAL_VERSIONS 3.12 3.11 3.10 3.9 3.8 3.7 3.6)
+      # search for interpreter first, so we have a consistent library
+      find_package(PythonInterp) # Deprecated since version 3.12
+      if(PYTHONINTERP_FOUND)
+        set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
+      endif()
+    endif()
+    # search for the library matching the selected interpreter
+    set(Python_ADDITIONAL_VERSIONS ${PYTHON_VERSION_MAJOR}.${PYTHON_VERSION_MINOR})
     find_package(PythonLibs QUIET) # Deprecated since version 3.12
     if(PYTHONLIBS_FOUND)
+      if(NOT (PYTHON_VERSION_STRING STREQUAL PYTHONLIBS_VERSION_STRING))
+        message(FATAL_ERROR "Python Library version ${PYTHONLIBS_VERSION_STRING} does not match Interpreter version ${PYTHON_VERSION_STRING}")
+      endif()
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   else()
@@ -43,9 +55,9 @@ if(DOWNLOAD_MDI)
   # support cross-compilation and ninja-build
   include(ExternalProject)
   ExternalProject_Add(mdi_build
-    URL     ${MDI_URL} ${MDI_FALLBACK}
+    URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
-    CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+    CMAKE_ARGS
     -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
     -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
@@ -55,6 +67,7 @@ if(DOWNLOAD_MDI)
     -Dlanguage=C
     -Dlibtype=STATIC
     -Dmpi=${MDI_USE_MPI}
+    -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
     INSTALL_COMMAND ""

cmake/Modules/Packages/MISC.cmake

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

cmake/Modules/Packages/ML-HDNNP.cmake

@@ -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

@@ -2,13 +2,7 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
-    find_package(Python COMPONENTS NumPy QUIET)
-  else()
-    # assume we have NumPy
-    set(Python_NumPy_FOUND ON)
-  endif()
-  if(Cythonize_FOUND AND Python_NumPy_FOUND)
+  if(Cythonize_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
 endif()
@@ -17,9 +11,6 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
-  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
-    find_package(Python COMPONENTS NumPy REQUIRED)
-  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -3,23 +3,9 @@ set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2
 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(
@@ -36,8 +22,8 @@ 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 ${CONFIGURE_DEPENDS} ${lib-pace}/ML-PACE)
-file(GLOB PACE_EVALUATOR_SOURCES ${CONFIGURE_DEPENDS} ${lib-pace}/ML-PACE/*.cpp)
+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})

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

@@ -47,23 +47,22 @@ if(DOWNLOAD_PLUMED)
   endif()
   message(STATUS "PLUMED download requested - we will build our own")
   if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   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>
@@ -79,12 +78,12 @@ if(DOWNLOAD_PLUMED)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
   file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
@@ -97,7 +96,7 @@ else()
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

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/Packages/VTK.cmake

@@ -1,9 +1,4 @@
 find_package(VTK REQUIRED NO_MODULE)
+include(${VTK_USE_FILE})
 target_compile_definitions(lammps PRIVATE -DLAMMPS_VTK)
-if (VTK_MAJOR_VERSION VERSION_LESS 9.0)
-  include(${VTK_USE_FILE})
-  target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})
-else()
-  target_link_libraries(lammps PRIVATE VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
-  vtk_module_autoinit(TARGETS lammps MODULES VTK::CommonCore VTK::IOCore VTK::CommonDataModel VTK::IOXML VTK::IOLegacy VTK::IOParallelXML)
-endif()
+target_link_libraries(lammps PRIVATE ${VTK_LIBRARIES})

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

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

cmake/presets/all_on.cmake

@@ -5,6 +5,7 @@
 
 set(ALL_PACKAGES
   ADIOS
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -13,7 +14,7 @@ set(ALL_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/clang.cmake

@@ -28,3 +28,10 @@ set(MPI_CXX "clang++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 
 unset(HAVE_OMP_H_INCLUDE CACHE)
+set(OpenMP_C "clang" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "clang++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/gcc.cmake

@@ -19,3 +19,11 @@ set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Og -g -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" 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

@@ -1,4 +1,5 @@
 set(WIN_PACKAGES
+  AMOEBA
   ASPHERE
   ATC
   AWPMD
@@ -7,7 +8,7 @@ set(WIN_PACKAGES
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

cmake/presets/most.cmake

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

cmake/presets/nvhpc.cmake

@@ -1,9 +0,0 @@
-# preset that will enable Nvidia HPC SDK compilers with support for MPI and OpenMP (on Linux boxes)
-
-set(CMAKE_CXX_COMPILER "nvc++" CACHE STRING "" FORCE)
-set(CMAKE_C_COMPILER "nvc" CACHE STRING "" FORCE)
-set(CMAKE_Fortran_COMPILER "nvfortran" CACHE STRING "" FORCE)
-set(MPI_CXX "nvc++" CACHE STRING "" FORCE)
-set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
-unset(HAVE_OMP_H_INCLUDE CACHE)
-

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/pedantic.cmake

@@ -1,4 +1,4 @@
-# preset that will set gcc/g++ with extra warnings enabled and support for MPI and OpenMP (on Linux boxes)
+# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
 
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
@@ -17,3 +17,10 @@ set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
 set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
+set(OpenMP_C "gcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "g++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-fopenmp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "gomp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libgomp.so" CACHE PATH "" FORCE)

cmake/presets/pgi.cmake

@@ -7,3 +7,10 @@ set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
 set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
 unset(HAVE_OMP_H_INCLUDE CACHE)
 
+set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

cmake/presets/windows.cmake

@@ -1,11 +1,12 @@
 set(WIN_PACKAGES
+  AMOEBA
   ASPHERE
   BOCS
   BODY
   BPM
   BROWNIAN
   CG-DNA
-  CG-SDK
+  CG-SPICA
   CLASS2
   COLLOID
   COLVARS

doc/Makefile

@@ -38,14 +38,16 @@ endif
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
+#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
+
 # temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
-SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
 
 # grab list of sources from doxygen config file.
 # 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 rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -87,8 +89,6 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
-		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;\
@@ -96,7 +96,6 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		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 ;\
@@ -115,9 +114,7 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@mkdir -p fasthtml
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
-		touch $(RSTDIR)/Fortran.rst ;\
-		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
 	@rm -rf fasthtml/_sources
@@ -147,8 +144,6 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
-		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
-		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -168,15 +163,12 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(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= \
-		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
-		touch $(RSTDIR)/Fortran.rst ;\
-		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		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 ;\
@@ -222,9 +214,6 @@ 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

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" "23 June 2022 - Update 3" "2022-6-23"
+.TH LAMMPS "1" "15 September 2022" "2022-9-15"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 23 June 2022 - Update 3
+\- Molecular Dynamics Simulator.  Version 15 September 2022
 
 .SH SYNOPSIS
 .B lmp

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)

doc/src/Build_basics.rst

@@ -276,7 +276,7 @@ LAMMPS.
 
       Parallel build (see ``src/MAKE/Makefile.mpi``):
 
-      .. code-block:: make
+      .. code-block:: bash
 
          CC =            mpicxx
          CCFLAGS =       -g -O3
@@ -296,7 +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,

doc/src/Build_development.rst

@@ -140,62 +140,36 @@ 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
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
-.. admonition:: Software version requirements for testing
-   :class: note
-
-   The compiler and library version requirements for the testing
-   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.
-
 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 +200,11 @@ 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 +238,9 @@ 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 +520,7 @@ 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 +529,3 @@ 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.
 
@@ -28,16 +28,14 @@ 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>`
@@ -150,9 +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>`_
@@ -184,10 +180,17 @@ set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
+Using CHIP-SPV implementation of HIP is now supported. It allows one to run HIP
+code on Intel GPUs via the OpenCL or Level Zero backends. To use CHIP-SPV, you must
+set :code:`-DHIP_USE_DEVICE_SORT=OFF` in your CMake command line as CHIP-SPV does not
+yet support hipCUB. The use of HIP for Intel GPUs is still experimental so you
+should only use this option in preparations to run on Aurora system at ANL.
+
 .. code:: bash
 
    # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
+   export HIP_PATH=/path/to/HIP/install
    export HCC_AMDGPU_TARGET=gfx906
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
@@ -196,6 +199,7 @@ and the linker to work correctly.
 
    # AMDGPU target (ROCm >= 4.1)
    export HIP_PLATFORM=amd
+   export HIP_PATH=/path/to/HIP/install
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
    make -j 4
 
@@ -204,10 +208,20 @@ and the linker to work correctly.
    # CUDA target (not recommended, use GPU_ARCH=cuda)
    # !!! DO NOT set CMAKE_CXX_COMPILER !!!
    export HIP_PLATFORM=nvcc
+   export HIP_PATH=/path/to/HIP/install
    export CUDA_PATH=/usr/local/cuda
    cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=sm_70 ..
    make -j 4
 
+.. code:: bash
+
+   # SPIR-V target (Intel GPUs)
+   export HIP_PLATFORM=spirv
+   export HIP_PATH=/path/to/HIP/install
+   export CMAKE_CXX_COMPILER=<hipcc/clang++>
+   cmake -D PKG_GPU=on -D GPU_API=HIP ..
+   make -j 4
+
 Traditional make
 ^^^^^^^^^^^^^^^^
 
@@ -220,15 +234,15 @@ LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG``\ ,
 Makefile you use.
 
 You can also build the library in one step from the ``lammps/src`` dir,
-using a command like these, which simply invokes the ``lib/gpu/Install.py``
+using a command like these, which simply invoke the ``lib/gpu/Install.py``
 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
@@ -300,7 +314,7 @@ detailed information is available at:
 
 In addition to installing the KIM API, it is also necessary to install the
 library of KIM models (interatomic potentials).
-See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
+See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
 learn how to install a pre-build binary of the OpenKIM Repository of Models.
 See the list of all KIM models here: https://openkim.org/browse/models
 
@@ -336,18 +350,18 @@ minutes to hours) to build.  Of course you only need to do that once.)
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
       this in one step from the lammps/src directory, using a command like
-      these, which simply invokes the ``lib/kim/Install.py`` script with
+      these, which simply invoke the ``lib/kim/Install.py`` script with
       the specified args.
 
       .. 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
@@ -359,7 +373,7 @@ 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
@@ -418,7 +432,7 @@ Enabling the extra unit tests have some requirements,
   ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
   ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
   ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
-  See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_
+  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
   to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
   `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
@@ -793,8 +807,10 @@ library.
 
       .. code-block:: bash
 
-         -D DOWNLOAD_LATTE=value    # download LATTE for build, value = no (default) or yes
-         -D LATTE_LIBRARY=path      # LATTE library file (only needed if a custom location)
+         -D DOWNLOAD_LATTE=value      # download LATTE for build, value = no (default) or yes
+         -D LATTE_LIBRARY=path        # LATTE library file (only needed if a custom location)
+         -D USE_INTERNAL_LINALG=value # Use the internal linear algebra library instead of LAPACK
+                                      #   value = no (default) or yes
 
       If ``DOWNLOAD_LATTE`` is set, the LATTE library will be downloaded
       and built inside the CMake build directory.  If the LATTE library
@@ -802,6 +818,13 @@ library.
       ``LATTE_LIBRARY`` is the filename (plus path) of the LATTE library
       file, not the directory the library file is in.
 
+      The LATTE library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the LATTE build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
+
    .. tab:: Traditional make
 
       You can download and build the LATTE library manually if you
@@ -812,11 +835,11 @@ 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
@@ -910,17 +933,17 @@ more details.
       You can download and build the MS-CG library manually if you
       prefer; follow the instructions in ``lib/mscg/README``\ .  You can
       also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
+      command like these, which simply invoke the
       ``lib/mscg/Install.py`` script with the specified args:
 
       .. 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
@@ -967,15 +990,15 @@ POEMS package
       ``lib/poems``\ .  You can do this manually if you prefer; follow
       the instructions in ``lib/poems/README``\ .  You can also do it in
       one step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/poems/Install.py`` script with the
+      which simply invoke the ``lib/poems/Install.py`` script with the
       specified args:
 
       .. 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
@@ -1030,7 +1053,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
+`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
 binary package provided by your operating system.
 
 .. tabs::
@@ -1056,15 +1079,15 @@ binary package provided by your operating system.
       You can download and build the Voro++ library manually if you
       prefer; follow the instructions in ``lib/voronoi/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
+      command like these, which simply invoke the
       ``lib/voronoi/Install.py`` script with the specified args:
 
       .. 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++
@@ -1105,13 +1128,13 @@ 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
 
 ----------
 
@@ -1135,15 +1158,15 @@ The ATC package requires the MANYBODY package also be installed.
       ``lib/atc``.  You can do this manually if you prefer; follow the
       instructions in ``lib/atc/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/atc/Install.py`` script with the
+      which simply invoke the ``lib/atc/Install.py`` script with the
       specified args:
 
       .. 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
@@ -1162,17 +1185,17 @@ 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::
 
@@ -1186,15 +1209,15 @@ AWPMD package
       ``lib/awpmd``.  You can do this manually if you prefer; follow the
       instructions in ``lib/awpmd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/awpmd/Install.py`` script with the
+      which simply invoke the ``lib/awpmd/Install.py`` script with the
       specified args:
 
       .. 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
@@ -1213,20 +1236,21 @@ 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::
@@ -1248,15 +1272,15 @@ module included in the LAMMPS source distribution.
 
       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
+      directory using a command like these, which simply invoke 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 to use as build recipe.  If it does not already
@@ -1268,8 +1292,8 @@ module included in the LAMMPS source distribution.
 
       .. 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``
       (which also includes Lepton objects if enabled) and the specification file
@@ -1289,40 +1313,27 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
-      ``-D PKG_ELECTRODE=yes``.
+      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
+      PKG_ELECTRODE=yes``.
 
    .. tab:: Traditional make
 
-      Before building LAMMPS, you must configure the ELECTRODE support
-      libraries and settings in ``lib/electrode``.  You can do this
-      manually, if you prefer, or do it in one step from the
-      ``lammps/src`` dir, using a command like these, which simply
-      invokes the ``lib/electrode/Install.py`` script with the specified
-      args:
+      The package is activated with ``make yes-KSPACE`` and ``make
+      yes-ELECTRODE``
+
+
+      Note that the ``Makefile.lammps`` file has settings for the BLAS and
+      LAPACK linear algebra libraries.  As explained in ``lib/awpmd/README``
+      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-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
-      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 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``
+         $ 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
 
 ----------
 
@@ -1359,8 +1370,8 @@ 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.
 
@@ -1459,10 +1470,10 @@ 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``
@@ -1475,8 +1486,8 @@ 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
@@ -1523,13 +1534,13 @@ the HDF5 library.
       ``lib/h5md``.  You can do this manually if you prefer; follow the
       instructions in ``lib/h5md/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/h5md/Install.py`` script with the
+      which simply invoke the ``lib/h5md/Install.py`` script with the
       specified args:
 
       .. 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
@@ -1579,14 +1590,14 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
       You can download and build the *n2p2* library manually if you prefer;
       follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
       one step from the ``lammps/src`` dir, using a command like these, which
-      simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
+      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
 
       .. 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
@@ -1686,8 +1697,8 @@ 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``\ .
@@ -1716,14 +1727,14 @@ they will be downloaded the first time this package is installed.
       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
+      invoke 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
+         $ 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
@@ -1836,22 +1847,6 @@ 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:
@@ -1901,15 +1896,15 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       ``lib/qmmm``.  You can do this manually if you prefer; follow the
       first two steps explained in ``lib/qmmm/README``.  You can also do
       it in one step from the ``lammps/src`` dir, using a command like
-      these, which simply invokes the ``lib/qmmm/Install.py`` script with
+      these, which simply invoke the ``lib/qmmm/Install.py`` script with
       the specified args:
 
       .. 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
@@ -1948,12 +1943,23 @@ 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.
+      CMake will try to download and build the QUIP library from GitHub,
+      if it is not found on the local machine. This requires to have git
+      installed. It will use the same compilers and flags as used for
+      compiling LAMMPS.  Currently this is only supported for the GNU
+      and the Intel compilers. Set the ``QUIP_LIBRARY`` variable if you
+      want to use a previously compiled and installed QUIP library and
+      CMake cannot find it.
+
+      The QUIP library requires LAPACK (and BLAS) and CMake can identify
+      their locations and pass that info to the QUIP build script. But
+      on some systems this triggers a (current) limitation of CMake and
+      the configuration will fail. Try enabling ``USE_INTERNAL_LINALG`` in
+      those cases to use the bundled linear algebra library and work around
+      the limitation.
 
    .. tab:: Traditional make
 
@@ -1998,7 +2004,7 @@ To build with this package, you must download and build the
       You can download and build the ScaFaCoS library manually if you
       prefer; follow the instructions in ``lib/scafacos/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invokes the
+      command like these, which simply invoke the
       ``lib/scafacos/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -2042,14 +2048,14 @@ Eigen3 is a template library, so you do not need to build it.
       You can download the Eigen3 library manually if you prefer; follow
       the instructions in ``lib/smd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invokes the ``lib/smd/Install.py`` script with the
+      which simply invoke the ``lib/smd/Install.py`` script with the
       specified args:
 
       .. 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

@@ -209,7 +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)
@@ -222,7 +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_manual.rst

@@ -125,29 +125,38 @@ 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 +176,7 @@ math expressions transparently into embedded images.
 For converting the generated ePUB file to a MOBI format file (for e-book
 readers, like Kindle, that cannot read ePUB), you also need to have the
 ``ebook-convert`` tool from the "calibre" software
-installed. `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 +216,9 @@ 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:

doc/src/Build_package.rst

@@ -30,16 +30,14 @@ 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>`
@@ -47,10 +45,7 @@ packages:
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
    * :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-QUIP <ml-quip>`
    * :ref:`MOLFILE <molfile>`

doc/src/Build_settings.rst

@@ -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

doc/src/Commands.rst

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

doc/src/Commands_all.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 General commands
 ================
@@ -62,6 +63,7 @@ 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>`

doc/src/Commands_bond.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 .. _bond:
 
@@ -43,6 +44,7 @@ OPT.
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
    * :doc:`harmonic/shift/cut (o) <bond_harmonic_shift_cut>`
+   * :doc:`mesocnt <bond_mesocnt>`
    * :doc:`mm3 <bond_mm3>`
    * :doc:`morse (o) <bond_morse>`
    * :doc:`nonlinear (o) <bond_nonlinear>`
@@ -74,6 +76,7 @@ OPT.
    *
    *
    *
+   * :doc:`amoeba <angle_amoeba>`
    * :doc:`charmm (iko) <angle_charmm>`
    * :doc:`class2 (ko) <angle_class2>`
    * :doc:`class2/p6 <angle_class2>`
@@ -90,9 +93,10 @@ OPT.
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
    * :doc:`gaussian <angle_gaussian>`
    * :doc:`harmonic (iko) <angle_harmonic>`
+   * :doc:`mesocnt <angle_mesocnt>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
-   * :doc:`sdk (o) <angle_sdk>`
+   * :doc:`spica (o) <angle_spica>`
    * :doc:`table (o) <angle_table>`
 
 .. _dihedral:
@@ -152,6 +156,7 @@ OPT.
    *
    *
    *
+   * :doc:`amoeba <improper_amoeba>`
    * :doc:`class2 (ko) <improper_class2>`
    * :doc:`cossq (o) <improper_cossq>`
    * :doc:`cvff (io) <improper_cvff>`

doc/src/Commands_compute.rst

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

doc/src/Commands_dump.rst

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

doc/src/Commands_fix.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Fix commands
 ============
@@ -28,6 +29,8 @@ OPT.
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
    * :doc:`addtorque <fix_addtorque>`
+   * :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
+   * :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
    * :doc:`append/atoms <fix_append_atoms>`
    * :doc:`atc <fix_atc>`
    * :doc:`atom/swap <fix_atom_swap>`
@@ -40,6 +43,9 @@ OPT.
    * :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>`
@@ -47,9 +53,6 @@ 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>`
@@ -103,7 +106,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
-   * :doc:`mdi/aimd <fix_mdi_aimd>`
+   * :doc:`mdi/qm <fix_mdi_qm>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
@@ -162,6 +165,7 @@ OPT.
    * :doc:`orient/fcc <fix_orient>`
    * :doc:`orient/eco <fix_orient_eco>`
    * :doc:`pafi <fix_pafi>`
+   * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
    * :doc:`pimd <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`

doc/src/Commands_kspace.rst

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

doc/src/Commands_pair.rst

@@ -10,6 +10,7 @@
    * :ref:`Dihedral styles <dihedral>`
    * :ref:`Improper styles <improper>`
    * :doc:`KSpace styles <Commands_kspace>`
+   * :doc:`Dump styles <Commands_dump>`
 
 Pair_style potentials
 ======================
@@ -38,6 +39,7 @@ OPT.
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
    * :doc:`airebo/morse (io) <pair_airebo>`
+   * :doc:`amoeba <pair_amoeba>`
    * :doc:`atm <pair_atm>`
    * :doc:`awpmd/cut <pair_awpmd>`
    * :doc:`beck (go) <pair_beck>`
@@ -91,8 +93,8 @@ 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>`
@@ -124,6 +126,7 @@ OPT.
    * :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
    * :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
    * :doc:`hdnnp <pair_hdnnp>`
+   * :doc:`hippo <pair_amoeba>`
    * :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
    * :doc:`ilp/tmd (t) <pair_ilp_tmd>`
    * :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@@ -179,9 +182,9 @@ OPT.
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
    * :doc:`lj/relres (o) <pair_lj_relres>`
-   * :doc:`lj/sdk (gko) <pair_sdk>`
-   * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
-   * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
+   * :doc:`lj/spica (gko) <pair_spica>`
+   * :doc:`lj/spica/coul/long (go) <pair_spica>`
+   * :doc:`lj/spica/coul/msm (o) <pair_spica>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
    * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
@@ -194,10 +197,11 @@ OPT.
    * :doc:`lubricateU/poly <pair_lubricateU>`
    * :doc:`mdpd <pair_mesodpd>`
    * :doc:`mdpd/rhosum <pair_mesodpd>`
-   * :doc:`meam <pair_meam>`
+   * :doc:`meam (k) <pair_meam>`
    * :doc:`meam/spline (o) <pair_meam_spline>`
    * :doc:`meam/sw/spline <pair_meam_sw_spline>`
    * :doc:`mesocnt <pair_mesocnt>`
+   * :doc:`mesocnt/viscous <pair_mesocnt>`
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
@@ -268,6 +272,7 @@ OPT.
    * :doc:`spin/magelec <pair_spin_magelec>`
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
+   * :doc:`srp/react <pair_srp>`
    * :doc:`sw (giko) <pair_sw>`
    * :doc:`sw/angle/table <pair_sw_angle_table>`
    * :doc:`sw/mod (o) <pair_sw>`

doc/src/Commands_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
@@ -33,21 +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.
+: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
 -----------------
@@ -66,6 +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_code_design.rst

@@ -50,7 +50,7 @@ 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();
@@ -78,7 +78,7 @@ 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
@@ -87,9 +87,9 @@ 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
@@ -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 *);
@@ -360,7 +360,7 @@ characters; "{:<8}" would do this as left aligned, "{:^8}" as centered,
 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",

doc/src/Developer_notes.rst

@@ -105,7 +105,7 @@ list, where each pair of atoms is listed only once (except when the
 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);
 

doc/src/Developer_parallel.rst

@@ -3,9 +3,9 @@ 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 sub-domain assigned to an MPI
 process.  For clarity, most of the following illustrations show the 2d

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)
    {
@@ -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

@@ -7,7 +7,7 @@ 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
+contact developer@lammps.org in case you run across an issue that is not
 (yet) listed here.  Please also review the latest information about the
 LAMMPS :doc:`programming style conventions <Modify_style>`, especially
 if you are considering to submit the updated version for inclusion into
@@ -61,7 +61,7 @@ header file needs to be updated accordingly.
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    int PairEAM::pack_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -75,7 +75,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    int PairEAM::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
    {
@@ -112,14 +112,14 @@ Example from a pair style:
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    if (eflag || vflag) ev_setup(eflag, vflag);
    else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    ev_init(eflag, vflag);
 
@@ -142,14 +142,14 @@ when they are called from only one or a subset of the MPI processes.
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
     val = force->numeric(FLERR, arg[1]);
     num = force->inumeric(FLERR, arg[2]);
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
     val = utils::numeric(FLERR, true, arg[1], lmp);
     num = utils::inumeric(FLERR, false, arg[2], lmp);
@@ -183,14 +183,14 @@ copy them around for simulations.
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    fp = force->open_potential(filename);
    fp = fopen(filename, "r");
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    fp = utils::open_potential(filename, lmp);
 
@@ -207,7 +207,7 @@ Example:
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    if (fptr == NULL) {
      char str[128];
@@ -217,7 +217,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    if (fptr == nullptr)
      error->one(FLERR, "Cannot open AEAM potential file {}: {}", filename, utils::getsyserror());
@@ -237,7 +237,7 @@ an example from the ``FixWallReflect`` class:
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    FixWallReflect(class LAMMPS *, int, char **);
    virtual ~FixWallReflect();
@@ -247,7 +247,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    FixWallReflect(class LAMMPS *, int, char **);
    ~FixWallReflect() override;
@@ -271,7 +271,7 @@ the type of the "this" pointer argument.
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    comm->forward_comm_pair(this);
    comm->forward_comm_fix(this);
@@ -284,7 +284,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    comm->forward_comm(this);
    comm->reverse_comm(this);
@@ -304,7 +304,7 @@ requests can be :doc:`found here <Developer_notes>`. Example from the
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    int irequest = neighbor->request(this,instance_me);
    neighbor->requests[irequest]->pair = 0;
@@ -317,7 +317,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    auto req = neighbor->add_request(this, NeighConst::REQ_OCCASIONAL);
    if (cutflag) req->set_cutoff(mycutneigh);
@@ -340,7 +340,7 @@ these are internal fixes, there is no user visible change.
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    #include "fix_store.h"
 
@@ -351,7 +351,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    #include "fix_store_peratom.h"
 
@@ -362,7 +362,7 @@ New:
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    #include "fix_store.h"
 
@@ -373,7 +373,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. code-block:: C++
 
    #include "fix_store_global.h"
 
@@ -396,7 +396,7 @@ the dump directly.  Example:
 
 Old:
 
-.. code-block:: c++
+.. code-block:: C++
 
    int idump = output->find_dump(arg[iarg+1]);
    if (idump < 0)
@@ -412,7 +412,7 @@ Old:
 
 New:
 
-.. code-block:: c++
+.. 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]);

doc/src/Developer_utils.rst

@@ -154,6 +154,9 @@ and parsing files or arguments.
 .. doxygenfunction:: trim_and_count_words
    :project: progguide
 
+.. doxygenfunction:: join_words
+   :project: progguide
+
 .. doxygenfunction:: split_words
    :project: progguide
 
@@ -172,6 +175,12 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
+.. doxygenfunction:: is_id
+   :project: progguide
+
+.. doxygenfunction:: is_type
+   :project: progguide
+
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 
@@ -202,6 +211,9 @@ Argument processing
 .. doxygenfunction:: expand_args
    :project: progguide
 
+.. doxygenfunction:: expand_type
+   :project: progguide
+
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
@@ -305,7 +317,7 @@ 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"
@@ -337,7 +349,7 @@ 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"
@@ -415,7 +427,7 @@ 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;
@@ -464,7 +476,7 @@ 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");
@@ -543,7 +555,7 @@ 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"

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_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/sdk/kk*
+*Cannot use chosen neighbor list style with lj/spica/kk*
    That style is not supported by Kokkos.
 
 *Cannot use chosen neighbor list style with pair eam/kk*
@@ -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/sdk/coul/long/gpu pair style*
+*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
    Self-explanatory.
 
-*Cannot use newton pair with lj/sdk/gpu pair style*
+*Cannot use newton pair with lj/spica/gpu pair style*
    Self-explanatory.
 
 *Cannot use newton pair with lj96/cut/gpu pair style*
@@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    Mass command must set a type from 1-N where N is the number of atom
    types.
 
+*Invalid label2type() function syntax in variable formula*
+   The first argument must be a label map kind (atom, bond, angle,
+   dihedral, or improper) and the second argument must be a valid type
+   label that has been assigned to a numeric type.
+
 *Invalid use of library file() function*
    This function is called through the library interface.  This
    error should not occur.  Contact the developers if it does.
@@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *LJ6 off not supported in pair_style buck/long/coul/long*
    Self-explanatory.
 
+*Label map is incomplete: all types must be assigned a unique type label*
+   For a given type-kind (atom types, bond types, etc.) to be written to
+   the data file, all associated types must be assigned a type label, and
+   each type label can be assigned to only one numeric type.
+
 *Label wasn't found in input script*
    Self-explanatory.
 
+*Labelmap command before simulation box is defined*
+   The labelmap command cannot be used before a read_data,
+   read_restart, or create_box command.
+
 *Lattice orient vectors are not orthogonal*
    The three specified lattice orientation vectors must be mutually
    orthogonal.
@@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
 *Must not have multiple fixes change box parameter ...*
    Self-explanatory.
 
+*Must read Angle Type Labels before Angles*
+   An Angle Type Labels section of a data file must come before the Angles section.
+
+*Must read Atom Type Labels before Atoms*
+   An Atom Type Labels section of a data file must come before the Atoms section.
+
 *Must read Atoms before Angles*
    The Atoms section of a data file must come before an Angles section.
 
@@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
    The Atoms section of a data file must come before a Velocities
    section.
 
+*Must read Bond Type Labels before Bonds*
+   A Bond Type Labels section of a data file must come before the Bonds section.
+
+*Must read Dihedral Type Labels before Dihedrals*
+   An Dihedral Type Labels section of a data file must come before the Dihedrals section.
+
+*Must read Improper Type Labels before Impropers*
+   An Improper Type Labels section of a data file must come before the Impropers section.
+
 *Must re-specify non-restarted pair style (xxx) after read_restart*
    For pair styles, that do not store their settings in a restart file,
    it must be defined with a new 'pair_style' command after read_restart.
@@ -6782,7 +6811,7 @@ keyword to allow for additional bonds to be formed
    This is because the computation of constraint forces within a water
    molecule adds forces to atoms owned by other processors.
 
-*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
+*Pair style lj/spica/coul/long/gpu requires atom attribute q*
    The atom style defined does not have this attribute.
 
 *Pair style nb3b/harmonic requires atom IDs*
@@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
    Number of local atoms times number of columns must fit in a 32-bit
    integer for dump.
 
+*Topology type exceeds system topology type*
+   The number of bond, angle, etc types exceeds the system setting. See
+   the create_box or read_data command for how to specify these values.
+
 *Tree structure in joint connections*
    Fix poems cannot (yet) work with coupled bodies whose joints connect
    the bodies in a tree structure.
@@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
 *Two groups cannot be the same in fix spring couple*
    Self-explanatory.
 
+*The %s type label %s is already in use for type %s*
+   For a given type-kind (atom types, bond types, etc.), a given type
+   label can be assigned to only one numeric type.
+
+*Type label string %s for %s type %s is invalid*
+   See the labelmap command documentation for valid type labels.
+
 *Unable to initialize accelerator for use*
    There was a problem initializing an accelerator for the gpu package
 

doc/src/Errors_warnings.rst

@@ -470,6 +470,12 @@ This will most likely cause errors in kinetic fluctuations.
 *More than one compute sna/atom*
    Self-explanatory.
 
+*More than one compute sna/grid*
+   Self-explanatory.
+
+*More than one compute sna/grid/local*
+   Self-explanatory.
+
 *More than one compute snad/atom*
    Self-explanatory.
 

doc/src/Fortran.rst

@@ -1,51 +1,32 @@
-The :f:mod:`LIBLAMMPS` Fortran Module
-*************************************
+The ``LIBLAMMPS`` Fortran Module
+********************************
 
-The :f:mod:`LIBLAMMPS` module provides an interface to call LAMMPS from
-Fortran.  It is based on the LAMMPS C library interface and requires a
-fully Fortran 2003-compatible compiler to be compiled.  It is designed
-to be self-contained and not require any support functions written in C,
-C++, or Fortran other than those in the C library interface and the
-LAMMPS Fortran module itself.
+The ``LIBLAMMPS`` module provides an interface to call LAMMPS from a
+Fortran code.  It is based on the LAMMPS C-library interface and
+requires a Fortran 2003 compatible compiler to be compiled.
 
 While C libraries have a defined binary interface (ABI) and can thus be
-used from multiple compiler versions from different vendors as long as
-they are compatible with the hosting operating system, the same is not
-true for Fortran programs.  Thus, the LAMMPS Fortran module needs to be
+used from multiple compiler versions from different vendors for as long
+as they are compatible with the hosting operating system, the same is
+not true for Fortran codes.  Thus the LAMMPS Fortran module needs to be
 compiled alongside the code using it from the source code in
-``fortran/lammps.f90`` *and* with the same compiler used to build the
-rest of the Fortran code that interfaces to LAMMPS.  When linking, you
-also need to :doc:`link to the LAMMPS library <Build_link>`.  A typical
-command line for a simple program using the Fortran interface would be:
+``fortran/lammps.f90``.  When linking, you also need to
+:doc:`link to the LAMMPS library <Build_link>`.  A typical command line
+for a simple program using the Fortran interface would be:
 
 .. code-block:: bash
 
-   mpifort -o testlib.x lammps.f90 testlib.f90 -L. -llammps
+   mpifort -o testlib.x  lammps.f90 testlib.f90 -L. -llammps
 
-Please note that the MPI compiler wrapper is only required when the
-calling the library *from* an MPI-parallelized program.  Otherwise,
-using the plain Fortran compiler (gfortran, ifort, flang, etc.) will
-suffice, since there are no direct references to MPI library features,
-definitions and subroutine calls; MPI communicators are referred to by
-their integer index representation as required by the Fortran MPI
-interface.  It may be necessary to link to additional libraries,
-depending on how LAMMPS was configured and whether the LAMMPS library
-:doc:`was compiled as a static or dynamic library <Build_link>`.
+Please note, that the MPI compiler wrapper is only required when the
+calling the library from an MPI parallel code.  Please also note the
+order of the source files: the ``lammps.f90`` file needs to be compiled
+first, since it provides the ``LIBLAMMPS`` module that is imported by
+the Fortran code using the interface.  A working example code can be
+found together with equivalent examples in C and C++ in the
+``examples/COUPLE/simple`` folder of the LAMMPS distribution.
 
-If the LAMMPS library itself has been compiled with MPI support, the
-resulting executable will be able to run LAMMPS in parallel with
-``mpirun``, ``mpiexec``, or equivalent.  This may be either on the
-"world" communicator or a sub-communicator created by the calling
-Fortran code.  If, on the other hand, the LAMMPS library has been
-compiled **without** MPI support, each LAMMPS instance will run
-independently using just one processor.
-
-Please also note that the order of the source files matters: the
-``lammps.f90`` file needs to be compiled first, since it provides the
-:f:mod:`LIBLAMMPS` module that would need to be imported by the calling
-Fortran code in order to uses the Fortran interface.
-A working example can be found together with equivalent examples in C and
-C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
+.. versionadded:: 9Oct2020
 
 .. admonition:: Work in Progress
    :class: note
@@ -57,53 +38,53 @@ C++ in the ``examples/COUPLE/simple`` folder of the LAMMPS distribution.
 
 .. note::
 
-   A contributed (and complete!) Fortran interface that more
-   closely resembles the C-library interface is available
-   in the ``examples/COUPLE/fortran2`` folder.  Please see the
-   ``README`` file in that folder for more information about it
-   and how to contact its author and maintainer.
+   A contributed (and more complete!) Fortran interface that more
+   closely resembles the C-library interface is available in the
+   ``examples/COUPLE/fortran2`` folder.  Please see the ``README`` file
+   in that folder for more information about it and how to contact its
+   author and maintainer.
 
 ----------
 
 Creating or deleting a LAMMPS object
 ************************************
 
-With the Fortran interface, the creation of a :cpp:class:`LAMMPS
+With the Fortran interface the creation of a :cpp:class:`LAMMPS
 <LAMMPS_NS::LAMMPS>` instance is included in the constructor for
 creating the :f:func:`lammps` derived type.  To import the definition of
-that type and its type-bound procedures, you need to add a ``USE LIBLAMMPS``
-statement.  Internally, it will call either
+that type and its type bound procedures you need to add a ``USE
+LIBLAMMPS`` statement.  Internally it will call either
 :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi` from
 the C library API to create the class instance.  All arguments are
-optional and :cpp:func:`lammps_mpi_init` will be called automatically
-if it is needed.  Similarly, a possible call to
-:cpp:func:`lammps_mpi_finalize` is integrated into the :f:func:`close`
-function and triggered with the optional logical argument set to
-``.TRUE.``. Here is a simple example:
+optional and :cpp:func:`lammps_mpi_init` will be called automatically,
+if it is needed.  Similarly, a possible call to :cpp:func:`lammps_finalize`
+is integrated into the :f:func:`close` function and triggered with
+the optional logical argument set to ``.true.``. Here is a simple example:
 
 .. code-block:: fortran
 
    PROGRAM testlib
      USE LIBLAMMPS                 ! include the LAMMPS library interface
      IMPLICIT NONE
-     TYPE(lammps) :: lmp           ! derived type to hold LAMMPS instance
-     CHARACTER(LEN=12), PARAMETER :: args(3) = &
-         [ CHARACTER(LEN=12) :: 'liblammps', '-log', 'none' ]
+     TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
+     CHARACTER(len=*), PARAMETER :: args(3) = &
+         [ CHARACTER(len=12) :: 'liblammps', '-log', 'none' ]
 
      ! create a LAMMPS instance (and initialize MPI)
      lmp = lammps(args)
      ! get and print numerical version code
      PRINT*, 'LAMMPS Version: ', lmp%version()
-     ! delete LAMMPS instance (and shutdown MPI)
-     CALL lmp%close(.TRUE.)
+     ! delete LAMMPS instance (and shuts down MPI)
+     CALL lmp%close(.true.)
+
    END PROGRAM testlib
 
 It is also possible to pass command line flags from Fortran to C/C++ and
-thus make the resulting executable behave similarly to the standalone
-executable (it will ignore the `-in/-i` flag, though).  This allows
-using the command line to configure accelerator and suffix settings,
+thus make the resulting executable behave similar to the standalone
+executable (it will ignore the `-in/-i` flag, though).  This allows to
+use the command line to configure accelerator and suffix settings,
 configure screen and logfile output, or to set index style variables
-from the command line and more.  Here is a correspondingly adapted
+from the command line and more. Here is a correspondingly adapted
 version of the previous example:
 
 .. code-block:: fortran
@@ -111,8 +92,8 @@ version of the previous example:
    PROGRAM testlib2
      USE LIBLAMMPS                 ! include the LAMMPS library interface
      IMPLICIT NONE
-     TYPE(lammps) :: lmp           ! derived type to hold LAMMPS instance
-     CHARACTER(LEN=128), ALLOCATABLE :: command_args(:)
+     TYPE(lammps)     :: lmp       ! derived type to hold LAMMPS instance
+     CHARACTER(len=128), ALLOCATABLE :: command_args(:)
      INTEGER :: i, argc
 
      ! copy command line flags to `command_args()`
@@ -130,34 +111,35 @@ version of the previous example:
      ! delete LAMMPS instance (and shuts down MPI)
      CALL lmp%close(.TRUE.)
      DEALLOCATE(command_args)
+
    END PROGRAM testlib2
 
 --------------------
 
 Executing LAMMPS commands
-*************************
+=========================
 
 Once a LAMMPS instance is created, it is possible to "drive" the LAMMPS
-simulation by telling LAMMPS to read commands from a file or to pass
+simulation by telling LAMMPS to read commands from a file, or pass
 individual or multiple commands from strings or lists of strings.  This
-is done similarly to how it is implemented in the :doc:`C library
-interface <Library_execute>`. Before handing off the calls to the
-C library interface, the corresponding Fortran versions of the calls
+is done similar to how it is implemented in the `C-library
+<pg_lib_execute>` interface. Before handing off the calls to the
+C-library interface, the corresponding Fortran versions of the calls
 (:f:func:`file`, :f:func:`command`, :f:func:`commands_list`, and
-:f:func:`commands_string`) have to make copies of the strings passed as
+:f:func:`commands_string`) have to make a copy of the strings passed as
 arguments so that they can be modified to be compatible with the
 requirements of strings in C without affecting the original strings.
 Those copies are automatically deleted after the functions return.
-Below is a small demonstration of the uses of the different functions.
+Below is a small demonstration of the uses of the different functions:
 
 .. code-block:: fortran
 
    PROGRAM testcmd
      USE LIBLAMMPS
-     TYPE(lammps) :: lmp
-     CHARACTER(LEN=512) :: cmds
-     CHARACTER(LEN=40), ALLOCATABLE :: cmdlist(:)
-     CHARACTER(LEN=10) :: trimmed
+     TYPE(lammps)     :: lmp
+     CHARACTER(len=512) :: cmds
+     CHARACTER(len=40), ALLOCATABLE :: cmdlist(:)
+     CHARACTER(len=10) :: trimmed
      INTEGER :: i
 
      lmp = lammps()
@@ -166,9 +148,9 @@ Below is a small demonstration of the uses of the different functions.
      ! define 10 groups of 10 atoms each
      ALLOCATE(cmdlist(10))
      DO i=1, 10
-       WRITE(trimmed,'(I10)') 10*i
-       WRITE(cmdlist(i),'(A,I1,A,I10,A,A)')       &
-           'group g', i-1, ' id ', 10*(i-1)+1, ':', ADJUSTL(trimmed)
+         WRITE(trimmed,'(I10)') 10*i
+         WRITE(cmdlist(i),'(A,I1,A,I10,A,A)')       &
+             'group g', i-1, ' id ', 10*(i-1)+1, ':', ADJUSTL(trimmed)
      END DO
      CALL lmp%commands_list(cmdlist)
      ! run multiple commands from multi-line string
@@ -178,6 +160,7 @@ Below is a small demonstration of the uses of the different functions.
          'create_atoms 1 single 1.0 1.0 ${zpos}'
      CALL lmp%commands_string(cmds)
      CALL lmp%close(.TRUE.)
+
    END PROGRAM testcmd
 
 ---------------
@@ -190,9 +173,9 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
 
 .. f:type:: lammps
 
-   Derived type that is the general class of the Fortran interface.
-   It holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
-   that any of the included calls are forwarded to.
+   Derived type that is the general class of the Fortran interface.  It
+   holds a reference to the :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>`
+   class instance that any of the included calls are forwarded to.
 
    :f c_ptr handle: reference to the LAMMPS class
    :f close: :f:func:`close`
@@ -255,7 +238,7 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    This method will call :cpp:func:`lammps_commands_list` to have LAMMPS
    execute a list of input lines.
 
-   :p character(len=*) cmd(*): list of LAMMPS input lines
+   :p character(len=*) cmd(:): list of LAMMPS input lines
 
 .. f:subroutine:: commands_string(str)
 
@@ -263,4 +246,3 @@ of the contents of the ``LIBLAMMPS`` Fortran interface to LAMMPS.
    execute a block of commands from a string.
 
    :p character(len=*) str: LAMMPS input in string
-

doc/src/Howto.rst

@@ -34,6 +34,7 @@ Settings howto
    :maxdepth: 1
 
    Howto_2d
+   Howto_type_labels
    Howto_triclinic
    Howto_thermostat
    Howto_barostat
@@ -65,6 +66,7 @@ Force fields howto
    :maxdepth: 1
 
    Howto_bioFF
+   Howto_amoeba
    Howto_tip3p
    Howto_tip4p
    Howto_spc
@@ -83,7 +85,6 @@ Packages howto
    Howto_coreshell
    Howto_drude
    Howto_drude2
-   Howto_peri
    Howto_manifold
    Howto_spins
 

doc/src/Howto_amoeba.rst

@@ -0,0 +1,324 @@
+AMOEBA and HIPPO force fields
+=============================
+
+The AMOEBA and HIPPO polarizable force fields were developed by Jay
+Ponder's group at the U Washington at St Louis.  The LAMMPS
+implementation is based on Fortran 90 code provided by the Ponder
+group in their `Tinker MD software <https://dasher.wustl.edu/tinker/>`_.
+
+The current implementation (July 2022) of AMOEBA in LAMMPS matches the
+version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
+<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`.  Likewise the current
+implementation of HIPPO in LAMMPS matches the version discussed in
+:ref:`(Rackers) <amoeba-Rackers>`.
+
+These force fields can be used when polarization effects are desired
+in simulations of water, organic molecules, and biomolecules including
+proteins, provided that parameterizations (Tinker PRM force field
+files) are available for the systems you are interested in.  Files in
+the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
+be used.  The Tinker distribution and website have additional force
+field files as well:
+`https://github.com/TinkerTools/tinker/tree/release/params
+<https://github.com/TinkerTools/tinker/tree/release/params>`_.
+
+Note that currently, HIPPO can only be used for water systems, but
+HIPPO files for a variety of small organic and biomolecules are in
+preparation by the Ponder group.  Those force field files will be
+included in the LAMMPS distribution when available.
+
+To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
+fully periodic or fully non-periodic, and use an orthogonal (not
+triclinic) simulation box.
+
+----------
+
+The AMOEBA and HIPPO force fields contain the following terms in their
+energy (U) computation.  Further details for AMOEBA equations are in
+:ref:`(Ponder) <amoeba-Ponder>`, further details for the HIPPO
+equations are in :ref:`(Rackers) <amoeba-Rackers>`.
+
+.. math::
+
+  U & = U_{intermolecular} + U_{intramolecular} \\
+  U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
+  U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
+
+For intermolecular terms, the AMOEBA force field includes only the
+:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms.  The
+HIPPO force field includes all but the :math:`U_{hal}` term.  In
+LAMMPS, these are all computed by the :doc:`pair_style amoeba or hippo
+<pair_style>` command.  Note that the :math:`U_{multipole}` and
+:math:`U_{polar}` terms in this formula are not the same for the
+AMOEBA and HIPPO force fields.
+
+For intramolecular terms, the :math:`U_{bond}`, :math:`U_{angle}`,
+:math:`U_{torsion}`, :math:`U_{oop}` terms are computed by the
+:doc:`bond_style class2 <bond_class2>` :doc:`angle_style amoeba
+<angle_amoeba>`, :doc:`dihedral_style fourier <dihedral_fourier>`, and
+:doc:`improper_style amoeba <improper_amoeba>` commands respectively.
+The :doc:`angle_style amoeba <angle_amoeba>` command includes the
+:math:`U_{b\theta}` bond-angle cross term, and the :math:`U_{UB}` term
+for a Urey-Bradley bond contribution between the I,K atoms in the IJK
+angle.
+
+The :math:`U_{pitorsion}` term is computed by the :doc:`fix
+amoeba/pitorsion <fix_amoeba_pitorsion>` command.  It computes 6-body
+interaction between a pair of bonded atoms which each have 2
+additional bond partners.
+
+The :math:`U_{bitorsion}` term is computed by the :doc:`fix
+amoeba/bitorsion <fix_amoeba_bitorsion>` command.  It computes 5-body
+interaction between two 4-body torsions (dihedrals) which overlap,
+having 3 atoms in common.
+
+These command doc pages have additional details on the terms they
+compute:
+
+* :doc:`pair_style amoeba or hippo <pair_amoeba>`
+* :doc:`bond_style class2 <bond_class2>`
+* :doc:`angle_style amoeba <angle_amoeba>`
+* :doc:`dihedral_style fourier <dihedral_fourier>`
+* :doc:`improper_style amoeba <improper_amoeba>`
+* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
+* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
+
+----------
+
+To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
+the following appropriately in your input script.  The only change
+needed for AMOEBA vs HIPPO simulation is for the :doc:`pair_style
+<pair_style>` and :doc:`pair_coeff <pair_coeff>` commands, as shown
+below.  See examples/amoeba for example input scripts for both AMOEBA
+and HIPPO.
+
+.. code-block:: LAMMPS
+
+   units              real                           # required
+   atom_style         amoeba
+   bond_style         class2                         # CLASS2 package
+   angle_style        amoeba
+   dihedral_style     fourier                        # EXTRA-MOLECULE package
+   improper_style     amoeba
+                                                     # required per-atom data
+   fix                amtype all property/atom i_amtype ghost yes
+   fix                extra all property/atom &
+                      i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
+   fix                polaxe all property/atom i_polaxe
+
+   fix                pit all amoeba/pitorsion       # PiTorsion terms in FF
+   fix_modify         pit energy yes
+                                                     # Bitorsion terms in FF
+   fix                bit all amoeba/bitorsion bitorsion.ubiquitin.data
+   fix_modify         bit energy yes
+
+   read_data          data.ubiquitin fix amtype NULL "Tinker Types" &
+                      fix pit "pitorsion types" "PiTorsion Coeffs" &
+                      fix pit pitorsions PiTorsions &
+                      fix bit bitorsions BiTorsions
+
+   pair_style         amoeba                          # AMOEBA FF
+   pair_coeff         * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
+
+   pair_style         hippo                           # HIPPO FF
+   pair_coeff         * * hippo_water.prm hippo_water.key
+
+   special_bonds      lj/coul 0.5 0.5 0.5 one/five yes     # 1-5 neighbors
+
+The data file read by the :doc:`read_data <read_data>` command should
+be created by the tools/tinker/tinker2lmp.py conversion program
+described below.  It will create a section in the data file with the
+header "Tinker Types".  A :doc:`fix property/atom <fix_property_atom>`
+command for the data must be specified before the read_data command.
+In the example above the fix ID is *amtype*.
+
+Similarly, if the system you are simulating defines AMOEBA/HIPPO
+pitorsion or bitorsion interactions, there will be entries in the data
+file for those interactions.  They require a :doc:`fix
+amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
+amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined.  In the
+example above, the IDs for these two fixes are *pit* and *bit*.
+
+Of course, if the system being modeled does not have one or more of
+the following -- bond, angle, dihedral, improper, pitorsion,
+bitorsion interactions -- then the corresponding style and fix
+commands above do not need to be used.  See the example scripts in
+examples/amoeba for water systems as examples; they are simpler than
+what is listed above.
+
+The two :doc:`fix property/atom <fix_property_atom>` commands with IDs
+(in the example above) *extra* and *polaxe* are also needed to define
+internal per-atom quantities used by the AMOEBA and HIPPO force
+fields.
+
+The :doc:`pair_coeff <pair_coeff>` command used for either the AMOEBA
+or HIPPO force field takes two arguments for Tinker force field files,
+namely a PRM and KEY file.  The keyfile can be specified as NULL and
+default values for a various settings will be used.  Note that these 2
+files are meant to allow use of native Tinker files as-is.  However
+LAMMPS does not support all the options which can be included
+in a Tinker PRM or KEY file.  See specifics below.
+
+A :doc:`special_bonds <special_bonds>` command with the *one/five*
+option is required, since the AMOEBA/HIPPO force fields define
+weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
+1-5 interactions.  This command will trigger a per-atom list of 1-5
+neighbors to be generated.  The AMOEBA and HIPPO force fields define
+their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
+terms which in the Tinker PRM and KEY files; they can be different for
+different terms in the force field.
+
+In addition to the list above, these command doc pages have additional
+details:
+
+* :doc:`atom_style amoeba <atom_style>`
+* :doc:`fix property/atom <fix_property_atom>`
+* :doc:`special_bonds <special_bonds>`
+
+----------
+
+Tinker PRM and KEY files
+
+A Tinker PRM file is composed of sections, each of which has multiple
+lines.  This is the list of PRM sections LAMMPS knows how to parse and
+use.  Any other sections are skipped:
+
+* Angle Bending Parameters
+* Atom Type Definitions
+* Atomic Multipole Parameters
+* Bond Stretching Parameters
+* Charge Penetration Parameters
+* Charge Transfer Parameters
+* Dipole Polarizability Parameters
+* Dispersion Parameters
+* Force Field Definition
+* Literature References
+* Out-of-Plane Bend Parameters
+* Pauli Repulsion Parameters
+* Pi-Torsion Parameters
+* Stretch-Bend Parameters
+* Torsion-Torsion Parameters
+* Torsional Parameters
+* Urey-Bradley Parameters
+* Van der Waals Pair Parameters
+* Van der Waals Parameters
+
+A Tinker KEY file is composed of lines, each of which has a keyword
+followed by zero or more parameters.  This is the list of keywords
+LAMMPS knows how to parse and use in the same manner Tinker does.  Any
+other keywords are skipped.  The value in parenthesis is the default
+value for the keyword if it is not specified, or if the keyfile in the
+:doc:`pair_coeff <pair_coeff>` command is specified as NULL:
+
+* a-axis (0.0)
+* b-axis (0.0)
+* c-axis (0.0)
+* ctrn-cutoff (6.0)
+* ctrn-taper (0.9 * ctrn-cutoff)
+* cutoff
+* delta-halgren (0.07)
+* dewald (no long-range dispersion unless specified)
+* dewald-alpha (0.4)
+* dewald-cutoff (7.0)
+* dispersion-cutoff (9.0)
+* dispersion-taper (9.0 * dispersion-cutoff)
+* dpme-grid
+* dpme-order (4)
+* ewald (no long-range electrostatics unless specified)
+* ewald-alpha (0.4)
+* ewald-cutoff (7.0)
+* gamma-halgren (0.12)
+* mpole-cutoff (9.0)
+* mpole-taper (0.65 * mpole-cutoff)
+* pcg-guess (enabled by default)
+* pcg-noguess (disable pcg-guess if specified)
+* pcg-noprecond (disable pcg-precond if specified)
+* pcg-peek (1.0)
+* pcg-precond (enabled by default)
+* pewald-alpha (0.4)
+* pme-grid
+* pme-order (5)
+* polar-eps (1.0e-6)
+* polar-iter (100)
+* polar-predict (no prediction operation unless specified)
+* ppme-order (5)
+* repulsion-cutoff (6.0)
+* repulsion-taper (0.9 * repulsion-cutoff)
+* taper
+* usolve-cutoff (4.5)
+* usolve-diag (2.0)
+* vdw-cutoff (9.0)
+* vdw-taper (0.9 * vdw-cutoff)
+
+----------
+
+Tinker2lmp.py tool
+
+This conversion tool is found in the tools/tinker directory.
+As shown in examples/amoeba/README, these commands produce
+the data files found in examples/amoeba, and also illustrate
+all the options available to use with the tinker2lmp.py script:
+
+.. code-block:: bash
+
+   % python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba                # AMOEBA non-periodic system
+   % python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo                   # HIPPO non-periodic system
+   % python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643    # AMOEBA periodic system
+   % python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643       # HIPPO periodic system
+   % python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new   # system with bitorsions
+
+Switches and their arguments may be specified in any order.
+
+The -xyz switch is required and specifies an input XYZ file as an
+argument.  The format of this file is an extended XYZ format defined
+and used by Tinker for its input.  Example \*.xyz files are in the
+examples/amoeba directory.  The file lists the atoms in the system.
+Each atom has the following information: Tinker species name (ignored
+by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
+IDs the atom is bonded to.
+
+Here is more information about the extended XYZ format defined and
+used by Tinker, and links to programs that convert standard PDB files
+to the extended XYZ format:
+
+* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
+* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
+* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
+
+The -amoeba or -hippo switch is required.  It specifies an input
+AMOEBA or HIPPO PRM force field file as an argument.  This should be
+the same file used by the :doc:`pair_style <pair_style>` command in
+the input script.
+
+The -data switch is required.  It specifies an output file name for
+the LAMMPS data file that will be produced.
+
+For periodic systems, the -pbc switch is required.  It specifies the
+periodic box size for each dimension (x,y,z).  For a Tinker simulation
+these are specified in the KEY file.
+
+The -bitorsion switch is only needed if the system contains Tinker
+bitorsion interactions.  The data for each type of bitorsion
+interaction will be written to the specified file, and read by the
+:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>` command.  The data
+includes 2d arrays of values to which splines are fit, and thus is not
+compatible with the LAMMPS data file format.
+
+----------
+
+.. _howto-Ponder:
+
+**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque,  Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark,  Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
+
+.. _howto-Rackers:
+
+**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
+
+.. _howto-Ren:
+
+**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
+
+.. _howto-Shi:
+
+**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.
+

doc/src/Howto_bioFF.rst

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

doc/src/Howto_cmake.rst

@@ -46,7 +46,7 @@ This tutorial assumes that you are operating in a command-line environment
 using a shell like Bash.
 
 - Linux: any Terminal window will work
-- macOS: launch the Terminal application.
+- MacOS X: launch the Terminal application.
 - Windows 10: install and run the :doc:`Windows Subsystem for Linux <Howto_wsl>`
 
 We also assume that you have downloaded and unpacked a recent LAMMPS source code package
@@ -56,7 +56,7 @@ You should change into the top level directory of the LAMMPS source tree all
 paths mentioned in the tutorial are relative to that.  Immediately after downloading
 it should look like this:
 
-.. code-block:: console
+.. code-block:: bash
 
     $ ls
     bench  doc       lib      potentials  README  tools
@@ -104,7 +104,7 @@ the progress of the configuration printed to the screen followed by a
 summary of the enabled features, options and compiler settings. A typical
 summary screen will look like this:
 
-.. code-block:: console
+.. code-block::
 
    $ cmake ../cmake/
    -- The CXX compiler identification is GNU 8.2.0

doc/src/Howto_github.rst

@@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
 distribution.  It uses the process of updating this very tutorial as an
 example to describe the individual steps and options.  You need to be
 familiar with git and you may want to have a look at the `git book
-<https://git-scm.com/book/>`_ to familiarize yourself with some of the
+<http://git-scm.com/book/>`_ to familiarize yourself with some of the
 more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests
@@ -78,13 +78,13 @@ machine via HTTPS:
 
 .. code-block:: bash
 
-     git clone https://github.com/<your user name>/lammps.git <some name>
+     $ git clone https://github.com/<your user name>/lammps.git <some name>
 
 or, if you have set up your GitHub account for using SSH keys, via SSH:
 
 .. code-block:: bash
 
-     git clone git@github.com:<your user name>/lammps.git
+     $ git clone git@github.com:<your user name>/lammps.git
 
 You can find the proper URL by clicking the "Clone or download"-button:
 
@@ -103,21 +103,21 @@ and use git pull:
 
 .. code-block:: bash
 
-     cd mylammps
-     git checkout develop
-     git pull https://github.com/lammps/lammps develop
+     $ cd mylammps
+     $ git checkout develop
+     $ git pull https://github.com/lammps/lammps develop
 
 You can also add this URL as a remote:
 
 .. code-block:: bash
 
-     git remote add upstream https://www.github.com/lammps/lammps
+     $ git remote add upstream https://www.github.com/lammps/lammps
 
 From then on you can update your upstream branches with:
 
 .. code-block:: bash
 
-     git fetch upstream
+     $ git fetch upstream
 
 and then refer to the upstream repository branches with
 `upstream/develop` or `upstream/release` and so on.
@@ -129,8 +129,8 @@ workflow that updated this tutorial, and hence we will call the branch
 
 .. code-block:: bash
 
-    git fetch upstream
-    git checkout -b github-tutorial-update upstream/develop
+    $ git fetch upstream
+    $ git checkout -b github-tutorial-update upstream/develop
 
 Now that we have changed branches, we can make our changes to our local
 repository. Just remember that if you want to start working on another,
@@ -150,8 +150,8 @@ After everything is done, add the files to the branch and commit them:
 
 .. code-block:: bash
 
-    git add doc/src/Howto_github.txt
-    git add doc/src/JPG/tutorial*.png
+    $ git add doc/src/Howto_github.txt
+    $ git add doc/src/JPG/tutorial*.png
 
 .. warning::
 
@@ -174,13 +174,13 @@ useful message that explains the change.
 
 .. code-block:: bash
 
-   git commit -m 'Finally updated the GitHub tutorial'
+     $ git commit -m 'Finally updated the GitHub tutorial'
 
 After the commit, the changes can be pushed to the same branch on GitHub:
 
 .. code-block:: bash
 
-   git push
+   $ git push
 
 Git will ask you for your user name and password on GitHub if you have
 not configured anything. If your local branch is not present on GitHub yet,
@@ -188,7 +188,7 @@ it will ask you to add it by running
 
 .. code-block:: bash
 
-   git push --set-upstream origin github-tutorial-update
+     $ git push --set-upstream origin github-tutorial-update
 
 If you correctly type your user name and
 password, the feature branch should be added to your fork on GitHub.
@@ -198,13 +198,13 @@ If you want to make really sure you push to the right repository
 
 .. code-block:: bash
 
-   git push origin
+   $ git push origin
 
 or using an explicit URL:
 
 .. code-block:: bash
 
-   git push git@github.com:Pakketeretet2/lammps.git
+   $ git push git@github.com:Pakketeretet2/lammps.git
 
 ----------
 
@@ -412,10 +412,10 @@ we need to pull Axel's change back into our branch, and merge them:
 
 .. code-block:: bash
 
-    git add Howto_github.txt
-    git add JPG/tutorial_reverse_pull_request*.png
-    git commit -m "Updated text and images on reverse pull requests"
-    git pull
+    $ git add Howto_github.txt
+    $ git add JPG/tutorial_reverse_pull_request*.png
+    $ git commit -m "Updated text and images on reverse pull requests"
+    $ git pull
 
 In this case, the merge was painless because git could auto-merge:
 
@@ -428,10 +428,10 @@ commit and push again:
 
 .. code-block:: bash
 
-    git add Howto_github.txt
-    git add JPG/tutorial_reverse_pull_request6.png
-    git commit -m "Merged Axel's suggestions and updated text"
-    git push git@github.com:Pakketeretet2/lammps
+    $ git add Howto_github.txt
+    $ git add JPG/tutorial_reverse_pull_request6.png
+    $ git commit -m "Merged Axel's suggestions and updated text"
+    $ git push git@github.com:Pakketeretet2/lammps
 
 This merge also shows up on the lammps GitHub page:
 
@@ -456,9 +456,9 @@ branch!
 
 .. code-block:: bash
 
-   git checkout develop
-   git pull https://github.com/lammps/lammps develop
-   git branch -d github-tutorial-update
+   $ git checkout develop
+   $ git pull https://github.com/lammps/lammps develop
+   $ git branch -d github-tutorial-update
 
 If you do not pull first, it is not really a problem but git will warn
 you at the next statement that you are deleting a local branch that
@@ -472,7 +472,7 @@ to your remote(s) as well:
 
 .. code-block:: bash
 
-   git push origin :github-tutorial-update
+   $ git push origin :github-tutorial-update
 
 **Recent changes in the workflow**
 
@@ -486,6 +486,5 @@ simplify comparisons between releases.  Finally, all patches and
 submissions are subject to automatic testing and code checks to make
 sure they at the very least compile.
 
-A discussion of the LAMMPS developer GitHub workflow can be found in the
-file `doc/github-development-workflow.md
-<https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_
+A discussion of the LAMMPS developer GitHub workflow can be found in the file
+`doc/github-development-workflow.md <https://github.com/lammps/lammps/blob/develop/doc/github-development-workflow.md>`_

doc/src/Howto_manifold.rst

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

doc/src/Howto_mdi.rst

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

doc/src/Howto_output.rst

@@ -22,11 +22,10 @@ commands you specify.
 As discussed below, LAMMPS gives you a variety of ways to determine
 what quantities are computed and printed when the thermodynamics,
 dump, or fix commands listed above perform output.  Throughout this
-discussion, note that users can also :doc:`add their own computes and
-fixes to LAMMPS <Modify>` which can then generate values that can then
-be output with these commands.
+discussion, note that users can also :doc:`add their own computes and fixes to LAMMPS <Modify>` which can then generate values that can then be
+output with these commands.
 
-The following sub-sections discuss different LAMMPS commands related
+The following sub-sections discuss different LAMMPS command related
 to output and the kind of data they operate on and produce:
 
 * :ref:`Global/per-atom/local data <global>`
@@ -95,11 +94,11 @@ script references the data determines which style is meant. Example: if
 a compute provides both a global scalar and a per-atom vector, the
 former will be accessed by using ``c_ID`` in an equal-style variable,
 while the latter will be accessed by using ``c_ID`` in an atom-style
-variable.  Note that atom-style variable formulas can also access
-global scalars, but in this case it is not possible to do this
-directly because of the ambiguity.  Instead, an equal-style variable
-can be defined which accesses the global scalar, and that variable can
-be used in the atom-style variable formula in place of ``c_ID``.
+variable.  Note that atom-style variable formulas can also access global
+scalars, but in this case it is not possible to do directly because of
+the ambiguity.  Instead, an equal-style variable can be defined which
+accesses the global scalar, and that variable used in the atom-style
+variable formula in place of ``c_ID``.
 
 .. _thermo:
 
@@ -142,10 +141,9 @@ There is also a :doc:`dump custom <dump>` format where the user
 specifies what values are output with each atom.  Pre-defined atom
 attributes can be specified (id, x, fx, etc).  Three additional kinds
 of keywords can also be specified (c_ID, f_ID, v_name), where a
-:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable
-<variable>` provides the values to be output.  In each case, the
-compute, fix, or variable must generate per-atom values for input to
-the :doc:`dump custom <dump>` command.
+:doc:`compute <compute>` or :doc:`fix <fix>` or :doc:`variable <variable>`
+provides the values to be output.  In each case, the compute, fix, or
+variable must generate per-atom values for input to the :doc:`dump custom <dump>` command.
 
 There is also a :doc:`dump local <dump>` format where the user specifies
 what local values to output.  A pre-defined index keyword can be
@@ -162,13 +160,12 @@ Fixes that write output files
 -----------------------------
 
 Several fixes take various quantities as input and can write output
-files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk
-<fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`, :doc:`fix
-ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
+files: :doc:`fix ave/time <fix_ave_time>`, :doc:`fix ave/chunk <fix_ave_chunk>`, :doc:`fix ave/histo <fix_ave_histo>`,
+:doc:`fix ave/correlate <fix_ave_correlate>`, and :doc:`fix print <fix_print>`.
 
-The :doc:`fix ave/time <fix_ave_time>` command enables direct output
-to a file and/or time-averaging of global scalars or vectors.  The
-user specifies one or more quantities as input.  These can be global
+The :doc:`fix ave/time <fix_ave_time>` command enables direct output to
+a file and/or time-averaging of global scalars or vectors.  The user
+specifies one or more quantities as input.  These can be global
 :doc:`compute <compute>` values, global :doc:`fix <fix>` values, or
 :doc:`variables <variable>` of any style except the atom style which
 produces per-atom values.  Since a variable can refer to keywords used
@@ -187,8 +184,8 @@ atoms, e.g. individual molecules.  The per-atom quantities can be atom
 density (mass or number) or atom attributes such as position,
 velocity, force.  They can also be per-atom quantities calculated by a
 :doc:`compute <compute>`, by a :doc:`fix <fix>`, or by an atom-style
-:doc:`variable <variable>`.  The chunk-averaged output of this fix is
-global and can also be used as input to other output commands.
+:doc:`variable <variable>`.  The chunk-averaged output of this fix can
+also be used as input to other output commands.
 
 The :doc:`fix ave/histo <fix_ave_histo>` command enables direct output
 to a file of histogrammed quantities, which can be global or per-atom
@@ -205,35 +202,32 @@ written to the screen and log file or to a separate file, periodically
 during a running simulation.  The line can contain one or more
 :doc:`variable <variable>` values for any style variable except the
 vector or atom styles).  As explained above, variables themselves can
-contain references to global values generated by :doc:`thermodynamic
-keywords <thermo_style>`, :doc:`computes <compute>`, :doc:`fixes
-<fix>`, or other :doc:`variables <variable>`, or to per-atom values
-for a specific atom.  Thus the :doc:`fix print <fix_print>` command is
-a means to output a wide variety of quantities separate from normal
-thermodynamic or dump file output.
+contain references to global values generated by :doc:`thermodynamic keywords <thermo_style>`, :doc:`computes <compute>`,
+:doc:`fixes <fix>`, or other :doc:`variables <variable>`, or to per-atom
+values for a specific atom.  Thus the :doc:`fix print <fix_print>`
+command is a means to output a wide variety of quantities separate
+from normal thermodynamic or dump file output.
 
 .. _computeoutput:
 
 Computes that process output quantities
 ---------------------------------------
 
-The :doc:`compute reduce <compute_reduce>` and :doc:`compute
-reduce/region <compute_reduce>` commands take one or more per-atom or
-local vector quantities as inputs and "reduce" them (sum, min, max,
+The :doc:`compute reduce <compute_reduce>` and :doc:`compute reduce/region <compute_reduce>` commands take one or more per-atom
+or local vector quantities as inputs and "reduce" them (sum, min, max,
 ave) to scalar quantities.  These are produced as output values which
 can be used as input to other output commands.
 
-The :doc:`compute slice <compute_slice>` command take one or more
-global vector or array quantities as inputs and extracts a subset of
-their values to create a new vector or array.  These are produced as
-output values which can be used as input to other output commands.
+The :doc:`compute slice <compute_slice>` command take one or more global
+vector or array quantities as inputs and extracts a subset of their
+values to create a new vector or array.  These are produced as output
+values which can be used as input to other output commands.
 
-The :doc:`compute property/atom <compute_property_atom>` command takes
-a list of one or more pre-defined atom attributes (id, x, fx, etc) and
+The :doc:`compute property/atom <compute_property_atom>` command takes a
+list of one or more pre-defined atom attributes (id, x, fx, etc) and
 stores the values in a per-atom vector or array.  These are produced
 as output values which can be used as input to other output commands.
-The list of atom attributes is the same as for the :doc:`dump custom
-<dump>` command.
+The list of atom attributes is the same as for the :doc:`dump custom <dump>` command.
 
 The :doc:`compute property/local <compute_property_local>` command takes
 a list of one or more pre-defined local attributes (bond info, angle

doc/src/Howto_pylammps.rst

@@ -152,14 +152,14 @@ Creating a new instance of PyLammps
 To create a PyLammps object you need to first import the class from the lammps
 module. By using the default constructor, a new *lammps* instance is created.
 
-.. code-block:: python
+.. code-block:: Python
 
    from lammps import PyLammps
    L = PyLammps()
 
 You can also initialize PyLammps on top of this existing *lammps* object:
 
-.. code-block:: python
+.. code-block:: Python
 
    from lammps import lammps, PyLammps
    lmp = lammps()
@@ -180,14 +180,14 @@ For instance, let's take the following LAMMPS command:
 In the original interface this command can be executed with the following
 Python code if *L* was a lammps instance:
 
-.. code-block:: python
+.. code-block:: Python
 
    L.command("region box block 0 10 0 5 -0.5 0.5")
 
 With the PyLammps interface, any command can be split up into arbitrary parts
 separated by white-space, passed as individual arguments to a region method.
 
-.. code-block:: python
+.. code-block:: Python
 
    L.region("box block", 0, 10, 0, 5, -0.5, 0.5)
 
@@ -199,14 +199,14 @@ The benefit of this approach is avoiding redundant command calls and easier
 parameterization. In the original interface parameterization needed to be done
 manually by creating formatted strings.
 
-.. code-block:: python
+.. code-block:: Python
 
    L.command("region box block %f %f %f %f %f %f" % (xlo, xhi, ylo, yhi, zlo, zhi))
 
 In contrast, methods of PyLammps accept parameters directly and will convert
 them automatically to a final command string.
 
-.. code-block:: python
+.. code-block:: Python
 
    L.region("box block", xlo, xhi, ylo, yhi, zlo, zhi)
 
@@ -256,7 +256,7 @@ LAMMPS variables can be both defined and accessed via the PyLammps interface.
 
 To define a variable you can use the :doc:`variable <variable>` command:
 
-.. code-block:: python
+.. code-block:: Python
 
    L.variable("a index 2")
 
@@ -265,14 +265,14 @@ A dictionary of all variables is returned by L.variables
 you can access an individual variable by retrieving a variable object from the
 L.variables dictionary by name
 
-.. code-block:: python
+.. code-block:: Python
 
    a = L.variables['a']
 
 The variable value can then be easily read and written by accessing the value
 property of this object.
 
-.. code-block:: python
+.. code-block:: Python
 
    print(a.value)
    a.value = 4
@@ -284,7 +284,7 @@ LAMMPS expressions can be immediately evaluated by using the eval method. The
 passed string parameter can be any expression containing global thermo values,
 variables, compute or fix data.
 
-.. code-block:: python
+.. code-block:: Python
 
    result = L.eval("ke") # kinetic energy
    result = L.eval("pe") # potential energy
@@ -298,7 +298,7 @@ All atoms in the current simulation can be accessed by using the L.atoms list.
 Each element of this list is an object which exposes its properties (id, type,
 position, velocity, force, etc.).
 
-.. code-block:: python
+.. code-block:: Python
 
    # access first atom
    L.atoms[0].id
@@ -311,7 +311,7 @@ position, velocity, force, etc.).
 
 Some properties can also be used to set:
 
-.. code-block:: python
+.. code-block:: Python
 
    # set position in 2D simulation
    L.atoms[0].position = (1.0, 0.0)
@@ -328,7 +328,7 @@ after a run via the L.runs list. This list contains a growing list of run data.
 The first element is the output of the first run, the second element that of
 the second run.
 
-.. code-block:: python
+.. code-block:: Python
 
    L.run(1000)
    L.runs[0] # data of first 1000 time steps
@@ -339,14 +339,14 @@ the second run.
 Each run contains a dictionary of all trajectories. Each trajectory is
 accessible through its thermo name:
 
-.. code-block:: python
+.. code-block:: Python
 
    L.runs[0].thermo.Step # list of time steps in first run
    L.runs[0].thermo.Ke   # list of kinetic energy values in first run
 
 Together with matplotlib plotting data out of LAMMPS becomes simple:
 
-.. code-block:: python
+.. code-block:: Python
 
    import matplotlib.plot as plt
    steps = L.runs[0].thermo.Step
@@ -406,7 +406,7 @@ Four atoms are placed in the simulation and the dihedral potential is applied on
 them using a datafile. Then one of the atoms is rotated along the central axis by
 setting its position from Python, which changes the dihedral angle.
 
-.. code-block:: python
+.. code-block:: Python
 
    phi = [d \* math.pi / 180 for d in range(360)]
 
@@ -439,7 +439,7 @@ Initially, a 2D system is created in a state with minimal energy.
 
 It is then disordered by moving each atom by a random delta.
 
-.. code-block:: python
+.. code-block:: Python
 
    random.seed(27848)
    deltaperturb = 0.2
@@ -458,7 +458,7 @@ It is then disordered by moving each atom by a random delta.
 Finally, the Monte Carlo algorithm is implemented in Python. It continuously
 moves random atoms by a random delta and only accepts certain moves.
 
-.. code-block:: python
+.. code-block:: Python
 
    estart = L.eval("pe")
    elast = estart
@@ -517,7 +517,7 @@ PyLammps can be run in parallel using mpi4py. This python package can be install
 The following is a short example which reads in an existing LAMMPS input file and
 executes it in parallel.  You can find in.melt in the examples/melt folder.
 
-.. code-block:: python
+.. code-block:: Python
 
    from mpi4py import MPI
    from lammps import PyLammps

doc/src/Howto_spc.rst

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

doc/src/Howto_spins.rst

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

doc/src/Howto_structured_data.rst

@@ -43,7 +43,7 @@ JSON
      "ke": $(ke)
    }""" file current_state.json screen no
 
-.. code-block:: json
+.. code-block:: JSON
    :caption: current_state.json
 
    {

doc/src/Howto_tip3p.rst

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

doc/src/Howto_tip4p.rst

@@ -8,28 +8,18 @@ This site M is located at a fixed distance away from the oxygen along
 the bisector of the HOH bond angle.  A bond style of *harmonic* and an
 angle style of *harmonic* or *charmm* should also be used.
 
-A TIP4P model is run with LAMMPS using either these commands
+A TIP4P model is run with LAMMPS using either this command
 for a cutoff model:
 
-* :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
 * :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
-or these commands for a long-range model:
+or these two commands for a long-range model:
 
-* :doc:`pair_style tip4p/long <pair_coul>`
 * :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
-* :doc:`pair_style lj/long/tip4p/long <pair_lj_long>`
-* :doc:`pair_style tip4p/long/soft <pair_fep_soft>`
-* :doc:`pair_style lj/cut/tip4p/long/soft <pair_fep_soft>`
 * :doc:`kspace_style pppm/tip4p <kspace_style>`
-* :doc:`kspace_style pppm/disp/tip4p <kspace_style>`
 
-The bond lengths and bond angles should be held fixed using the
-:doc:`fix shake <fix_shake>` or :doc:`fix rattle <fix_shake>` command,
-unless a parameterization for a flexible TIP4P model is used.  The
-parameter sets listed below are all for rigid TIP4P model variants and
-thus the bond and angle force constants are not used and can be set to
-any legal value; only equilibrium length and angle are used.
+For both models, the bond lengths and bond angles should be held fixed
+using the :doc:`fix shake <fix_shake>` command.
 
 These are the additional parameters (in real units) to set for O and H
 atoms and the water molecule to run a rigid TIP4P model with a cutoff
@@ -97,18 +87,17 @@ solver (e.g. Ewald or PPPM in LAMMPS):
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 |
 
-Note that the when using the TIP4P pair style, the neighbor list cutoff
-for Coulomb interactions is effectively extended by a distance 2 \* (OM
-distance), to account for the offset distance of the fictitious charges
-on O atoms in water molecules.  Thus it is typically best in an
-efficiency sense to use a LJ cutoff >= Coulomb cutoff + 2\*(OM
-distance), to shrink the size of the neighbor list.  This leads to
-slightly larger cost for the long-range calculation, so you can test the
-trade-off for your model.  The OM distance and the LJ and Coulombic
-cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
-<pair_lj_cut_tip4p>` command.
+Note that the when using the TIP4P pair style, the neighbor list
+cutoff for Coulomb interactions is effectively extended by a distance
+2 \* (OM distance), to account for the offset distance of the
+fictitious charges on O atoms in water molecules.  Thus it is
+typically best in an efficiency sense to use a LJ cutoff >= Coulomb
+cutoff + 2\*(OM distance), to shrink the size of the neighbor list.
+This leads to slightly larger cost for the long-range calculation, so
+you can test the trade-off for your model.  The OM distance and the LJ
+and Coulombic cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>` command.
 
-Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
+Wikipedia also has a nice article on `water models <http://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 

doc/src/Howto_type_labels.rst

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

doc/src/Howto_viz.rst

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

doc/src/Install_conda.rst

@@ -1,25 +1,24 @@
 Download an executable for Linux or Mac via Conda
 -------------------------------------------------
 
-Pre-compiled LAMMPS binaries are available for macOS or Linux via the
-`Conda <conda_>`_ package management system.
+Binaries are available for MacOS or Linux via `Conda <conda_>`_.
 
 First, one must setup the Conda package manager on your system.  Follow the
 instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
-environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
+environment (named `my-lammps-env` or whatever you prefer) for your lammps
 install:
 
 .. code-block:: bash
 
-   conda config --add channels conda-forge
-   conda create -n my-lammps-env
+   % conda config --add channels conda-forge
+   % conda create -n my-lammps-env
 
-Then, you can install LAMMPS on your system with the following command:
+Then, you can install lammps on your system with the following command:
 
 .. code-block:: bash
 
-   conda activate my-lammps-env
-   conda install lammps
+   % conda activate my-lammps-env
+   % conda install lammps
 
 The LAMMPS binary is built with the :ref:`KIM package <kim>` which
 results in Conda also installing the `kim-api` binaries when LAMMPS is
@@ -28,7 +27,7 @@ install the `openkim-models` package
 
 .. code-block:: bash
 
-   conda install openkim-models
+   % conda install openkim-models
 
 If you have problems with the installation you can post issues to
 `this link <conda_forge_lammps_>`_.

doc/src/Install_git.rst

@@ -41,7 +41,7 @@ create a local copy of the LAMMPS repository with a command like:
 
 .. code-block:: bash
 
-   git clone -b release https://github.com/lammps/lammps.git mylammps
+   $ git clone -b release https://github.com/lammps/lammps.git mylammps
 
 where "mylammps" is the name of the directory you wish to create on
 your machine and "release" is one of the 3 branches listed above.
@@ -78,10 +78,10 @@ from within the "mylammps" directory:
 
 .. code-block:: bash
 
-   git checkout release      # not needed if you always stay in this branch
-   git checkout stable       # use one of these 3 checkout commands
-   git checkout develop      # to choose the branch to follow
-   git pull
+   $ git checkout release      # not needed if you always stay in this branch
+   $ git checkout stable       # use one of these 3 checkout commands
+   $ git checkout develop      # to choose the branch to follow
+   $ git pull
 
 Doing a "pull" will not change any files you have added to the LAMMPS
 directory structure.  It will also not change any existing LAMMPS
@@ -97,7 +97,7 @@ this is as follows.
 
 .. code-block:: bash
 
-   git checkout tagID
+   $ git checkout tagID
 
 Stable versions and what tagID to use for a particular stable version
 are discussed on `this page <https://www.lammps.org/bug.html#version>`_.
@@ -138,13 +138,13 @@ changed.  How to do this depends on the build system you are using.
 
       .. code-block:: bash
 
-         make purge             # remove any deprecated src files
-         make package-update    # sync package files with src files
-         make foo               # re-build for your machine (mpi, serial, etc)
+         $ make purge             # remove any deprecated src files
+         $ make package-update    # sync package files with src files
+         $ make foo               # re-build for your machine (mpi, serial, etc)
 
       to enforce consistency of the source between the src folder
       and package directories.  This is OK to do even if you don't
-      use any packages. The ``make purge`` command removes any deprecated
+      use any packages. The "make purge" command removes any deprecated
       src files if they were removed by the patch from a package
       sub-directory.
 
@@ -160,9 +160,9 @@ changed.  How to do this depends on the build system you are using.
    :class: note
 
    The servers at github.com support the "https://" access protocol for
-   anonymous, read-only access.  If you have a suitably configured
-   GitHub account, you may also use SSH protocol with the URL
-   "git@github.com:lammps/lammps.git".
+   anonymous, read-only access.  If you have a suitably configured GitHub
+   account, you may also use SSH protocol with the
+   URL "git@github.com:lammps/lammps.git".
 
 The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
 (Temple U, akohlmey at gmail.com).

doc/src/Install_linux.rst

@@ -34,7 +34,7 @@ To install LAMMPS do the following once:
 
 .. code-block:: bash
 
-   sudo apt-get install lammps
+   $ sudo apt-get install lammps
 
 This downloads an executable named ``lmp`` to your box and multiple
 packages with supporting data, examples and libraries as well as any
@@ -43,13 +43,13 @@ to run input scripts:
 
 .. code-block:: bash
 
-   lmp -in in.lj
+   $ lmp -in in.lj
 
 To update LAMMPS to the latest packaged version, do the following:
 
 .. code-block:: bash
 
-   sudo apt-get update
+   $ sudo apt-get update
 
 which will also update other packages on your system.
 
@@ -61,14 +61,14 @@ package
 
 .. code-block:: bash
 
-   sudo apt-get install openkim-models
+   $ sudo apt-get install openkim-models
 
 Or use the KIM-API commands to download and install individual models.
 To un-install LAMMPS, do the following:
 
 .. code-block:: bash
 
-   sudo apt-get remove lammps
+   $ sudo apt-get remove lammps
 
 Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
@@ -103,9 +103,9 @@ To install LAMMPS with OpenMPI and run an input ``in.lj`` with 2 CPUs do:
 
 .. code-block:: bash
 
-   dnf install lammps-openmpi
-   module load mpi/openmpi-x86_64
-   mpirun -np 2 lmp -in in.lj
+   $ dnf install lammps-openmpi
+   $ module load mpi/openmpi-x86_64
+   $ mpirun -np 2 lmp -in in.lj
 
 The ``dnf install`` command is needed only once. In case of a new LAMMPS
 stable release, ``dnf update`` will automatically update to the newer
@@ -121,7 +121,7 @@ can install the `openkim-models` package
 
 .. code-block:: bash
 
-   dnf install openkim-models
+   $ dnf install openkim-models
 
 Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
@@ -162,14 +162,14 @@ in OpenSuse as of Leap 15.0. You can install the package with:
 
 .. code-block:: bash
 
-   zypper install lammps
+   $ zypper install lammps
 
 This includes support for OpenMPI. The name of the LAMMPS executable
 is ``lmp``. Thus to run an input in parallel on 2 CPUs you would do:
 
 .. code-block:: bash
 
-   mpirun -np 2 lmp -in in.lj
+   $ mpirun -np 2 lmp -in in.lj
 
 Please use ``lmp -help`` to see which compilation options, packages,
 and styles are included in the binary.
@@ -181,7 +181,7 @@ can install the `openkim-models` package
 
 .. code-block:: bash
 
-   zypper install openkim-models
+   $ zypper install openkim-models
 
 Thanks to Christoph Junghans (LANL) for making LAMMPS available in OpenSuse.
 
@@ -197,7 +197,7 @@ typing:
 
 .. code-block:: bash
 
-   emerge --ask lammps
+   % emerge --ask lammps
 
 Note that in Gentoo the LAMMPS source is downloaded and the package is
 built on the your machine.
@@ -206,7 +206,7 @@ Certain LAMMPS packages can be enable via USE flags, type
 
 .. code-block:: bash
 
-   equery uses lammps
+   % equery uses lammps
 
 for details.
 
@@ -229,10 +229,10 @@ any of the above names in-place of lammps.
 
 .. code-block:: bash
 
-   git clone https://aur.archlinux.org/lammps.git
-   cd lammps
-   makepkg -s
-   makepkg -i
+   $ git clone https://aur.archlinux.org/lammps.git
+   $ cd lammps
+   $ makepkg -s
+   $ makepkg -i
 
 To update, you may repeat the above, or change into the cloned directory,
 and execute the following, after which, if there are any changes, you may
@@ -240,7 +240,7 @@ use makepkg as above.
 
 .. code-block:: bash
 
-   git pull
+   $ git pull
 
 Alternatively, you may use an AUR helper to install these packages.
 

doc/src/Install_mac.rst

@@ -12,7 +12,7 @@ the following commands:
 
 .. code-block:: bash
 
-   brew install lammps
+   % brew install lammps
 
 This will install the executables "lammps_serial" and "lammps_mpi", as well as
 the LAMMPS "doc", "potentials", "tools", "bench", and "examples" directories.
@@ -22,7 +22,7 @@ Lennard-Jones benchmark file:
 
 .. code-block:: bash
 
-   brew test lammps -v
+   % brew test lammps -v
 
 The LAMMPS binary is built with the :ref:`KIM package <kim>` which
 results in Homebrew also installing the `kim-api` binaries when LAMMPS is
@@ -31,7 +31,7 @@ install the `openkim-models` package
 
 .. code-block:: bash
 
-   brew install openkim-models
+   % brew install openkim-models
 
 If you have problems with the installation you can post issues to
 `this link <https://github.com/Homebrew/homebrew-core/issues>`_.

doc/src/Install_tarball.rst

@@ -26,7 +26,7 @@ command:
 
 .. code-block:: bash
 
-   tar -xzvf lammps*.tar.gz
+   $ tar -xzvf lammps*.tar.gz
 
 This will create a LAMMPS directory with the version date
 in its name, e.g. lammps-23Jun18.
@@ -40,7 +40,7 @@ with the following command, to create a lammps-<version> dir:
 
 .. code-block:: bash
 
-   unzip lammps*.zip
+   $ unzip lammps*.zip
 
 This version corresponds to the selected LAMMPS patch or stable
 release.