Merge pull request #2766 from akohlmey/next_patch_release

Step version strings for the next patch release

.gitattributes

@@ -1,3 +1,4 @@
 .gitattributes export-ignore
 .gitignore export-ignore
 .github export-ignore
+.lgtm.yml export-ignore

.github/CONTRIBUTING.md

@@ -26,11 +26,11 @@ __
 
 ## I don't want to read this whole thing I just have a question!
 
-> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using.
+> **Note:** Please do not file an issue to ask a general question about LAMMPS, its features, how to use specific commands, or how perform simulations or analysis in LAMMPS. Instead post your question to either the ['lammps-users' mailing list](https://lammps.sandia.gov/mail.html) or the [LAMMPS Material Science Discourse forum](https://matsci.org/lammps). You do not need to be subscribed to post to the list (but a mailing list subscription avoids having your post delayed until it is approved by a mailing list moderator). Most posts to the mailing list receive a response within less than 24 hours. Before posting to the mailing list, please read the [mailing list guidelines](https://lammps.sandia.gov/guidelines.html). Following those guidelines will help greatly to get a helpful response. Always mention which LAMMPS version you are using. The LAMMPS forum was recently created as part of a larger effort to build a materials science community and have discussions not just about using LAMMPS. Thus the forum may be also used for discussions that would be off-topic for the mailing list. Those will just have to be moved to a more general category.
 
 ## How Can I Contribute?
 
-There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list), and you can contribute by submitting pull requests on GitHub or e-mail your code
+There are several ways how you can actively contribute to the LAMMPS project: you can discuss compiling and using LAMMPS, and solving LAMMPS related problems with other LAMMPS users on the lammps-users mailing list, you can report bugs or suggest enhancements by creating issues on GitHub (or posting them to the lammps-users mailing list or posting in the LAMMPS Materials Science Discourse forum), and you can contribute by submitting pull requests on GitHub or e-mail your code
 to one of the [LAMMPS core developers](https://lammps.sandia.gov/authors.html). As you may see from the aforementioned developer page, the LAMMPS software package includes the efforts of a very large number of contributors beyond the principal authors and maintainers.
 
 ### Discussing How To Use LAMMPS
@@ -42,6 +42,8 @@ Anyone can browse/search previous questions/answers in the archives. You do not
 
 If you post a message and you are a subscriber, your message will appear immediately. If you are not a subscriber, your message will be moderated, which typically takes one business day. Either way, when someone replies the reply will usually be sent to both, your personal email address and the mailing list. When replying to people, that responded to your post to the list, please always included the mailing list in your replies (i.e. use "Reply All" and **not** "Reply"). Responses will appear on the list in a few minutes, but it can take a few hours for postings and replies to show up in the SourceForge archive. Sending replies also to the mailing list is important, so that responses are archived and people with a similar issue can search for possible solutions in the mailing list archive.
 
+The LAMMPS Materials Science Discourse forum was created recently to facilitate discussion not just about LAMMPS and as part of a larger effort  towards building a materials science community. The forum contains a read-only sub-category with the continually updated mailing list archive, so you won't miss anything by joining only the forum and not the mailing list.
+
 ### Reporting Bugs
 
 While developers writing code for LAMMPS are careful to test their code, LAMMPS is such a large and complex software, that it is impossible to test for all combinations of features under all normal and not so normal circumstances. Thus bugs do happen, and if you suspect, that you have encountered one, please try to document it and report it as an [Issue](https://github.com/lammps/lammps/issues) on the LAMMPS GitHub project web page. However, before reporting a bug, you need to check whether this is something that may have already been corrected. The [Latest Features and Bug Fixes in LAMMPS](https://lammps.sandia.gov/bug.html) web page lists all significant changes to LAMMPS over the years. It also tells you what the current latest development version of LAMMPS is, and you should test whether your issue still applies to that version.

.github/codeql/cpp.yml

@@ -0,0 +1,4 @@
+paths:
+ - src
+ - lib
+ - tools

.github/codeql/python.yml

@@ -0,0 +1,5 @@
+paths:
+ - python/lammps
+
+queries:
+ - uses: security-and-quality

.github/workflows/codeql-analysis.yml

@@ -31,16 +31,18 @@ jobs:
       uses: github/codeql-action/init@v1
       with:
         languages: ${{ matrix.language }}
+        config-file: ./.github/codeql/${{ matrix.language }}.yml
 
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      if: ${{ matrix.language == 'cpp' }}
+      run: mkdir build
 
     - name: Building LAMMPS via CMake
       if: ${{ matrix.language == 'cpp' }}
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
+        cmake -C ../cmake/presets/most.cmake ../cmake
         cmake --build . --parallel 2
 
     - name: Perform CodeQL Analysis

.github/workflows/unittest-macos.yml

@@ -10,6 +10,8 @@ jobs:
     name: MacOS Unit Test
     if: ${{ github.repository == 'lammps/lammps' }}
     runs-on: macos-latest
+    env:
+      CCACHE_DIR: ${{ github.workspace }}/.ccache
 
     steps:
     - name: Checkout repository
@@ -17,18 +19,36 @@ jobs:
       with:
         fetch-depth: 2
 
+    - name: Install ccache
+      run: brew install ccache
+
     - name: Create Build Environment
-      run: cmake -E make_directory ${{github.workspace}}/build
+      run: mkdir build
+
+    - name: Set up ccache
+      uses: actions/cache@v2
+      with:
+        path: ${{ env.CCACHE_DIR }}
+        key: macos-ccache-${{ github.sha }}
+        restore-keys: macos-ccache-
 
     - name: Building LAMMPS via CMake
       shell: bash
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       run: |
-        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
-              -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
+        ccache -z
+        cmake -C ../cmake/presets/clang.cmake \
+              -C ../cmake/presets/most.cmake \
+              -D CMAKE_CXX_COMPILER_LAUNCHER=ccache \
+              -D CMAKE_C_COMPILER_LAUNCHER=ccache \
+              -D ENABLE_TESTING=on \
+              -D BUILD_SHARED_LIBS=on \
+              -D LAMMPS_EXCEPTIONS=on \
+              ../cmake
         cmake --build . --parallel 2
+        ccache -s
 
     - name: Run Tests
-      working-directory: ${{github.workspace}}/build
+      working-directory: build
       shell: bash
       run: ctest -V

.lgtm.yml

@@ -0,0 +1,14 @@
+extraction:
+  cpp:
+    configure:
+      command:
+      - "mkdir build"
+      - "cd build"
+      - "cmake -G Ninja -C ../cmake/presets/minimal.cmake ../cmake"
+    index:
+      build_command:
+      - "cd build"
+      - "ninja"
+  python:
+    python_setup:
+      version: 3

SECURITY.md

@@ -0,0 +1,35 @@
+# Security Policy
+
+LAMMPS is designed as a user-level application to conduct computer
+simulations for research using classical mechanics.  As such LAMMPS
+depends to some degrees on users providing correctly formatted input and
+LAMMPS needs to read and write files based on uncontrolled user input.
+As a parallel application for use in high-performance computing
+environments, performance critical steps are also done without checking
+data.
+
+LAMMPS also is interfaced to a number of external libraries, including
+libraries with experimental research software, that are not validated
+and tested by the LAMMPS developers, so it is easy to import bad
+behavior from calling functions in one of those libraries.
+
+Thus is is quite easy to crash LAMMPS through malicious input and do all
+kinds of filesystem manipulations.  And because of that LAMMPS should
+**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).
+
+
+# Version Updates
+
+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

@@ -22,6 +22,11 @@ set(LAMMPS_TOOLS_DIR      ${LAMMPS_DIR}/tools)
 set(LAMMPS_PYTHON_DIR     ${LAMMPS_DIR}/python)
 set(LAMMPS_POTENTIALS_DIR ${LAMMPS_DIR}/potentials)
 
+set(LAMMPS_DOWNLOADS_URL "https://download.lammps.org" CACHE STRING "Base URL for LAMMPS downloads")
+set(LAMMPS_POTENTIALS_URL "${LAMMPS_DOWNLOADS_URL}/potentials")
+set(LAMMPS_THIRDPARTY_URL "${LAMMPS_DOWNLOADS_URL}/thirdparty")
+mark_as_advanced(LAMMPS_DOWNLOADS_URL)
+
 find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
@@ -31,7 +36,7 @@ endif()
 
 # If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
 option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
-if (LAMMPS_INSTALL_RPATH)
+if(LAMMPS_INSTALL_RPATH)
   set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
@@ -113,13 +118,13 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
-  QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
+  PLUGIN QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
   USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
   USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
+  USER-LB USER-MANIFOLD USER-MDI USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
   USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
   USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
+  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-PACE USER-BROWNIAN)
 
 set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
 
@@ -240,68 +245,6 @@ if(BUILD_OMP)
   target_link_libraries(lammps PRIVATE OpenMP::OpenMP_CXX)
 endif()
 
-# Compiler specific features for testing
-if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
-  mark_as_advanced(ENABLE_COVERAGE)
-  if(ENABLE_COVERAGE)
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC --coverage)
-      target_link_options(lammps PUBLIC --coverage)
-    endif()
-  endif()
-endif()
-
-#######################################
-# add custom target for IWYU analysis
-#######################################
-set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
-mark_as_advanced(ENABLE_IWYU)
-if(ENABLE_IWYU)
-  find_program(IWYU_EXE NAMES include-what-you-use iwyu)
-  find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
-  if (IWYU_EXE AND IWYU_TOOL)
-    add_custom_target(
-      iwyu
-      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
-      COMMENT "Running IWYU")
-    add_dependencies(iwyu lammps)
-  else()
-    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
-      "and the iwyu-tool/iwyu_tool script installed in your PATH")
-  endif()
-endif()
-
-set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
-mark_as_advanced(ENABLE_SANITIZER)
-set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
-set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
-validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
-string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
-if(NOT ENABLE_SANITIZER STREQUAL "none")
-  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
-    if(CMAKE_VERSION VERSION_LESS 3.13)
-      if(CMAKE_CXX_FLAGS)
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      else()
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
-      endif()
-    else()
-      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
-    endif()
-  else()
-    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
-    set(ENABLE_SANITIZER "none")
-  endif()
-endif()
-
 if(PKG_MSCG OR PKG_USER-ATC OR PKG_USER-AWPMD OR PKG_USER-QUIP OR PKG_LATTE)
   enable_language(C)
   find_package(LAPACK)
@@ -381,10 +324,10 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
-        USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS)
+foreach(PKG_WITH_INCL KSPACE PYTHON MLIAP VORONOI USER-COLVARS USER-MDI USER-MOLFILE USER-NETCDF USER-PLUMED
+        USER-QMMM USER-QUIP USER-SCAFACOS USER-SMD USER-VTK KIM LATTE MESSAGE MSCG COMPRESS USER-PACE)
   if(PKG_${PKG_WITH_INCL})
-    include(Packages/${PKG_WITH_INCL})
+    include(Packages/${PKG_WITH_INCL}) 
   endif()
 endforeach()
 
@@ -533,6 +476,18 @@ foreach(PKG_WITH_INCL CORESHELL QEQ USER-OMP USER-SDPD KOKKOS OPT USER-INTEL GPU
   endif()
 endforeach()
 
+if(PKG_PLUGIN)
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
+endif()
+
 ######################################################################
 # the windows version of LAMMPS requires a couple extra libraries
 # and the MPI library - if use - has to be linked right before those
@@ -713,7 +668,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Operating System: ${CMAKE_SYSTEM_NAME}
+   Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    Build type:       ${CMAKE_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")
@@ -782,9 +737,12 @@ if(BUILD_MPI)
 endif()
 if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
--- GPU API:          ${GPU_API}")
+-- GPU API:                  ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
+    message(STATUS "CUDA Compiler:            ${CUDA_NVCC_EXECUTABLE}")
     message(STATUS "GPU default architecture: ${GPU_ARCH}")
+    message(STATUS "GPU binning with CUDPP:   ${CUDPP_OPT}")
+    message(STATUS "CUDA MPS support:         ${CUDA_MPS_SUPPORT}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")
@@ -794,7 +752,7 @@ if(PKG_GPU)
       message(STATUS "HIP GPU sorting: off")
     endif()
   endif()
-  message(STATUS "GPU precision:    ${GPU_PREC}")
+  message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
 if(PKG_KOKKOS)
   message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")

cmake/Modules/Documentation.cmake

@@ -55,11 +55,15 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
+  mark_as_advanced(MATHJAX_URL)
+
   # download mathjax distribution and unpack to folder "mathjax"
   if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/mathjax/es5)
-    file(DOWNLOAD "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz"
+    file(DOWNLOAD ${MATHJAX_URL}
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 a4a6a093a89bc2ccab1452d766b98e53)
+      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 ${CMAKE_CURRENT_BINARY_DIR}/MathJax-*)
     execute_process(COMMAND ${CMAKE_COMMAND} -E rename ${MATHJAX_VERSION_DIR} ${DOC_BUILD_STATIC_DIR}/mathjax)

cmake/Modules/GTest.cmake

@@ -8,10 +8,12 @@ endif()
 
 include(ExternalProject)
 set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
 mark_as_advanced(GTEST_URL)
+mark_as_advanced(GTEST_MD5)
 ExternalProject_Add(googletest
-                    URL ${GTEST_URL}
-                    URL_MD5         ecd1fa65e7de707cd5c00bdac56022cd
+                    URL             ${GTEST_URL}
+                    URL_MD5         ${GTEST_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/gtest-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/gtest-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_GTEST_OPTS}

cmake/Modules/GenerateOpenCLHeader.cmake

@@ -0,0 +1,3 @@
+# utility script to call WriteOpenCLHeader function
+include(${SOURCE_DIR}/Modules/OpenCLUtils.cmake)
+WriteOpenCLHeader(${VARNAME} ${HEADER_FILE} ${SOURCE_FILES})

cmake/Modules/LAMMPSUtils.cmake

@@ -86,7 +86,6 @@ endfunction(GenerateBinaryHeader)
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
   if (EXISTS "${pkgfolder}/potentials.txt")
-    set(LAMMPS_POTENTIALS_URL "https://download.lammps.org/potentials")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)
@@ -105,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
     endforeach()
   endif()
 endfunction(FetchPotentials)
+
+# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
+if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
+  file(STRINGS /etc/os-release distro REGEX "^NAME=")
+  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
+  string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
+  set(CMAKE_LINUX_DISTRO ${distro})
+  set(CMAKE_DISTRO_VERSION ${disversion})
+endif()

cmake/Modules/MPI4WIN.cmake

@@ -1,16 +1,25 @@
 # 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 https://download.lammps.org/thirdparty/mpich2-win64-devel.tar.gz
-    URL_MD5 4939fdb59d13182fd5dd65211e469f14
+    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 https://download.lammps.org/thirdparty/mpich2-win32-devel.tar.gz
-    URL_MD5 a61d153500dce44e21b755ee7257e031
+    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()

cmake/Modules/OpenCLLoader.cmake

@@ -1,11 +1,13 @@
 message(STATUS "Downloading and building OpenCL loader library")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2021.05.02.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "29180b05056578afda92f0d394c3a373" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+mark_as_advanced(OPENCL_LOADER_MD5)
 
 include(ExternalProject)
-set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
-mark_as_advanced(OPENCL_LOADER_URL)
 ExternalProject_Add(opencl_loader
-                    URL ${OPENCL_LOADER_URL}
-                    URL_MD5         011cdcbd41030be94f3fced6d763a52a
+                    URL             ${OPENCL_LOADER_URL}
+                    URL_MD5         ${OPENCL_LOADER_MD5}
                     SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
                     BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
                     CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}

cmake/Modules/OpenCLUtils.cmake

@@ -1,10 +1,8 @@
-function(GenerateOpenCLHeader varname outfile files)
-    message("Creating ${outfile}...")
+function(WriteOpenCLHeader varname outfile files)
     file(WRITE ${outfile} "const char * ${varname} = \n")
-    math(EXPR ARG_END   "${ARGC}-1")
+    separate_arguments(files)
 
-    foreach(IDX RANGE 2 ${ARG_END})
-        list(GET ARGV ${IDX} filename)
+    foreach(filename ${files})
         file(READ ${filename} content)
         string(REGEX REPLACE "\\s*//[^\n]*\n" "\n" content "${content}")
         string(REGEX REPLACE "\\\\" "\\\\\\\\" content "${content}")
@@ -15,4 +13,16 @@ function(GenerateOpenCLHeader varname outfile files)
     endforeach()
 
     file(APPEND ${outfile} ";\n")
+endfunction(WriteOpenCLHeader)
+
+function(GenerateOpenCLHeader varname outfile files)
+    list(REMOVE_AT ARGV 0 1)
+    add_custom_command(OUTPUT ${outfile}
+      COMMAND ${CMAKE_COMMAND} -D SOURCE_DIR=${CMAKE_CURRENT_SOURCE_DIR}
+                               -D VARNAME=${varname}
+                               -D HEADER_FILE=${outfile}
+                               -D SOURCE_FILES="${ARGV}"
+                               -P ${CMAKE_CURRENT_SOURCE_DIR}/Modules/GenerateOpenCLHeader.cmake
+      DEPENDS ${ARGV}
+      COMMENT "Generating ${outfile}...")
 endfunction(GenerateOpenCLHeader)

cmake/Modules/Packages/GPU.cmake

@@ -35,7 +35,7 @@ if(GPU_API STREQUAL "CUDA")
   if(NOT BIN2C)
     message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
   endif()
-  option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+  option(CUDPP_OPT "Enable GPU binning via CUDAPP (should be off for modern GPUs)" OFF)
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
     if(CUDPP_OPT)
@@ -112,10 +112,10 @@ if(GPU_API STREQUAL "CUDA")
   endif()
 
   cuda_compile_fatbin(GPU_GEN_OBJS ${GPU_LIB_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DNV_KERNEL -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   cuda_compile(GPU_OBJS ${GPU_LIB_CUDPP_CU} OPTIONS ${CUDA_REQUEST_PIC}
-          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING})
+          -DUNIX -O3 --use_fast_math -Wno-deprecated-gpu-targets -DUCL_CUDADR ${GPU_CUDA_GENCODE} -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES})
 
   foreach(CU_OBJ ${GPU_GEN_OBJS})
     get_filename_component(CU_NAME ${CU_OBJ} NAME_WE)
@@ -131,7 +131,7 @@ if(GPU_API STREQUAL "CUDA")
   add_library(gpu STATIC ${GPU_LIB_SOURCES} ${GPU_LIB_CUDPP_SOURCES} ${GPU_OBJS})
   target_link_libraries(gpu PRIVATE ${CUDA_LIBRARIES} ${CUDA_CUDA_LIBRARY})
   target_include_directories(gpu PRIVATE ${LAMMPS_LIB_BINARY_DIR}/gpu ${CUDA_INCLUDE_DIRS})
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
+  target_compile_definitions(gpu PRIVATE -DUSE_CUDA -D_${GPU_PREC_SETTING} -DMPI_GERYON -DUCL_NO_EXIT ${GPU_CUDA_MPS_FLAGS})
   if(CUDPP_OPT)
     target_include_directories(gpu PRIVATE ${LAMMPS_LIB_SOURCE_DIR}/gpu/cudpp_mini)
     target_compile_definitions(gpu PRIVATE -DUSE_CUDPP)
@@ -145,7 +145,14 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
+  # the static OpenCL loader doesn't seem to work on macOS. use the system provided
+  # version by default instead (for as long as it will be available)
+  if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(_opencl_static_default OFF)
+  else()
+    set(_opencl_static_default ON)
+  endif()
+  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ${_opencl_static_default})
   mark_as_advanced(USE_STATIC_OPENCL_LOADER)
   if (USE_STATIC_OPENCL_LOADER)
     include(OpenCLLoader)
@@ -218,7 +225,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   if(NOT DEFINED HIP_PLATFORM)
       if(NOT DEFINED ENV{HIP_PLATFORM})
-          set(HIP_PLATFORM "hcc" CACHE PATH "HIP Platform to be used during compilation")
+          set(HIP_PLATFORM "amd" CACHE PATH "HIP Platform to be used during compilation")
       else()
           set(HIP_PLATFORM $ENV{HIP_PLATFORM} CACHE PATH "HIP Platform used during compilation")
       endif()
@@ -226,7 +233,7 @@ elseif(GPU_API STREQUAL "HIP")
 
   set(ENV{HIP_PLATFORM} ${HIP_PLATFORM})
 
-  if(HIP_PLATFORM STREQUAL "hcc")
+  if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
     set(HIP_ARCH "gfx906" CACHE STRING "HIP target architecture")
   elseif(HIP_PLATFORM STREQUAL "nvcc")
     find_package(CUDA REQUIRED)
@@ -284,23 +291,23 @@ elseif(GPU_API STREQUAL "HIP")
     set(CUBIN_FILE   "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}.cubin")
     set(CUBIN_H_FILE "${LAMMPS_LIB_BINARY_DIR}/gpu/${CU_NAME}_cubin.h")
 
-    if(HIP_PLATFORM STREQUAL "hcc")
+    if(HIP_PLATFORM STREQUAL "hcc" OR HIP_PLATFORM STREQUAL "amd")
         configure_file(${CU_FILE} ${CU_CPP_FILE} COPYONLY)
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()
     elseif(HIP_PLATFORM STREQUAL "nvcc")
         add_custom_command(OUTPUT ${CUBIN_FILE}
-          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
+          VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --fatbin --use_fast_math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} ${HIP_CUDA_GENCODE} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_FILE}
           DEPENDS ${CU_FILE}
           COMMENT "Generating ${CU_NAME}.cubin")
     endif()
@@ -338,11 +345,16 @@ elseif(GPU_API STREQUAL "HIP")
 
       if(DOWNLOAD_CUB)
         message(STATUS "CUB download requested")
+        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)
+
         include(ExternalProject)
 
         ExternalProject_Add(CUB
-          GIT_REPOSITORY https://github.com/NVlabs/cub
-          TIMEOUT 5
+          URL     ${CUB_URL}
+          URL_MD5 ${CUB_MD5}
           PREFIX "${CMAKE_CURRENT_BINARY_DIR}"
           CONFIGURE_COMMAND ""
           BUILD_COMMAND ""
@@ -354,7 +366,7 @@ elseif(GPU_API STREQUAL "HIP")
       else()
         find_package(CUB)
         if(NOT CUB_FOUND)
-          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_VORO=ON to download it")
+          message(FATAL_ERROR "CUB library not found. Help CMake to find it by setting CUB_INCLUDE_DIR, or set DOWNLOAD_CUB=ON to download it")
         endif()
       endif()
 
@@ -381,6 +393,12 @@ elseif(GPU_API STREQUAL "HIP")
 
     target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_HCC__)
     target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
+  elseif(HIP_PLATFORM STREQUAL "amd")
+    target_compile_definitions(gpu PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(gpu PRIVATE ${HIP_ROOT_DIR}/../include)
+
+    target_compile_definitions(hip_get_devices PRIVATE -D__HIP_PLATFORM_AMD__)
+    target_include_directories(hip_get_devices PRIVATE ${HIP_ROOT_DIR}/../include)
   endif()
 
   target_link_libraries(lammps PRIVATE gpu)

cmake/Modules/Packages/KIM.cmake

@@ -35,9 +35,13 @@ if(DOWNLOAD_KIM)
   include(ExternalProject)
   enable_language(C)
   enable_language(Fortran)
+  set(KIM_URL "https://s3.openkim.org/kim-api/kim-api-2.2.1.txz" CACHE STRING "URL for KIM tarball")
+  set(KIM_MD5 "ae1ddda2ef7017ea07934e519d023dca" CACHE STRING "MD5 checksum of KIM tarball")
+  mark_as_advanced(KIM_URL)
+  mark_as_advanced(KIM_MD5)
   ExternalProject_Add(kim_build
-    URL https://s3.openkim.org/kim-api/kim-api-2.2.1.txz
-    URL_MD5 ae1ddda2ef7017ea07934e519d023dca
+    URL     ${KIM_URL}
+    URL_MD5 ${KIM_MD5}
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

cmake/Modules/Packages/KOKKOS.cmake

@@ -37,9 +37,13 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.4.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "c2fdcedb6953e6160c765366f6045abb" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  mark_as_advanced(KOKKOS_URL)
+  mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
-    URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
+    URL     ${KOKKOS_URL}
+    URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -51,10 +55,12 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
+  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.3.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.4.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
+  target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -66,6 +72,7 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
+  target_link_libraries(lmp PRIVATE kokkos)
 endif()
 target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
 

cmake/Modules/Packages/LATTE.cmake

@@ -15,10 +15,14 @@ endif()
 option(DOWNLOAD_LATTE "Download the LATTE library instead of using an already installed one" ${DOWNLOAD_LATTE_DEFAULT})
 if(DOWNLOAD_LATTE)
   message(STATUS "LATTE download requested - we will build our own")
+  set(LATTE_URL "https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz" CACHE STRING "URL for LATTE tarball")
+  set(LATTE_MD5 "820e73a457ced178c08c71389a385de7" CACHE STRING "MD5 checksum of LATTE tarball")
+  mark_as_advanced(LATTE_URL)
+  mark_as_advanced(LATTE_MD5)
   include(ExternalProject)
   ExternalProject_Add(latte_build
-    URL https://github.com/lanl/LATTE/archive/v1.2.2.tar.gz
-    URL_MD5 820e73a457ced178c08c71389a385de7
+    URL     ${LATTE_URL}
+    URL_MD5 ${LATTE_MD5}
     SOURCE_SUBDIR cmake
     CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> ${CMAKE_REQUEST_PIC} -DCMAKE_INSTALL_LIBDIR=lib
     -DBLAS_LIBRARIES=${BLAS_LIBRARIES} -DLAPACK_LIBRARIES=${LAPACK_LIBRARIES}

cmake/Modules/Packages/MSCG.cmake

@@ -7,10 +7,15 @@ else()
 endif()
 option(DOWNLOAD_MSCG "Download MSCG library instead of using an already installed one)" ${DOWNLOAD_MSCG_DEFAULT})
 if(DOWNLOAD_MSCG)
+  set(MSCG_URL "https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz" CACHE STRING "URL for MSCG tarball")
+  set(MSCG_MD5 "8c45e269ee13f60b303edd7823866a91" CACHE STRING "MD5 checksum of MSCG tarball")
+  mark_as_advanced(MSCG_URL)
+  mark_as_advanced(MSCG_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(mscg_build
-    URL https://github.com/uchicago-voth/MSCG-release/archive/1.7.3.1.tar.gz
-    URL_MD5 8c45e269ee13f60b303edd7823866a91
+    URL     ${MSCG_URL}
+    URL_MD5 ${MSCG_MD5}
     SOURCE_SUBDIR src/CMake
     CMAKE_ARGS ${CMAKE_REQUEST_PIC} ${EXTRA_MSCG_OPTS}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}

cmake/Modules/Packages/USER-INTEL.cmake

@@ -30,7 +30,12 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
   endif()
 endif()
 if(INTEL_LRT_MODE STREQUAL "C++11")
-  target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+  if(Threads_FOUND)
+    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+    target_link_libraries(lammps PRIVATE Threads::Threads)
+  else()
+    message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+  endif()
 endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
@@ -74,9 +79,11 @@ if(INTEL_ARCH STREQUAL "KNL")
 else()
   if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     include(CheckCXXCompilerFlag)
-    foreach(_FLAG -O2 -fp-model fast=2 -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
-      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAG})
-      if(COMPILER_SUPPORTS${_FLAG})
+    foreach(_FLAG -O2 "-fp-model fast=2" -no-prec-div -qoverride-limits -qopt-zmm-usage=high -qno-offload -fno-alias -ansi-alias -restrict)
+      string(REGEX REPLACE "[ =\"]" "" _FLAGX ${_FLAG})
+      check_cxx_compiler_flag("${_FLAG}" COMPILER_SUPPORTS${_FLAGX})
+      if(COMPILER_SUPPORTS${_FLAGX})
+          separate_arguments(_FLAG UNIX_COMMAND "${_FLAG}")
           target_compile_options(lammps PRIVATE ${_FLAG})
       endif()
     endforeach()

cmake/Modules/Packages/USER-MDI.cmake

@@ -0,0 +1,66 @@
+find_package(mdi QUIET)
+if(${mdi_FOUND})
+  set(DOWNLOAD_MDI_DEFAULT OFF)
+else()
+  set(DOWNLOAD_MDI_DEFAULT ON)
+endif()
+option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
+
+if(DOWNLOAD_MDI)
+  message(STATUS "MDI download requested - we will build our own")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.2.9.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_MD5 "ddfa46d6ee15b4e59cfd527ec7212184" CACHE STRING "MD5 checksum for MDI tarball")
+  mark_as_advanced(MDI_URL)
+  mark_as_advanced(MDI_MD5)
+
+  set(LAMMPS_LIB_MDI_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/mdi)
+
+  include(ExternalProject)
+  message(STATUS "Building mdi.")
+  ExternalProject_Add(mdi_external
+      URL     ${MDI_URL}
+      URL_MD5 ${MDI_MD5}
+      UPDATE_COMMAND ""
+      CMAKE_ARGS ${CMAKE_REQUEST_PIC}
+                 -DCMAKE_INSTALL_PREFIX=${LAMMPS_LIB_MDI_BIN_DIR}
+                 -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                 -DCMAKE_INSTALL_LIBDIR=${CMAKE_INSTALL_LIBDIR}
+                 -DCMAKE_INSTALL_INCLUDEDIR=${CMAKE_INSTALL_INCLUDEDIR}
+                 -DBUILD_SHARED_LIBS=${BUILD_SHARED_LIBS}
+                 -Dlanguage=C
+      CMAKE_CACHE_ARGS -DCMAKE_C_FLAGS:STRING=${CMAKE_C_FLAGS}
+                       -DCMAKE_CXX_FLAGS:STRING=${CMAKE_CXX_FLAGS}
+                       -DTargetOpenMP_FIND_COMPONENTS:STRING=C;CXX)
+
+  # Link the lammps library against MDI
+  target_include_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
+  target_link_directories(lammps PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  target_link_libraries(lammps PRIVATE mdi)
+  add_dependencies(lammps mdi_external)
+
+  # Link the lammps executable against MDI
+  target_include_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_INCLUDEDIR}/mdi)
+  target_link_directories(lmp PRIVATE ${LAMMPS_LIB_MDI_BIN_DIR}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  target_link_libraries(lmp PRIVATE mdi)
+  add_dependencies(lmp mdi_external)
+
+else()
+
+  find_package(mdi)
+  if(NOT mdi_FOUND)
+    message(FATAL_ERROR "MDI library not found. Help CMake to find it "
+      "by setting mdi_LIBRARY and mdi_INCLUDE_DIR, or set DOWNLOAD_MDI=ON "
+      "to download and compile it")
+  endif()
+
+  # Link the lammps library against MDI
+  target_include_directories(lammps PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lammps PRIVATE ${mdi_LIBRARY})
+
+  # Link the lammps executable against MDI
+  target_include_directories(lmp PRIVATE ${mdi_INCLUDE_DIR})
+  target_link_libraries(lmp PRIVATE ${mdi_LIBRARY})
+endif()
+
+target_compile_definitions(lammps PRIVATE -DLMP_USER_MDI)
+target_compile_definitions(lmp PRIVATE -DLMP_USER_MDI)

cmake/Modules/Packages/USER-MOLFILE.cmake

@@ -2,8 +2,4 @@ set(MOLFILE_INCLUDE_DIR "${LAMMPS_LIB_SOURCE_DIR}/molfile" CACHE STRING "Path to
 set(MOLFILE_INCLUDE_DIRS "${MOLFILE_INCLUDE_DIR}")
 add_library(molfile INTERFACE)
 target_include_directories(molfile INTERFACE ${MOLFILE_INCLUDE_DIRS})
-# no need to link with -ldl on windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-  target_link_libraries(molfile INTERFACE ${CMAKE_DL_LIBS})
-endif()
 target_link_libraries(lammps PRIVATE molfile)

cmake/Modules/Packages/USER-PACE.cmake

@@ -0,0 +1,26 @@
+
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+mark_as_advanced(PACELIB_URL)
+mark_as_advanced(PACELIB_MD5)
+
+# download library sources to build folder
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
+
+# uncompress downloaded sources
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E remove_directory lammps-user-pace*
+  COMMAND ${CMAKE_COMMAND} -E tar xzf libpace.tar.gz
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+)
+
+
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
+list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
+
+add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
+set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
+target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -53,10 +53,17 @@ if(DOWNLOAD_PLUMED)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
+
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+
+  mark_as_advanced(PLUMED_URL)
+  mark_as_advanced(PLUMED_MD5)
+
   include(ExternalProject)
   ExternalProject_Add(plumed_build
-    URL https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz
-    URL_MD5 95f29dd0c067577f11972ff90dfc7d12
+    URL     ${PLUMED_URL}
+    URL_MD5 ${PLUMED_MD5}
     BUILD_IN_SOURCE 1
     CONFIGURE_COMMAND <SOURCE_DIR>/configure --prefix=<INSTALL_DIR>
                                              ${CONFIGURE_REQUEST_PIC}

cmake/Modules/Packages/USER-SCAFACOS.cmake

@@ -14,15 +14,19 @@ endif()
 option(DOWNLOAD_SCAFACOS "Download ScaFaCoS library instead of using an already installed one" ${DOWNLOAD_SCAFACOS_DEFAULT})
 if(DOWNLOAD_SCAFACOS)
   message(STATUS "ScaFaCoS download requested - we will build our own")
+  set(SCAFACOS_URL "https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz" CACHE STRING "URL for SCAFACOS tarball")
+  set(SCAFACOS_MD5 "bd46d74e3296bd8a444d731bb10c1738" CACHE STRING "MD5 checksum of SCAFACOS tarball")
+  mark_as_advanced(SCAFACOS_URL)
+  mark_as_advanced(SCAFACOS_MD5)
 
   # version 1.0.1 needs a patch to compile and linke cleanly with GCC 10 and later.
-  file(DOWNLOAD https://download.lammps.org/thirdparty/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
+  file(DOWNLOAD ${LAMMPS_THIRDPARTY_URL}/scafacos-1.0.1-fix.diff ${CMAKE_CURRENT_BINARY_DIR}/scafacos-1.0.1.fix.diff
           EXPECTED_HASH MD5=4baa1333bb28fcce102d505e1992d032)
 
   include(ExternalProject)
   ExternalProject_Add(scafacos_build
-    URL https://github.com/scafacos/scafacos/releases/download/v1.0.1/scafacos-1.0.1.tar.gz
-    URL_MD5 bd46d74e3296bd8a444d731bb10c1738
+    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
                                              --enable-fcs-solvers=fmm,p2nfft,direct,ewald,p3m

cmake/Modules/Packages/USER-SMD.cmake

@@ -7,10 +7,14 @@ endif()
 option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed one)" ${DOWNLOAD_EIGEN3_DEFAULT})
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
+  set(EIGEN3_URL "https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_MD5 "9e30f67e8531477de4117506fe44669b" CACHE STRING "MD5 checksum of Eigen3 tarball")
+  mark_as_advanced(EIGEN3_URL)
+  mark_as_advanced(EIGEN3_MD5)
   include(ExternalProject)
   ExternalProject_Add(Eigen3_build
-    URL https://gitlab.com/libeigen/eigen/-/archive/3.3.7/eigen-3.3.7.tar.gz
-    URL_MD5 9e30f67e8531477de4117506fe44669b
+    URL     ${EIGEN3_URL}
+    URL_MD5 ${EIGEN3_MD5}
     CONFIGURE_COMMAND "" BUILD_COMMAND "" INSTALL_COMMAND ""
   )
   ExternalProject_get_property(Eigen3_build SOURCE_DIR)

cmake/Modules/Packages/VORONOI.cmake

@@ -7,6 +7,11 @@ endif()
 option(DOWNLOAD_VORO "Download and compile the Voro++ library instead of using an already installed one" ${DOWNLOAD_VORO_DEFAULT})
 if(DOWNLOAD_VORO)
   message(STATUS "Voro++ download requested - we will build our own")
+  set(VORO_URL "${LAMMPS_THIRDPARTY_URL}/voro++-0.4.6.tar.gz" CACHE STRING "URL for Voro++ tarball")
+  set(VORO_MD5 "2338b824c3b7b25590e18e8df5d68af9" CACHE STRING "MD5 checksum for Voro++ tarball")
+  mark_as_advanced(VORO_URL)
+  mark_as_advanced(VORO_MD5)
+
   include(ExternalProject)
 
   if(BUILD_SHARED_LIBS)
@@ -22,8 +27,8 @@ if(DOWNLOAD_VORO)
   endif()
 
   ExternalProject_Add(voro_build
-    URL https://download.lammps.org/thirdparty/voro++-0.4.6.tar.gz
-    URL_MD5 2338b824c3b7b25590e18e8df5d68af9
+    URL     ${VORO_URL}
+    URL_MD5 ${VORO_MD5}
     PATCH_COMMAND patch -b -p0 < ${LAMMPS_LIB_SOURCE_DIR}/voronoi/voro-make.patch
     CONFIGURE_COMMAND ""
     BUILD_COMMAND make ${VORO_BUILD_OPTIONS}

cmake/Modules/Testing.cmake

@@ -16,11 +16,14 @@ if(ENABLE_TESTING)
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
-  # check if a faster linker is available.
-  # only verified with GNU and Clang compilers and new CMake
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+  # we need to build and link a LOT of tester executables, so it is worth checking if
+  # a faster linker is available. requires GNU or Clang compiler, newer CMake.
+  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
+  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+      AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
+    if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+        OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)
@@ -53,3 +56,76 @@ if(ENABLE_TESTING)
   get_filename_component(LAMMPS_UNITTEST_BIN ${CMAKE_BINARY_DIR}/unittest ABSOLUTE)
   add_subdirectory(${LAMMPS_UNITTEST_DIR} ${LAMMPS_UNITTEST_BIN})
 endif()
+
+# Compiler specific features for testing
+if(${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  option(ENABLE_COVERAGE "Enable collecting code coverage data" OFF)
+  mark_as_advanced(ENABLE_COVERAGE)
+  if(ENABLE_COVERAGE)
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} --coverage")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} --coverage")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC --coverage)
+      target_link_options(lammps PUBLIC --coverage)
+    endif()
+  endif()
+endif()
+
+#######################################
+# add custom target for IWYU analysis
+#######################################
+set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
+mark_as_advanced(ENABLE_IWYU)
+if(ENABLE_IWYU)
+  # enforce these settings
+  set(CMAKE_EXPORT_COMPILE_COMMANDS ON CACHE BOOL "Enable reporting compilation commands to compile_commands.json" FORCE)
+  if (NOT ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") OR (CMAKE_CXX_COMPILER_ID STREQUAL "GNU")))
+    message(FATAL_ERROR "IWYU is only supported with Clang or GNU compilers")
+  endif()
+  # detect the "native" header folder so we can include them first
+  execute_process(COMMAND ${CMAKE_CXX_COMPILER} --print-search-dirs OUTPUT_VARIABLE IWYU_SEARCH_PATHS)
+  string(REGEX REPLACE ".*libraries: *=([^:]+):.*" "\\1/include" IWYU_EXTRA_INCLUDE_DIR ${IWYU_SEARCH_PATHS})
+  find_program(IWYU_EXE NAMES include-what-you-use iwyu)
+  find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
+  if (IWYU_EXE AND IWYU_TOOL)
+    add_custom_target(
+      iwyu
+      ${IWYU_TOOL} -o clang -p ${CMAKE_CURRENT_BINARY_DIR} -- -I${IWYU_EXTRA_INCLUDE_DIR} -Xiwyu --mapping_file=${CMAKE_CURRENT_SOURCE_DIR}/iwyu/iwyu-extra-map.imp
+      COMMENT "Running IWYU")
+    add_dependencies(iwyu lammps)
+  else()
+    message(FATAL_ERROR "To use IWYU you need the include-what-you-use/iwyu executable"
+      "and the iwyu-tool/iwyu_tool script installed in your PATH")
+  endif()
+endif()
+
+#######################################
+# select code sanitizer options
+#######################################
+set(ENABLE_SANITIZER "none" CACHE STRING "Select a code sanitizer option (none (default), address, leak, thread, undefined)")
+mark_as_advanced(ENABLE_SANITIZER)
+set(ENABLE_SANITIZER_VALUES none address leak thread undefined)
+set_property(CACHE ENABLE_SANITIZER PROPERTY STRINGS ${ENABLE_SANITIZER_VALUES})
+validate_option(ENABLE_SANITIZER ENABLE_SANITIZER_VALUES)
+string(TOLOWER ${ENABLE_SANITIZER} ENABLE_SANITIZER)
+if(NOT ENABLE_SANITIZER STREQUAL "none")
+  if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU") OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+    if(CMAKE_VERSION VERSION_LESS 3.13)
+      if(CMAKE_CXX_FLAGS)
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      else()
+        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_${CMAKE_BUILD_TYPE}_FLAGS} -fsanitize=${ENABLE_SANITIZER}")
+      endif()
+    else()
+      target_compile_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+      target_link_options(lammps PUBLIC -fsanitize=${ENABLE_SANITIZER})
+    endif()
+  else()
+    message(WARNING "ENABLE_SANITIZER option not supported by ${CMAKE_CXX_COMPILER_ID} compilers. Ignoring.")
+    set(ENABLE_SANITIZER "none")
+  endif()
+endif()

cmake/Modules/YAML.cmake

@@ -2,10 +2,13 @@ message(STATUS "Downloading and building YAML library")
 
 include(ExternalProject)
 set(YAML_URL "https://pyyaml.org/download/libyaml/yaml-0.2.5.tar.gz" CACHE STRING "URL for libyaml tarball")
+set(YAML_MD5 "bb15429d8fb787e7d3f1c83ae129a999" CACHE STRING "MD5 checksum of libyaml tarball")
 mark_as_advanced(YAML_URL)
+mark_as_advanced(YAML_MD5)
+
 ExternalProject_Add(libyaml
                     URL               ${YAML_URL}
-                    URL_MD5           bb15429d8fb787e7d3f1c83ae129a999
+                    URL_MD5           ${YAML_MD5}
                     SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
                     BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
                     CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}

cmake/Modules/generate_lmpgitversion.cmake

@@ -17,7 +17,7 @@ if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified --always
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
     WORKING_DIRECTORY ${LAMMPS_DIR}

cmake/presets/all_off.cmake

@@ -2,16 +2,16 @@
 # an existing package selection without losing any other settings
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  SRD VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
+  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -4,16 +4,16 @@
 # with just a working C++ compiler and an MPI library.
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  SRD VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
+  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/most.cmake

@@ -4,10 +4,10 @@
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE
         GRANULAR KSPACE MANYBODY MC MISC MLIAP MOLECULE OPT PERI
-        POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
-        USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS USER-DIFFRACTION
-        USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC USER-MESODPD
-        USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
+        PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN SRD VORONOI
+        USER-BROWNIAN USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+        USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-MEAMC
+        USER-MESODPD USER-MISC USER-MOFFF USER-OMP USER-PHONON USER-REACTION
         USER-REAXC USER-SDPD USER-SPH USER-SMD USER-UEF USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})

cmake/presets/nolib.cmake

@@ -1,10 +1,11 @@
 # preset that turns off all packages that require some form of external
 # library or special compiler (fortran or cuda) or equivalent.
 
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
-        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
-        USER-SCAFACOS USER-SMD USER-VTK)
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
+  PYTHON VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
+  USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
+  USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/oneapi.cmake

@@ -0,0 +1,18 @@
+# preset that will enable the LLVM based Intel compilers with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "icpx" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "icx" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "ifx" CACHE STRING "" FORCE)
+set(MPI_CXX "icpx" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "icx" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-qopenmp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "icpx" 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" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libiomp5.so" CACHE PATH "" FORCE)
+

doc/Makefile

@@ -236,7 +236,7 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/graphviz/lammps-classes.dot

@@ -18,8 +18,8 @@ digraph lammps {
     Up [shape=box label="Update" color=blue]
     Un [shape=box label="Universe" color=blue]
     Ti [shape=box label="Timer" color=blue]
-    Lt [label="Lattice"]
     Rg [label="Region" color=red]
+    Lt [label="Lattice"]
     Rb [shape=box label="RegionBlock"]
     Rs [shape=box label="RegionSphere"]
     Av [label="AtomVec" color=red]
@@ -34,6 +34,7 @@ digraph lammps {
     Du [label="Dump" color=red]
     Fi [label="Fix" color=red]
     Cp [label="Compute" color=red]
+    Cm [label="Command" color=red]
     Th [label="Thermo"]
     Va [label="Variable"]
     Ew [shape=box label="Ewald"]
@@ -71,16 +72,19 @@ digraph lammps {
     Dg [shape=box label="DumpCFG"]
     Ve [shape=box label="Verlet"]
     Rr [shape=box label="Respa"]
+    Ru [shape=box label="Run"]
+    Se [shape=box label="Set"]
     Pt [shape=box label="PPPMTIP4P"]
     Vs [shape=box label="VerletSplit"]
     Ro [shape=box label="RespaOMP"]
     Mc [shape=box label="MinCG"]
     Mf [shape=box label="MinFire"]
     La -> {At Ci Co Do Er Fo Gr In Me Mo Ne Ou Ti Up Un} [penwidth=2]
-    Do -> {Lt Rg} [penwidth=2]
+    Do -> {Rg Lt} [penwidth=2]
     Rg -> {Rb Rs} [style=dashed penwidth=2]
     Co -> {Cb Ct} [style=dashed penwidth=2]
-    In -> Va [penwidth=2]
+    In -> {Va Cm} [penwidth=2]
+    Cm -> {Ru Se} [style=dashed penwidth=2]
     Mo -> {Fi Cp} [penwidth=2]
     Fo -> {Pa Bo An Di Im Ks} [penwidth=2]
     Ks -> {Ew Pp} [style=dashed penwidth=2]

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "10 March 2021" "2021-03-10"
+.TH LAMMPS "14 May 2021" "2021-05-14"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -1,7 +1,7 @@
 Basic build options
 ===================
 
-The following topics are covered on this page, for building both with
+The following topics are covered on this page, for building with both
 CMake and make:
 
 * :ref:`Serial vs parallel build <serial>`
@@ -234,6 +234,8 @@ LAMMPS.
          cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
          # Building with Intel Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         # Building with Intel oneAPI Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
          # Building with LLVM/Clang Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
          # Building with PGI/Nvidia Compilers:
@@ -243,8 +245,10 @@ LAMMPS.
       provided that can be loaded with
       `-C ../cmake/presets/clang.cmake`.  Similarly,
       `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
-      should switch the compiler to the PGI compilers.
+      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
+      will switch to the LLVM based oneAPI Intel compilers,
+      and `-C ../cmake/presets/pgi.cmake`
+      will switch the compiler to the PGI compilers.
 
       In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts. By

doc/src/Build_extras.rst

@@ -49,9 +49,11 @@ This is the list of packages that may require additional steps.
    * :ref:`USER-COLVARS <user-colvars>`
    * :ref:`USER-H5MD <user-h5md>`
    * :ref:`USER-INTEL <user-intel>`
+   * :ref:`USER-MDI <user-mdi>`
    * :ref:`USER-MESONT <user-mesont>`
    * :ref:`USER-MOLFILE <user-molfile>`
    * :ref:`USER-NETCDF <user-netcdf>`
+   * :ref:`USER-PACE <user-pace>`
    * :ref:`USER-PLUMED <user-plumed>`
    * :ref:`USER-OMP <user-omp>`
    * :ref:`USER-QMMM <user-qmmm>`
@@ -125,12 +127,12 @@ CMake build
                                 # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
+                                # default is 'gfx906' for HIP_PLATFORM=amd and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
-   -D CUDPP_OPT=value           # optimization setting for GPU_API=cuda
-                                # enables CUDA Performance Primitives Optimizations, must be "no" for CUDA_MPS_SUPPORT=yes
-                                # value = yes (default) or no
+   -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
+                                # enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
+                                # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
    -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
@@ -169,17 +171,24 @@ desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
 
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
-:code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
+:code:`HCC_AMDGPU_TARGET` (for ROCm <= 4.0) or :code:`CUDA_PATH` are necessary for :code:`hipcc`
 and the linker to work correctly.
 
 .. code:: bash
 
-   # AMDGPU target
+   # AMDGPU target (ROCm <= 4.0)
    export HIP_PLATFORM=hcc
    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
 
+.. code:: bash
+
+   # AMDGPU target (ROCm >= 4.1)
+   export HIP_PLATFORM=amd
+   cmake -D PKG_GPU=on -D GPU_API=HIP -D HIP_ARCH=gfx906 -D CMAKE_CXX_COMPILER=hipcc ..
+   make -j 4
+
 .. code:: bash
 
    # CUDA target (not recommended, use GPU_ARCH=cuda)
@@ -230,11 +239,12 @@ GPU architectures as supported by the CUDA toolkit in use. This is done
 through using the "--gencode " flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
-To include CUDA performance primitives set the Makefile variable
-``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.
+To enable GPU binning via CUDA performance primitives set the Makefile variable
+``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.  This should **not** be used with
+most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you should **not** use
+``-DCUDA_PROXY``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
@@ -458,6 +468,9 @@ They must be specified in uppercase.
    *  - ARMV8_THUNDERX2
       - HOST
       - ARMv8 Cavium ThunderX2 CPU
+   *  - A64FX
+      - HOST
+      - ARMv8.2 with SVE Support
    *  - WSM
       - HOST
       - Intel Westmere CPU (SSE 4.2)
@@ -530,6 +543,9 @@ They must be specified in uppercase.
    *  - AMPERE80
       - GPU
       - NVIDIA Ampere generation CC 8.0 GPU
+   *  - AMPERE86
+      - GPU
+      - NVIDIA Ampere generation CC 8.6 GPU
    *  - VEGA900
       - GPU
       - AMD GPU MI25 GFX900
@@ -538,12 +554,12 @@ They must be specified in uppercase.
       - AMD GPU MI50/MI60 GFX906
    *  - VEGA908
       - GPU
-      - AMD GPU GFX908
+      - AMD GPU MI100 GFX908
    *  - INTEL_GEN
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.3 of the Kokkos library.
+This list was last updated for version 3.4 of the Kokkos library.
 
 .. tabs::
 
@@ -1239,6 +1255,46 @@ be built for the most part with all major versions of the C++ language.
 
 ----------
 
+.. _user-pace:
+
+USER-PACE package
+-----------------------------
+
+This package requires a library that can be downloaded and built
+in lib/pace or somewhere else, which must be done before building
+LAMMPS with this package. The code for the library can be found
+at: `https://github.com/ICAMS/lammps-user-pace/ <https://github.com/ICAMS/lammps-user-pace/>`_
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      By default the library will be downloaded from the git repository
+      and built automatically when the USER-PACE package is enabled with
+      ``-D PKG_USER-PACE=yes``.  The location for the sources may be
+      customized by setting the variable ``PACELIB_URL`` when
+      configuring with CMake (e.g. to use a local archive on machines
+      without internet access).  Since CMake checks the validity of the
+      archive with ``md5sum`` you may also need to set ``PACELIB_MD5``
+      if you provide a different library version than what is downloaded
+      automatically.
+
+
+   .. tab:: Traditional make
+
+      You can download and build the USER-PACE library
+      in one step from the ``lammps/src`` dir, using these commands,
+      which invoke the ``lib/pace/Install.py`` script.
+
+      .. code-block:: bash
+
+         $ 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.
+
+----------
+
 .. _user-plumed:
 
 USER-PLUMED package
@@ -1484,6 +1540,35 @@ TBB and MKL.
 
 ----------
 
+.. _user-mdi:
+
+USER-MDI package
+-----------------------------
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D DOWNLOAD_MDI=value    # download MDI Library for build, value = no (default) or yes
+
+   .. tab:: Traditional make
+
+      Before building LAMMPS, you must build the MDI Library in
+      ``lib/mdi``\ .  You can do this by executing a command like one
+      of the following from the ``lib/mdi`` directory:
+
+      .. code-block:: bash
+
+         $ 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``\ .
+
+----------
+
 .. _user-mesont:
 
 USER-MESONT package

doc/src/Build_package.rst

@@ -30,17 +30,17 @@ steps, as explained on the :doc:`Build extras <Build_extras>` page.
 These links take you to the extra instructions for those select
 packages:
 
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`COMPRESS <compress>`       | :ref:`GPU <gpu>`                 | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`MSCG <mscg>`               | :ref:`OPT <opt>`                 | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-ATC <user-atc>`       | :ref:`USER-AWPMD <user-awpmd>`   | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-NETCDF <user-netcdf>` | :ref:`USER-PLUMED <user-plumed>` | :ref:`USER-OMP <user-omp>`         | :ref:`USER-QMMM <user-qmmm>` | :ref:`USER-QUIP <user-quip>`   | :ref:`USER-SCAFACOS <user-scafacos>` |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
-| :ref:`USER-SMD <user-smd>`       | :ref:`USER-VTK <user-vtk>`       |                                    |                              |                                |                                      |
-+----------------------------------+----------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`COMPRESS <compress>`           | :ref:`GPU <gpu>`               | :ref:`KIM <kim>`                   | :ref:`KOKKOS <kokkos>`       | :ref:`LATTE <latte>`           | :ref:`MESSAGE <message>`             |
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`MSCG <mscg>`                   | :ref:`OPT <opt>`               | :ref:`POEMS <poems>`               | :ref:`PYTHON <python>`       | :ref:`VORONOI <voronoi>`       | :ref:`USER-ADIOS <user-adios>`       |
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-ATC <user-atc>`           | :ref:`USER-AWPMD <user-awpmd>` | :ref:`USER-COLVARS <user-colvars>` | :ref:`USER-H5MD <user-h5md>` | :ref:`USER-INTEL <user-intel>` | :ref:`USER-MOLFILE <user-molfile>`   |
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-NETCDF <user-netcdf>`     | :ref:`USER-PACE <user-pace>`   | :ref:`USER-PLUMED <user-plumed>`   | :ref:`USER-OMP <user-omp>`   | :ref:`USER-QMMM <user-qmmm>`   | :ref:`USER-QUIP <user-quip>`         |
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
+| :ref:`USER-SCAFACOS <user-scafacos>` | :ref:`USER-SMD <user-smd>`     | :ref:`USER-VTK <user-vtk>`         |                              |                                |                                      |
++--------------------------------------+--------------------------------+------------------------------------+------------------------------+--------------------------------+--------------------------------------+
 
 The mechanism for including packages is simple but different for CMake
 versus make.

doc/src/Commands_all.rst

@@ -67,6 +67,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`lattice <lattice>`
    * :doc:`log <log>`
    * :doc:`mass <mass>`
+   * :doc:`mdi/engine <mdi_engine>`
    * :doc:`message <message>`
    * :doc:`minimize <minimize>`
    * :doc:`min_modify <min_modify>`
@@ -86,6 +87,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`pair_style <pair_style>`
    * :doc:`pair_write <pair_write>`
    * :doc:`partition <partition>`
+   * :doc:`plugin <plugin>`
    * :doc:`prd <prd>`
    * :doc:`print <print>`
    * :doc:`processors <processors>`

doc/src/Commands_bond.rst

@@ -126,7 +126,7 @@ OPT.
    * :doc:`quadratic (o) <dihedral_quadratic>`
    * :doc:`spherical <dihedral_spherical>`
    * :doc:`table (o) <dihedral_table>`
-   * :doc:`table/cut <dihedral_table_cut>`
+   * :doc:`table/cut <dihedral_table>`
 
 .. _improper:
 

doc/src/Commands_fix.rst

@@ -39,6 +39,9 @@ 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>`
@@ -46,6 +49,7 @@ OPT.
    * :doc:`bond/react <fix_bond_react>`
    * :doc:`bond/swap <fix_bond_swap>`
    * :doc:`box/relax <fix_box_relax>`
+   * :doc:`charge/regulation <fix_charge_regulation>`
    * :doc:`client/md <fix_client_md>`
    * :doc:`cmap <fix_cmap>`
    * :doc:`colvars <fix_colvars>`
@@ -97,6 +101,7 @@ OPT.
    * :doc:`lb/viscous <fix_lb_viscous>`
    * :doc:`lineforce <fix_lineforce>`
    * :doc:`manifoldforce <fix_manifoldforce>`
+   * :doc:`mdi/engine <fix_mdi_engine>`
    * :doc:`meso/move <fix_meso_move>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`

doc/src/Commands_pair.rst

@@ -26,6 +26,7 @@ OPT.
    * :doc:`zero <pair_zero>`
    * :doc:`hybrid (k) <pair_hybrid>`
    * :doc:`hybrid/overlay (k) <pair_hybrid>`
+   * :doc:`hybrid/scaled <pair_hybrid>`
    * :doc:`kim <pair_kim>`
    * :doc:`list <pair_list>`
    *
@@ -33,7 +34,6 @@ OPT.
    *
    *
    *
-   *
    * :doc:`adp (o) <pair_adp>`
    * :doc:`agni (o) <pair_agni>`
    * :doc:`airebo (io) <pair_airebo>`
@@ -69,6 +69,7 @@ OPT.
    * :doc:`comb3 <pair_comb>`
    * :doc:`cosine/squared <pair_cosine_squared>`
    * :doc:`coul/cut (gko) <pair_coul>`
+   * :doc:`coul/cut/global (o) <pair_coul>`
    * :doc:`coul/cut/soft (o) <pair_fep_soft>`
    * :doc:`coul/debye (gko) <pair_coul>`
    * :doc:`coul/diel (o) <pair_coul_diel>`
@@ -86,6 +87,8 @@ OPT.
    * :doc:`coul/wolf/cs <pair_cs>`
    * :doc:`dpd (gio) <pair_dpd>`
    * :doc:`dpd/fdt <pair_dpd_fdt>`
+   * :doc:`dpd/ext <pair_dpd_ext>`
+   * :doc:`dpd/ext/tstat <pair_dpd_ext>`
    * :doc:`dpd/fdt/energy (k) <pair_dpd_fdt>`
    * :doc:`dpd/tstat (go) <pair_dpd>`
    * :doc:`dsmc <pair_dsmc>`
@@ -168,7 +171,7 @@ OPT.
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
    * :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
-   * :doc:`lj/smooth (o) <pair_lj_smooth>`
+   * :doc:`lj/smooth (go) <pair_lj_smooth>`
    * :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`
    * :doc:`lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`lj96/cut (go) <pair_lj96>`
@@ -187,7 +190,7 @@ OPT.
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
    * :doc:`mliap <pair_mliap>`
-   * :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+   * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
    * :doc:`morse/smooth/linear (o) <pair_morse>`
@@ -215,6 +218,7 @@ OPT.
    * :doc:`oxrna2/stk <pair_oxrna2>`
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
+   * :doc:`pace <pair_pace>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
    * :doc:`peri/pmb (o) <pair_peri>`

doc/src/Developer.rst

@@ -14,6 +14,7 @@ of time and requests from the LAMMPS user community.
    Developer_flow
    Developer_write
    Developer_notes
+   Developer_plugins
    Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_org.rst

@@ -49,8 +49,8 @@ underscore character '_' to separate words. Outside of bundled libraries
 which may have different conventions, all C and C++ header files have a
 ``.h`` extension, all C++ files have a ``.cpp`` extension, and C files a
 ``.c`` extension. A small number of C++ classes and utility functions
-are implemented with only a ``.h`` file. Examples are the Pointer class
-or the MathVec functions.
+are implemented with only a ``.h`` file. Examples are the Pointers and
+Commands classes or the MathVec functions.
 
 Class topology
 --------------
@@ -144,7 +144,7 @@ implement specific commands that can be invoked before, after, or in
 between runs.  For these an instance of the class is created, its
 command() method called and then, after completion, the class instance
 deleted.  Examples for this are the create_box, create_atoms, minimize,
-run, or velocity command styles.
+run, set, or velocity command styles.
 
 For all those ``styles`` certain naming conventions are employed: for
 the fix nve command the class is called FixNVE and the source files are
@@ -175,11 +175,11 @@ follows:
 - The Input class reads and processes input input strings and files,
   stores variables, and invokes :doc:`commands <Commands_all>`.
 
-- As discussed above, command style classes are directly derived from
-  the Pointers class. They provide input script commands that perform
-  one-time operations before/after/between simulations or which invoke a
-  simulation.  They are instantiated from within the Input class,
-  invoked, then immediately destructed.
+- Command style classes are derived from the Command class. They provide
+  input script commands that perform one-time operations
+  before/after/between simulations or which invoke a simulation.  They
+  are usually instantiated from within the Input class, its ``command``
+  method invoked, and then immediately destructed.
 
 - The Finish class is instantiated to print statistics to the screen
   after a simulation is performed, by commands like run and minimize.

doc/src/Developer_plugins.rst

@@ -0,0 +1,251 @@
+Writing plugins
+---------------
+
+Plugins provide a mechanism to add functionality to a LAMMPS executable
+without recompiling LAMMPS.  The functionality for this and the
+:doc:`plugin command <plugin>` are implemented in the
+:ref:`PLUGIN package <PKG-PLUGIN>` which must be installed to use plugins.
+
+Plugins use the operating system's capability to load dynamic shared
+object (DSO) files in a way similar shared libraries and then reference
+specific functions in those DSOs.  Any DSO file with plugins has to include
+an initialization function with a specific name, "lammpsplugin_init", that
+has to follow specific rules described below.  When loading the DSO with
+the "plugin" command, this function is looked up and called and will then
+register the contained plugin(s) with LAMMPS.
+
+From the programmer perspective this can work because of the object
+oriented design of LAMMPS where all pair style commands are derived from
+the class Pair, all fix style commands from the class Fix and so on and
+usually only functions present in those base classes are called
+directly.  When a :doc:`pair_style` command or :doc:`fix` command is
+issued a new instance of such a derived class is created.  This is done
+by a so-called factory function which is mapped to the style name.  Thus
+when, for example, the LAMMPS processes the command ``pair_style lj/cut
+2.5``, LAMMPS will look up the factory function for creating the
+``PairLJCut`` class and then execute it.  The return value of that
+function is a ``Pair *`` pointer and the pointer will be assigned to the
+location for the currently active pair style.
+
+A DSO file with a plugin thus has to implement such a factory function
+and register it with LAMMPS so that it gets added to the map of available
+styles of the given category.  To register a plugin with LAMMPS an
+initialization function has to be present in the DSO file called
+``lammpsplugin_init`` which is called with three ``void *`` arguments:
+a pointer to the current LAMMPS instance, a pointer to the opened DSO
+handle, and a pointer to the registration function.  The registration
+function takes two arguments: a pointer to a ``lammpsplugin_t`` struct
+with information about the plugin and a pointer to the current LAMMPS
+instance.  Please see below for an example of how the registration is
+done.
+
+Members of ``lammpsplugin_t``
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+
+   * - Member
+     - Description
+   * - version
+     - LAMMPS Version string the plugin was compiled for
+   * - style
+     - Style of the plugin (pair, bond, fix, command, etc.)
+   * - name
+     - Name of the plugin style
+   * - info
+     - String with information about the plugin
+   * - author
+     - String with the name and email of the author
+   * - creator.v1
+     - Pointer to factory function for pair, bond, angle, dihedral, improper or command styles
+   * - creator.v2
+     - Pointer to factory function for compute, fix, or region styles
+   * - handle
+     - Pointer to the open DSO file handle
+
+Only one of the three alternate creator entries can be used at a time
+and which of those is determined by the style of plugin. The
+"creator.v1" element is for factory functions of supported styles
+computing forces (i.e.  command, pair, bond, angle, dihedral, or
+improper styles) and the function takes as single argument the pointer
+to the LAMMPS instance. The factory function is cast to the
+``lammpsplugin_factory1`` type before assignment.  The "creator.v2"
+element is for factory functions creating an instance of a fix, compute,
+or region style and takes three arguments: a pointer to the LAMMPS
+instance, an integer with the length of the argument list and a ``char
+**`` pointer to the list of arguments. The factory function pointer
+needs to be cast to the ``lammpsplugin_factory2`` type before
+assignment.
+
+Pair style example
+^^^^^^^^^^^^^^^^^^
+
+As an example, a hypothetical pair style plugin "morse2" implemented in
+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++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "pair_morse2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Pair *morse2creator(LAMMPS *lmp)
+  {
+    return new PairMorse2(lmp);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "pair";
+    plugin.name    = "morse2";
+    plugin.info    = "Morse2 variant pair style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v1 = (lammpsplugin_factory1 *) &morse2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+The factory function in this example is called ``morse2creator()``.  It
+receives a pointer to the LAMMPS class as only argument and thus has to
+be assigned to the *creator.v1* member of the plugin struct and cast to
+the ``lammpsplugin_factory1`` function pointer type.  It returns a
+pointer to the allocated class instance derived from the ``Pair`` class.
+This function may be declared static to avoid clashes with other
+plugins.  The name of the derived class, ``PairMorse2``, however must be
+unique inside the entire LAMMPS executable.
+
+Fix style example
+^^^^^^^^^^^^^^^^^
+
+If the factory function would be for a fix or compute, which take three
+arguments (a pointer to the LAMMPS class, the number of arguments and the
+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++
+
+  #include "lammpsplugin.h"
+  #include "version.h"
+  #include "fix_nve2.h"
+
+  using namespace LAMMPS_NS;
+
+  static Fix *nve2creator(LAMMPS *lmp, int argc, char **argv)
+  {
+    return new FixNVE2(lmp,argc,argv);
+  }
+
+  extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+  {
+    lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+    lammpsplugin_t plugin;
+
+    plugin.version = LAMMPS_VERSION;
+    plugin.style   = "fix";
+    plugin.name    = "nve2";
+    plugin.info    = "NVE2 variant fix style v1.0";
+    plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+    plugin.creator.v2 = (lammpsplugin_factory2 *) &nve2creator;
+    plugin.handle  = handle;
+    (*register_plugin)(&plugin,lmp);
+  }
+
+Command style example
+^^^^^^^^^^^^^^^^^^^^^
+Command styles also use the first variant of factory function as
+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++
+
+   #include "lammpsplugin.h"
+
+   #include "comm.h"
+   #include "error.h"
+   #include "command.h"
+   #include "version.h"
+
+   #include <cstring>
+
+   namespace LAMMPS_NS {
+     class Hello : public Command {
+      public:
+       Hello(class LAMMPS *lmp) : Command(lmp) {};
+       void command(int, char **);
+     };
+   }
+
+   using namespace LAMMPS_NS;
+
+   void Hello::command(int argc, char **argv)
+   {
+      if (argc != 1) error->all(FLERR,"Illegal hello command");
+      if (comm->me == 0)
+        utils::logmesg(lmp,fmt::format("Hello, {}!\n",argv[0]));
+   }
+
+   static void hellocreator(LAMMPS *lmp)
+   {
+     return new Hello(lmp);
+   }
+
+   extern "C" void lammpsplugin_init(void *lmp, void *handle, void *regfunc)
+   {
+     lammpsplugin_t plugin;
+     lammpsplugin_regfunc register_plugin = (lammpsplugin_regfunc) regfunc;
+
+     plugin.version = LAMMPS_VERSION;
+     plugin.style   = "command";
+     plugin.name    = "hello";
+     plugin.info    = "Hello world command v1.1";
+     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+     plugin.creator.v1 = (lammpsplugin_factory1 *) &hellocreator;
+     plugin.handle  = handle;
+     (*register_plugin)(&plugin,lmp);
+   }
+
+Additional Details
+^^^^^^^^^^^^^^^^^^
+
+The initialization function **must** be called ``lammpsplugin_init``, it
+**must** have C bindings and it takes three void pointers as arguments.
+The first is a pointer to the LAMMPS class that calls it and it needs to
+be passed to the registration function.  The second argument is a
+pointer to the internal handle of the DSO file, this needs to be added
+to the plugin info struct, so that the DSO can be closed and unloaded
+when all its contained plugins are unloaded.  The third argument is a
+function pointer to the registration function and needs to be stored
+in a variable of ``lammpsplugin_regfunc`` type and then called with a
+pointer to the ``lammpsplugin_t`` struct and the pointer to the LAMMPS
+instance as arguments to register a single plugin.  There may be multiple
+calls to multiple plugins in the same initialization function.
+
+To register a plugin a struct of the ``lammpsplugin_t`` needs to be filled
+with relevant info: current LAMMPS version string, kind of style, name of
+style, info string, author string, pointer to factory function, and the
+DSO handle.  The registration function is called with a pointer to the address
+of this struct and the pointer of the LAMMPS class.  The registration function
+will then add the factory function of the plugin style to the respective
+style map under the provided name.  It will also make a copy of the struct
+in a list of all loaded plugins and update the reference counter for loaded
+plugins from this specific DSO file.
+
+The pair style itself (i.e. the PairMorse2 class in this example) can be
+written just like any other pair style that is included in LAMMPS.  For
+a plugin, the use of the ``PairStyle`` macro in the section encapsulated
+by ``#ifdef PAIR_CLASS`` is not needed, since the mapping of the class
+name to the style name is done by the plugin registration function with
+the information from the ``lammpsplugin_t`` struct.  It may be included
+in case the new code is intended to be later included in LAMMPS directly.

doc/src/Developer_unittest.rst

@@ -4,10 +4,10 @@ Adding tests for unit testing
 This section discusses adding or expanding tests for the unit test
 infrastructure included into the LAMMPS source code distribution.
 Unlike example inputs, unit tests focus on testing the "local" behavior
-of individual features, tend to run very fast, and should be set up to
-cover as much of the added code as possible.  When contributing code to
-the distribution, the LAMMPS developers will appreciate if additions
-to the integrated unit test facility are included.
+of individual features, tend to run fast, and should be set up to cover
+as much of the added code as possible.  When contributing code to the
+distribution, the LAMMPS developers will appreciate if additions to the
+integrated unit test facility are included.
 
 Given the complex nature of MD simulations where many operations can
 only be performed when suitable "real" simulation environment has been
@@ -50,6 +50,9 @@ available:
    * - File name:
      - Test name:
      - Description:
+   * - ``test_argutils.cpp``
+     - ArgInfo
+     - Tests for ``ArgInfo`` class used by LAMMPS
    * - ``test_fmtlib.cpp``
      - FmtLib
      - Tests for ``fmtlib::`` functions used by LAMMPS
@@ -155,23 +158,27 @@ have the desired effect:
    {
        ASSERT_EQ(lmp->update->ntimestep, 0);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 10");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 10");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 10);
 
-       if (!verbose) ::testing::internal::CaptureStdout();
-       lmp->input->one("reset_timestep 0");
-       if (!verbose) ::testing::internal::GetCapturedStdout();
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 0");
+       END_HIDE_OUTPUT();
        ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       TEST_FAILURE(".*ERROR: Timestep must be >= 0.*", command("reset_timestep -10"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep"););
+       TEST_FAILURE(".*ERROR: Illegal reset_timestep .*", command("reset_timestep 10 10"););
+       TEST_FAILURE(".*ERROR: Expected integer .*", command("reset_timestep xxx"););
    }
 
-Please note the use of the (global) verbose variable to control whether
-the LAMMPS command will be silent by capturing the output or not.  In
-the default case, verbose == false, the test output will be compact and
-not mixed with LAMMPS output. However setting the verbose flag (via
-setting the ``TEST_ARGS`` environment variable, ``TEST_ARGS=-v``) can be
-helpful to understand why tests fail unexpectedly.
+Please note the use of the ``BEGIN_HIDE_OUTPUT`` and ``END_HIDE_OUTPUT``
+functions that will capture output from running LAMMPS.  This is normally
+discarded but by setting the verbose flag (via setting the ``TEST_ARGS``
+environment variable, ``TEST_ARGS=-v``) it can be printed and used to
+understand why tests fail unexpectedly.
 
 Another complexity of these tests stems from the need to capture
 situations where LAMMPS will stop with an error, i.e. handle so-called
@@ -210,6 +217,12 @@ The following test programs are currently available:
    * - ``test_lattice_region.cpp``
      - LatticeRegion
      - Tests to validate the :doc:`lattice <lattice>` and :doc:`region <region>` commands
+   * - ``test_groups.cpp``
+     - GroupTest
+     - Tests to validate the :doc:`group <group>` command
+   * - ``test_variables.cpp``
+     - VariableTest
+     - Tests to validate the :doc:`variable <variable>` command
    * - ``test_kim_commands.cpp``
      - KimCommands
      - Tests for several commands from the :ref:`KIM package <PKG-KIM>`

doc/src/Developer_utils.rst

@@ -9,14 +9,29 @@ reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
 reduces redundant implementations and encourages consistent behavior.
 
-I/O with status check
-^^^^^^^^^^^^^^^^^^^^^
+I/O with status check and similar functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-These are wrappers around the corresponding C library calls like
-``fgets()`` or ``fread()``.  They will check if there were errors
-on reading or an unexpected end-of-file state was reached.  In that
-case, the functions will stop the calculation with an error message,
-indicating the name of the problematic file, if possible.
+The the first two functions are wrappers around the corresponding C
+library calls ``fgets()`` or ``fread()``.  They will check if there
+were errors on reading or an unexpected end-of-file state was reached.
+In that case, the functions will stop with an error message, indicating
+the name of the problematic file, if possible unless the *error* argument
+is a NULL pointer.
+
+The :cpp:func:`fgets_trunc` function will work similar for ``fgets()``
+but it will read in a whole line (i.e. until the end of line or end
+of file), but store only as many characters as will fit into the buffer
+including a final newline character and the terminating NULL byte.
+If the line in the file is longer it will thus be truncated in the buffer.
+This function is used by :cpp:func:`read_lines_from_file` to read individual
+lines but make certain they follow the size constraints.
+
+The :cpp:func:`read_lines_from_file` function will read the requested
+number of lines of a maximum length into a buffer and will return 0
+if successful or 1 if not. It also guarantees that all lines are
+terminated with a newline character and the entire buffer with a
+NULL character.
 
 ----------
 
@@ -26,6 +41,12 @@ indicating the name of the problematic file, if possible.
 .. doxygenfunction:: sfread
    :project: progguide
 
+.. doxygenfunction:: fgets_trunc
+   :project: progguide
+
+.. doxygenfunction:: read_lines_from_file
+   :project: progguide
+
 ----------
 
 String to number conversions with validity check
@@ -101,6 +122,9 @@ and parsing files or arguments.
 .. doxygenfunction:: split_words
    :project: progguide
 
+.. doxygenfunction:: split_lines
+   :project: progguide
+
 .. doxygenfunction:: strmatch
    :project: progguide
 
@@ -161,7 +185,10 @@ Argument processing
 Convenience functions
 ^^^^^^^^^^^^^^^^^^^^^
 
-.. doxygenfunction:: logmesg
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const S &format, Args&&... args)
+   :project: progguide
+
+.. doxygenfunction:: logmesg(LAMMPS *lmp, const std::string &mesg)
    :project: progguide
 
 .. doxygenfunction:: getsyserror

doc/src/Examples.rst

@@ -108,6 +108,8 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | msst        | MSST shock dynamics                                              |
 +-------------+------------------------------------------------------------------+
+| multi       | multi neighboring for systems with large interaction disparities |
++-------------+------------------------------------------------------------------+
 | nb3b        | use of non-bonded 3-body harmonic pair style                     |
 +-------------+------------------------------------------------------------------+
 | neb         | nudged elastic band (NEB) calculation for barrier finding        |

doc/src/Howto.rst

@@ -23,6 +23,7 @@ General howto
    Howto_library
    Howto_couple
    Howto_client_server
+   Howto_mdi
 
 Settings howto
 ==============

doc/src/Howto_bioFF.rst

@@ -91,6 +91,7 @@ documentation for the formula it computes.
 * :doc:`bond_style <bond_harmonic>` harmonic
 * :doc:`bond_style <bond_morse>` morse
 
+* :doc:`angle_style <angle_cosine_squared>` cosine/squared
 * :doc:`angle_style <angle_harmonic>` harmonic
 * :doc:`angle_style <angle_cosine>` cosine
 * :doc:`angle_style <angle_cosine_periodic>` cosine/periodic

doc/src/Howto_cmake.rst

@@ -411,10 +411,10 @@ interface (``ccmake`` or ``cmake-gui``).
 .. note::
 
    Using a preset to select a compiler package (``clang.cmake``,
-   ``gcc.cmake``, or ``intel.cmake``) are an exception to the option
-   of updating the configuration incrementally, as they will trigger
-   a reset of cached internal CMake settings and thus reset them to
-   their default values.
+   ``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
+   are an exception to the mechanism of updating the configuration incrementally,
+   as they will trigger a reset of cached internal CMake settings and thus
+   reset settings to their default values.
 
 Compilation and build targets
 -----------------------------

doc/src/Howto_drude2.rst

@@ -9,6 +9,8 @@ USER-DRUDE package activated. Then, the data file and input scripts
 have to be modified to include the Drude dipoles and how to handle
 them.
 
+Example input scripts available: examples/USER/drude
+
 ----------
 
 **Overview of Drude induced dipoles**

doc/src/Howto_granular.rst

@@ -18,12 +18,13 @@ This compute
 
 calculates rotational kinetic energy which can be :doc:`output with thermodynamic info <Howto_output>`.
 
-Use one of these 3 pair potentials, which compute forces and torques
+Use one of these 4 pair potentials, which compute forces and torques
 between interacting pairs of particles:
 
-* :doc:`pair_style <pair_style>` gran/history
-* :doc:`pair_style <pair_style>` gran/no_history
-* :doc:`pair_style <pair_style>` gran/hertzian
+* :doc:`pair_style gran/history <pair_gran>`
+* :doc:`pair_style gran/no_history <pair_gran>`
+* :doc:`pair_style gran/hertzian <pair_gran>`
+* :doc:`pair_style granular <pair_granular>`
 
 These commands implement fix options specific to granular systems:
 
@@ -31,6 +32,7 @@ These commands implement fix options specific to granular systems:
 * :doc:`fix pour <fix_pour>`
 * :doc:`fix viscous <fix_viscous>`
 * :doc:`fix wall/gran <fix_wall_gran>`
+* :doc:`fix wall/gran/region <fix_wall_gran_region>`
 
 The fix style *freeze* zeroes both the force and torque of frozen
 atoms, and should be used for granular system instead of the fix style

doc/src/Howto_mdi.rst

@@ -0,0 +1,132 @@
+Using LAMMPS with the MDI library for code coupling
+===================================================
+
+..note::
+
+  This Howto doc page will eventually replace the
+  :doc:`Howto client/server <Howto_client_server>` doc page.
+
+Client/server coupling of two codes is where one code is the "client"
+and sends request messages (data) to a "server" code.  The server
+responds to each request with a reply message.  This enables the two
+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>`_,
+developed by the `Molecular Sciences Software Institute (MolSSI)
+<https://molssi.org>`_.
+
+Alternate methods for code coupling with LAMMPS are described on the
+:doc:`Howto couple <Howto_couple>` doc page.
+
+Some advantages of client/server coupling are that the two codes can run
+as stand-alone executables; they need not be linked together.  Thus
+neither code needs to have a library interface.  This also makes it easy
+to run the two codes on different numbers of processors.  If a message
+protocol (format and content) is defined for a particular kind of
+simulation, then in principle any code which implements the client-side
+protocol can be used in tandem with any code which implements the
+server-side protocol.  Neither code needs to know what specific other
+code it is working with.
+
+In MDI nomenclature, a client code is the "driver", and a server code is
+an "engine".  One driver code can communicate with one or more instances
+of one or more engine codes.  Driver and engine codes can be written in
+any language: C, C++, Fortran, Python, etc.
+
+In addition to allowing driver and engine(s) running to run as
+stand-alone executables, MDI also enables a server code to be a
+"plugin" to the client code.  In this scenario, server code(s) are
+compiled as shared libraries, and one (or more) instances of the
+server are instantiated by the driver code.  If the driver code runs
+in parallel, it can split its MPI communicator into multiple
+sub-communicators, and launch each plugin engine instance on a
+sub-communicator.  Driver processors in that sub-communicator exchange
+messages with that engine instance, and can also send MPI messages to
+other processors in the driver.  The driver code can also destroy
+engine instances and re-instantiate them.
+
+The way that a driver communicates with an engine is by making
+MDI_Send() and MDI_Recv() calls, which are conceptually similar to
+MPI_Send() and MPI_Recv() calls.  Each send or receive has a string
+which identifies the command name, and optionally some data, which can
+be a single value or vector of values of any data type.  Inside the
+MDI library, data is exchanged between the driver and engine via MPI
+calls or sockets.  This a run-time choice by the user.
+
+-------------
+
+As an example, LAMMPS and the ``pw.x`` command from Quantum Espresso (a
+suite of quantum DFT codes), can work together via the MDI library to
+perform an ab initio MD (AIMD) simulation, where LAMMPS runs an MD
+simulation and sends a message each timestep to ``pw.x`` asking it to
+compute quantum forces on the current configuration of atoms.  Here is
+how the 2 codes are launched to communicate by MPI:
+
+.. code-block:: bash
+
+% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method MPI" \
+   -in in.aimd : -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method MPI"
+
+In this case LAMMPS runs on 2 processors (MPI tasks), ``pw.x`` runs on 16
+processors.
+
+Here is how the 2 codes are launched to communicate by sockets:
+
+.. code-block:: bash
+
+% mpirun -np 2 lmp_mpi -mdi "-role DRIVER -name d -method TCP -port 8021" -in in.aimd
+% mpirun -np 16 pw.x -in qe.in -mdi "-role ENGINE -name e -method TCP -port 8021 -hostname localhost"
+
+These commands could be issued in different windows on a desktop
+machine.  Or in the same window, if the first command is ended with
+"&" so as to run in the background.  If "localhost" is replaced by an
+IP address, ``pw.x`` could be run on another machine on the same network, or
+even on another machine across the country.
+
+After both codes initialize themselves to model the same system, this is
+what occurs each timestep:
+
+* LAMMPS send a ">COORDS" message to ``pw.x`` with a 3*N vector of current atom coords
+* ``pw.x`` receives the message/coords and computes quantum forces on all the atoms
+* LAMMPS send a "<FORCES" message to ``pw.x`` and waits for the result
+* ``pw.x`` receives the message (after its computation finishes) and sends a 3*N vector of forces
+* LAMMPS receives the forces and time integrates to complete a single timestep
+
+-------------
+
+Examples scripts for using LAMMPS as an MDI engine are in the
+examples/mdi directory.  See the README file in that directory for
+instructions on how to run the examples.
+
+..note::
+
+  Work is underway to add commands that allow LAMMPS to be used as an
+  MDI driver, e.g. for the AIMD example discussed above.  Example
+  scripts for this usage mode will be added the same directory when
+  available.
+
+If LAMMPS is used as a stand-alone engine it should set up the system
+it will be modeling in its input script, then invoke the
+:doc:`mdi/engine <mdi_engine>` command.  This will put LAMMPS into
+engine mode where it waits for messages and data from the driver.
+When the driver sends an "EXIT" command, LAMMPS will exit engine mode
+and the input script will continue.
+
+If LAMMPS is used as a plugin engine it operates the same way, except
+that the driver will pass LAMMPS an input script to initialize itself.
+Upon receiving the "EXIT" command, LAMMPS will exit engine mode and the
+input script will continue.  After finishing execution of the input
+script, the instance of LAMMPS will be destroyed.
+
+LAMMPS supports the full set of MD-appropriate engine commands defined
+by the MDI library.  See the :doc:`mdi/engine <mdi_engine>` doc page for
+a list of these.
+
+If those commands are not sufficient for a user-developed driver to use
+LAMMPS as an engine, then new commands can be easily added.  See these
+two files which implement the definition of MDI commands and the logic
+for responding to them:
+
+* src/MDI/mdi_engine.cpp
+* src/MDI/fix_mdi_engine.cpp

doc/src/Howto_spins.rst

@@ -21,8 +21,8 @@ orientations and their associated inter-atomic distances.
 
 The command :doc:`fix precession/spin <fix_precession_spin>` allows to
 apply a constant magnetic torque on all the spins in the system. This
-torque can be an external magnetic field (Zeeman interaction), or an
-uniaxial magnetic anisotropy.
+torque can be an external magnetic field (Zeeman interaction), and an
+uniaxial or cubic magnetic anisotropy.
 
 A Langevin thermostat can be applied to those magnetic spins using
 :doc:`fix langevin/spin <fix_langevin_spin>`. Typically, this thermostat

doc/src/Install_git.rst

@@ -86,33 +86,59 @@ check out any other desired branch) first.
 
 Once you have updated your local files with a ``git pull`` (or ``git
 checkout``), you still need to re-build LAMMPS if any source files have
-changed.  To do this, you should cd to the src directory and type:
+changed.  How to do this depends on the build system you are using.
 
-.. code-block:: bash
+.. tabs::
 
-   $ 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)
+   .. tab:: CMake build
 
-just as described on the :doc:`Apply patch <Install_patch>` page,
-after a patch has been installed.
+      Change to your build folder and type:
 
-.. warning::
+      .. code-block:: bash
 
-   If you wish to edit/change a src file that is from a
-   package, you should edit the version of the file inside the package
-   sub-directory with src, then re-install the package.  The version in
-   the source directory is merely a copy and will be wiped out if you type "make
-   package-update".
+         cmake . --build
 
-.. warning::
+      CMake should auto-detect whether it needs to re-run the CMake
+      configuration step and otherwise redo the build for all files
+      that have been changed or files that depend on changed files.
+      In case some build options have been changed or renamed, you
+      may have to update those by running:
 
-   The GitHub servers support both the "git://" and
-   "https://" access protocols for anonymous read-only access.  If you
-   have a correspondingly configured GitHub account, you may also use
-   SSH access with the URL "git@github.com:lammps/lammps.git".
+      .. code-block:: bash
 
-The LAMMPS GitHub project is managed by Christoph Junghans (LANL,
-junghans at lanl.gov), Axel Kohlmeyer (Temple U, akohlmey at
-gmail.com) and Richard Berger (Temple U, richard.berger at
-temple.edu).
+         cmake .
+
+      and then rebuild.
+
+   .. tab:: Traditional make
+
+      Switch to the src directory and type:
+
+      .. 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)
+
+      Just as described on the :doc:`Apply patch <Install_patch>` page,
+      after a patch has been installed.
+
+      .. warning::
+
+         If you wish to edit/change a src file that is from a package,
+         you should edit the version of the file inside the package
+         sub-directory with src, then re-install the package.  The
+         version in the source directory is merely a copy and will be
+         wiped out if you type "make package-update".
+
+.. admonition:: Git protocols
+   :class: note
+
+   The servers at github.com support the "git://" and "https://" access
+   protocols 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".
+
+The LAMMPS GitHub project is currently managed by Axel Kohlmeyer
+(Temple U, akohlmey at gmail.com) and Richard Berger (Temple U,
+richard.berger at temple.edu).

doc/src/Install_patch.rst

@@ -43,24 +43,54 @@ up to date.
 * A list of updated files print out to the screen.  The -b switch
   creates backup files of your originals (e.g. src/force.cpp.orig), so
   you can manually undo the patch if something goes wrong.
-* Type the following from the src directory, to enforce consistency
-  between the src and package directories.  This is OK to do even if you
-  don't use one or more packages.  If you are applying several patches
-  successively, you only need to type this once at the end. The purge
-  command removes deprecated src files if any were removed by the patch
-  from package sub-directories.
 
-  .. code-block:: bash
+* Once you have updated your local files you need to re-build LAMMPS.
+  If you are applying several patches successively, you only need to
+  do the rebuild once at the end. How to do it depends on the build
+  system you are using.
 
-     $ make purge
-     $ make package-update
+  .. tabs::
 
-* Re-build LAMMPS via the "make" command.
+     .. tab:: CMake build
 
-.. warning::
+        Change to your build folder and type:
 
-   If you wish to edit/change a source file that is part of a package,
-   you should edit the version of the file inside the package folder in
-   src, and then re-install or update the package.  The version in the
-   src directory is merely a copy and will be wiped out when you type
-   "make package-update".
+        .. code-block:: bash
+
+           cmake . --build
+
+        CMake should auto-detect whether it needs to re-run the CMake
+        configuration step and otherwise redo the build for all files
+        that have been changed or files that depend on changed files.
+        In case some build options have been changed or renamed, you
+        may have to update those by running:
+
+        .. code-block:: bash
+
+           cmake .
+
+        and then rebuild.
+
+     .. tab:: Traditional make
+
+        Switch to the src directory and type:
+
+        .. 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)
+
+        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
+        src files if they were removed by the patch from a package
+        sub-directory.
+
+        .. warning::
+
+           If you wish to edit/change a src file that is from a package,
+           you should edit the version of the file inside the package
+           sub-directory with src, then re-install the package.  The
+           version in the source directory is merely a copy and will be
+           wiped out if you type "make package-update".

doc/src/Library_config.rst

@@ -15,6 +15,8 @@ This section documents the following functions:
 - :cpp:func:`lammps_config_package_count`
 - :cpp:func:`lammps_config_package_name`
 - :cpp:func:`lammps_config_accelerator`
+- :cpp:func:`lammps_has_gpu_device`
+- :cpp:func:`lammps_gpu_device_info`
 - :cpp:func:`lammps_has_style`
 - :cpp:func:`lammps_style_count`
 - :cpp:func:`lammps_style_name`
@@ -132,6 +134,16 @@ approach.
 
 -----------------------
 
+.. doxygenfunction:: lammps_has_gpu_device
+   :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_get_gpu_device_info
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_has_style
    :project: progguide
 

doc/src/Library_scatter.rst

@@ -76,7 +76,7 @@ It documents the following functions:
 
 -----------------------
 
-.. doxygenfunction:: lammps_create_atoms(void *handle, int n, int *id, int *type, double *x, double *v, int *image, int bexpand)
+.. doxygenfunction:: lammps_create_atoms(void *handle, int n, const int *id, const int *type, const double *x, const double *v, const int *image, int bexpand)
    :project: progguide
 
 

doc/src/Manual.rst

@@ -89,10 +89,15 @@ Programmer Guide
    Modify
    Developer
 
+*****************
+Command Reference
+*****************
+
+.. _command_reference:
 .. toctree::
-   :caption: Index
-   :name: index
-   :hidden:
+   :name: reference
+   :maxdepth: 1
+   :caption: Command Reference
 
    commands_list
    fixes
@@ -118,7 +123,7 @@ Indices and tables
 .. admonition:: Web Browser Compatibility
 
    The HTML version of the manual makes use of advanced features present
-   int "modern" web browsers.  This can lead to incompatibilities with older
+   in "modern" web browsers.  This can lead to incompatibilities with older
    web browsers (released more than 4 years ago) and specific vendor browsers
    (e.g. Internet Explorer on Windows; Microsoft Edge works well though)
    where parts of the pages are not rendered as expected (e.g. the layout is

doc/src/Modify_command.rst

@@ -1,14 +1,15 @@
 Input script command style
 ==========================
 
-New commands can be added to LAMMPS input scripts by adding new
-classes that have a "command" method.  For example, the create_atoms,
-read_data, velocity, and run commands are all implemented in this
-fashion.  When such a command is encountered in the LAMMPS input
-script, LAMMPS simply creates a class with the corresponding name,
-invokes the "command" method of the class, and passes it the arguments
-from the input script.  The command method can perform whatever
-operations it wishes on LAMMPS data structures.
+New commands can be added to LAMMPS input scripts by adding new classes
+that are derived from the Command class and thus must have a "command"
+method.  For example, the create_atoms, read_data, velocity, and run
+commands are all implemented in this fashion.  When such a command is
+encountered in the LAMMPS input script, LAMMPS simply creates a class
+instance with the corresponding name, invokes the "command" method of
+the class, and passes it the arguments from the input script.  The
+command method can perform whatever operations it wishes on LAMMPS data
+structures.
 
 The single method your new class must define is as follows:
 

doc/src/Modify_contribute.rst

@@ -10,15 +10,15 @@ Tutorial <Howto_github>` for a demonstration on how to do that.  An
 alternative is to contact the LAMMPS developers or the indicated
 developer of a package or feature directly and send in your contribution
 via e-mail, but that can add a significant delay on getting your
-contribution included, depending on how busy the developer is you
-contact, how complex a task it would be to integrate that code, and how
+contribution included, depending on how busy the respective developer
+is, how complex a task it would be to integrate that code, and how
 many - if any - changes are required before the code can be included.
 
 For any larger modifications or programming project, you are encouraged
-to contact the LAMMPS developers ahead of time, in order to discuss
-implementation strategies and coding guidelines, that will make it
-easier to integrate your contribution and result in less work for
-everybody involved. You are also encouraged to search through the list
+to contact the LAMMPS developers ahead of time in order to discuss
+implementation strategies and coding guidelines. That will make it
+easier to integrate your contribution and results in less work for
+everybody involved.  You are also encouraged to search through the list
 of `open issues on GitHub <https://github.com/lammps/lammps/issues>`_
 and submit a new issue for a planned feature, so you would not duplicate
 the work of others (and possibly get scooped by them) or have your work
@@ -34,18 +34,19 @@ installing, or using LAMMPS. Please contact the `lammps-users mailing
 list <https://lammps.sandia.gov/mail.html>`_ for those purposes instead.
 
 How quickly your contribution will be integrated depends largely on how
-much effort it will cause to integrate and test it, how much it requires
-changes to the core codebase, and of how much interest it is to the
-larger LAMMPS community.  Please see below for a checklist of typical
-requirements. Once you have prepared everything, see the :doc:`LAMMPS GitHub
-Tutorial <Howto_github>` page for instructions on
-how to submit your changes or new files through a GitHub pull
-request. If you prefer to submit patches or full files, you should first
-make certain, that your code works correctly with the latest patch-level
-version of LAMMPS and contains all bug fixes from it. Then create a
-gzipped tar file of all changed or added files or a corresponding patch
-file using 'diff -u' or 'diff -c' and compress it with gzip. Please only
-use gzip compression, as this works well on all platforms.
+much effort it will cause to integrate and test it, how many and what
+kind of changes it requires to the core codebase, and of how much
+interest it is to the larger LAMMPS community.  Please see below for a
+checklist of typical requirements.  Once you have prepared everything,
+see the :doc:`LAMMPS GitHub Tutorial <Howto_github>` page for
+instructions on how to submit your changes or new files through a GitHub
+pull request.  If you prefer to submit patches or full files, you should
+first make certain, that your code works correctly with the latest
+patch-level version of LAMMPS and contains all bug fixes from it.  Then
+create a gzipped tar file of all changed or added files or a
+corresponding patch file using 'diff -u' or 'diff -c' and compress it
+with gzip.  Please only use gzip compression, as this works well and is
+available on all platforms.
 
 If the new features/files are broadly useful we may add them as core
 files to LAMMPS or as part of a :doc:`standard package <Packages_standard>`.  Else we will add them as a
@@ -57,9 +58,12 @@ added to the LAMMPS distribution.  All the standard and user packages
 are listed and described on the :doc:`Packages details <Packages_details>` doc page.
 
 Note that by providing us files to release, you are agreeing to make
-them open-source, i.e. we can release them under the terms of the GPL,
-used as a license for the rest of LAMMPS.  See the :doc:`LAMMPS license
-<Intro_opensource>` doc page for details.
+them open-source, i.e. we can release them under the terms of the GPL
+(version 2), used as a license for the rest of LAMMPS.  And as part of
+a LGPL (version 2.1) distribution that we make available to developers
+on request only and with files that are authorized for that kind of
+distribution removed (e.g. interface to FFTW).  See the
+:doc:`LAMMPS license <Intro_opensource>` doc page for details.
 
 With user packages and files, all we are really providing (aside from
 the fame and fortune that accompanies having your name in the source
@@ -112,7 +116,7 @@ packages in the src directory for examples. If you are uncertain, please ask.
   your contribution(s) to be added to main LAMMPS code or one of its
   standard packages, it needs to be written in a style compatible with
   other LAMMPS source files. This means: 2-character indentation per
-  level, **no tabs**\ , no lines over 80 characters. I/O is done via
+  level, **no tabs**\ , no lines over 100 characters. I/O is done via
   the C-style stdio library (mixing of stdio and iostreams is generally
   discouraged), class header files should not import any system headers
   outside of <cstdio>, STL containers should be avoided in headers,
@@ -131,6 +135,31 @@ packages in the src directory for examples. If you are uncertain, please ask.
   LAMMPS source files, including the use of the error class for error
   and warning messages.
 
+* To simplify reformatting contributed code in a way that is compatible
+  with the LAMMPS formatting styles, you can use clang-format (version 8
+  or later).  The LAMMPS distribution includes a suitable ``.clang-format``
+  file which will be applied if you run ``clang-format -i some_file.cpp``
+  on your files inside the LAMMPS src tree.  Please only reformat files
+  that you have contributed.  For header files containing a
+  ``SomeStyle(keyword, ClassName)`` macros it is required to have this
+  macro embedded with a pair of ``// clang-format off``, ``// clang-format on``
+  commends and the line must be terminated with a semi-colon (;).
+  Example:
+
+  .. code-block:: c++
+
+     #ifdef COMMAND_CLASS
+     // clang-format off
+     CommandStyle(run,Run);
+     // clang-format on
+     #else
+
+     #ifndef LMP_RUN_H
+     [...]
+
+  You may also use ``// clang-format on/off`` throughout your file
+  to protect sections of the file from being reformatted.
+
 * If you want your contribution to be added as a user-contributed
   feature, and it's a single file (actually a \*.cpp and \*.h file) it can
   rapidly be added to the USER-MISC directory.  Send us the one-line

doc/src/Packages_details.rst

@@ -50,6 +50,7 @@ page gives those details.
    * :ref:`MSCG <PKG-MSCG>`
    * :ref:`OPT <PKG-OPT>`
    * :ref:`PERI <PKG-PERI>`
+   * :ref:`PLUGIN <PKG-PLUGIN>`
    * :ref:`POEMS <PKG-POEMS>`
    * :ref:`PYTHON <PKG-PYTHON>`
    * :ref:`QEQ <PKG-QEQ>`
@@ -68,6 +69,7 @@ page gives those details.
    * :ref:`USER-ATC <PKG-USER-ATC>`
    * :ref:`USER-AWPMD <PKG-USER-AWPMD>`
    * :ref:`USER-BOCS <PKG-USER-BOCS>`
+   * :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`
    * :ref:`USER-CGDNA <PKG-USER-CGDNA>`
    * :ref:`USER-CGSDK <PKG-USER-CGSDK>`
    * :ref:`USER-COLVARS <PKG-USER-COLVARS>`
@@ -80,6 +82,7 @@ page gives those details.
    * :ref:`USER-INTEL <PKG-USER-INTEL>`
    * :ref:`USER-LB <PKG-USER-LB>`
    * :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`
+   * :ref:`USER-MDI <PKG-USER-MDI>`
    * :ref:`USER-MEAMC <PKG-USER-MEAMC>`
    * :ref:`USER-MESODPD <PKG-USER-MESODPD>`
    * :ref:`USER-MESONT <PKG-USER-MESONT>`
@@ -89,6 +92,7 @@ page gives those details.
    * :ref:`USER-MOLFILE <PKG-USER-MOLFILE>`
    * :ref:`USER-NETCDF <PKG-USER-NETCDF>`
    * :ref:`USER-OMP <PKG-USER-OMP>`
+   * :ref:`USER-PACE <PKG-USER-PACE>`
    * :ref:`USER-PHONON <PKG-USER-PHONON>`
    * :ref:`USER-PLUMED <PKG-USER-PLUMED>`
    * :ref:`USER-PTM <PKG-USER-PTM>`
@@ -584,7 +588,7 @@ MC package
 Several fixes and a pair style that have Monte Carlo (MC) or MC-like
 attributes.  These include fixes for creating, breaking, and swapping
 bonds, for performing atomic swaps, and performing grand-canonical MC
-(GCMC) in conjunction with dynamics.
+(GCMC) or similar processes in conjunction with dynamics.
 
 **Supporting info:**
 
@@ -592,8 +596,12 @@ bonds, for performing atomic swaps, and performing grand-canonical MC
 * :doc:`fix atom/swap <fix_atom_swap>`
 * :doc:`fix bond/break <fix_bond_break>`
 * :doc:`fix bond/create <fix_bond_create>`
+* :doc:`fix bond/create/angle <fix_bond_create>`
 * :doc:`fix bond/swap <fix_bond_swap>`
+* :doc:`fix charge/regulation <fix_charge_regulation>`
 * :doc:`fix gcmc <fix_gcmc>`
+* :doc:`fix tfmc <fix_tfmc>`
+* :doc:`fix widom <fix_widom>`
 * :doc:`pair_style dsmc <pair_dsmc>`
 * https://lammps.sandia.gov/movies.html#gcmc
 
@@ -843,6 +851,28 @@ Foster (UTSA).
 
 ----------
 
+.. _PKG-PLUGIN:
+
+PLUGIN package
+--------------
+
+**Contents:**
+
+A :doc:`plugin <plugin>` command that can load and unload several
+kind of styles in LAMMPS from shared object files at runtime without
+having to recompile and relink LAMMPS.
+
+**Authors:** Axel Kohlmeyer (Temple U)
+
+**Supporting info:**
+
+* src/PLUGIN: filenames -> commands
+* :doc:`plugin command <plugin>`
+* :doc:`Information on writing plugins <Developer_plugins>`
+* examples/plugin
+
+----------
+
 .. _PKG-POEMS:
 
 POEMS package
@@ -1238,6 +1268,26 @@ Example inputs are in the examples/USER/bocs folder.
 
 ----------
 
+.. _PKG-USER-BROWNIAN:
+
+USER-BROWNIAN package
+---------------------
+
+**Contents:**
+
+This package provides :doc:`fix brownian, fix brownian/sphere, and
+fix brownian/asphere <fix_brownian>` as well as
+:doc:`fix propel/self <fix_propel_self>` which allow to do Brownian
+Dynamics time integration of point, spherical and aspherical particles
+and also support self-propelled particles.
+
+**Authors:** Sam Cameron (University of Bristol),
+Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
+
+Example inputs are in the examples/USER/brownian folder.
+
+----------
+
 .. _PKG-USER-CGDNA:
 
 USER-CGDNA package
@@ -1326,6 +1376,46 @@ This package has :ref:`specific installation instructions <user-colvars>` on the
 
 ----------
 
+.. _PKG-USER-PACE:
+
+USER-PACE package
+-------------------
+
+**Contents:**
+
+A pair style for the Atomic Cluster Expansion potential (ACE).
+ACE is a methodology for deriving a highly accurate classical potential
+fit to a large archive of quantum mechanical (DFT) data. The USER-PACE
+package provides an efficient implementation for running simulations
+with ACE potentials.
+
+**Authors:**
+
+This package was written by Yury Lysogorskiy^1,
+Cas van der Oord^2, Anton Bochkarev^1,
+Sarath Menon^1, Matteo Rinaldi^1, Thomas Hammerschmidt^1, Matous Mrovec^1,
+Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
+
+ ^1: Ruhr-University Bochum, Bochum, Germany
+
+ ^2: University of Cambridge, Cambridge, United Kingdom
+
+ ^3: Sandia National Laboratories, Albuquerque, New Mexico, USA
+
+ ^4: University of British Columbia, Vancouver, BC, Canada
+
+**Install:**
+
+This package has :ref:`specific installation instructions <user-pace>` on the :doc:`Build extras <Build_extras>` page.
+
+**Supporting info:**
+
+* src/USER-PACE: filenames -> commands
+* :doc:`pair_style pace <pair_pace>`
+* examples/USER/pace
+
+----------
+
 .. _PKG-USER-PLUMED:
 
 USER-PLUMED package
@@ -1702,6 +1792,28 @@ Waltham, MA, USA)
 
 ----------
 
+.. _PKG-USER-MDI:
+
+USER-MDI package
+----------------
+
+**Contents:**
+
+A LAMMPS command and fix to allow client-server coupling of LAMMPS to
+other atomic or molecular simulation codes via the `MolSSI Driver Interface
+(MDI) library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
+
+**Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
+
+**Supporting info:**
+
+* src/USER-MDI/README
+* :doc:`mdi/engine <mdi_engine>`
+* :doc:`fix mdi/engine <fix_mdi_engine>`
+* examples/USER/mdi
+
+----------
+
 .. _PKG-USER-MEAMC:
 
 USER-MEAMC package
@@ -2456,6 +2568,6 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 * :doc:`bond_style mm3 <bond_mm3>`
 * :doc:`improper_style distharm <improper_distharm>`
 * :doc:`improper_style sqdistharm <improper_sqdistharm>`
-* :doc:`pair_style mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
+* :doc:`pair_style mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * :doc:`pair_style lj/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
 * examples/USER/yaff

doc/src/Packages_standard.rst

@@ -71,6 +71,8 @@ package:
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PERI <PKG-PERI>`           | Peridynamics models                  | :doc:`pair_style peri <pair_peri>`                 | peri                                                 | no      |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`PLUGIN <PKG-PLUGIN>`       | Plugin loader command                | :doc:`plugin <plugin>`                             | plugins                                              | no      |
++----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`POEMS <PKG-POEMS>`         | coupled rigid body motion            | :doc:`fix poems <fix_poems>`                       | rigid                                                | int     |
 +----------------------------------+--------------------------------------+----------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`PYTHON <PKG-PYTHON>`       | embed Python code in an input script | :doc:`python <python>`                             | python                                               | sys     |

doc/src/Packages_user.rst

@@ -39,6 +39,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-BOCS <PKG-USER-BOCS>`               | BOCS bottom up coarse graining                                  | :doc:`fix bocs <fix_bocs>`                                                    | USER/bocs                                            | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-BROWNIAN <PKG-USER-BROWNIAN>`       | Brownian dynamics and self-propelled particles                  | :doc:`fix brownian <fix_brownian>`, :doc:`fix propel/self <fix_propel_self>`  | USER/brownian                                        | no      |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-CGDNA <PKG-USER-CGDNA>`             | coarse-grained DNA force fields                                 | src/USER-CGDNA/README                                                         | USER/cgdna                                           | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-CGSDK <PKG-USER-CGSDK>`             | SDK coarse-graining model                                       | :doc:`pair_style lj/sdk <pair_sdk>`                                           | USER/cgsdk                                           | no      |
@@ -63,6 +65,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MANIFOLD <PKG-USER-MANIFOLD>`       | motion on 2d surfaces                                           | :doc:`fix manifoldforce <fix_manifoldforce>`                                  | USER/manifold                                        | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-MDI <PKG-USER-MDI>`                 | client-server coupling                                          | :doc:`MDI Howto <Howto_mdi>`                                                  | USER/mdi                                             | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MEAMC <PKG-USER-MEAMC>`             | modified EAM potential (C++)                                    | :doc:`pair_style meam/c <pair_meamc>`                                         | meamc                                                | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-MESODPD <PKG-USER-MESODPD>`         | mesoscale DPD models                                            | :doc:`pair_style edpd <pair_mesodpd>`                                         | USER/mesodpd                                         | no      |
@@ -81,6 +85,8 @@ package:
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-OMP <PKG-USER-OMP>`                 | OpenMP-enabled styles                                           | :doc:`Speed omp <Speed_omp>`                                                  | `Benchmarks <https://lammps.sandia.gov/bench.html>`_ | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
+| :ref:`USER-PACE <PKG-USER-PACE>`               | Fast implementation of Atomic Cluster Expansion (ACE) potential | :doc:`pair pace <pair_pace>`                                                  | USER/pace                                            | ext     |
++------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PHONON <PKG-USER-PHONON>`           | phonon dynamical matrix                                         | :doc:`fix phonon <fix_phonon>`                                                | USER/phonon                                          | no      |
 +------------------------------------------------+-----------------------------------------------------------------+-------------------------------------------------------------------------------+------------------------------------------------------+---------+
 | :ref:`USER-PLUMED <PKG-USER-PLUMED>`           | :ref:`PLUMED <PLUMED>` free energy library                      | :doc:`fix plumed <fix_plumed>`                                                | USER/plumed                                          | ext     |

doc/src/Python_module.rst

@@ -142,7 +142,7 @@ Style Constants
 Type Constants
 --------------
 
-.. py:data:: LMP_TYPE_SCALAR, LMP_TYLE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
+.. py:data:: LMP_TYPE_SCALAR, LMP_TYPE_VECTOR, LMP_TYPE_ARRAY, LMP_SIZE_VECTOR, LMP_SIZE_ROWS, LMP_SIZE_COLS
    :type: int
 
    Constants in the :py:mod:`lammps` module to select what type of data

doc/src/Python_neighbor.rst

@@ -1,6 +1,43 @@
 Neighbor list access
 ====================
 
+Access to neighbor lists is handled through a couple of wrapper classes
+that allows to treat it like either a python list or a NumPy array.  The
+access procedure is similar to that of the C-library interface: use one
+of the "find" functions to look up the index of the neighbor list in the
+global table of neighbor lists and then get access to the neighbor list
+data. The code sample below demonstrates reading the neighbor list data
+using the NumPy access method.
+
+.. code-block:: python
+
+   from lammps import lammps
+   import numpy as np
+
+   lmp = lammps()
+   lmp.commands_string("""
+   region box block -2 2 -2 2 -2 2
+   lattice fcc 1.0
+   create_box 1 box
+   create_atoms 1 box
+   mass 1 1.0
+   pair_style lj/cut 2.5
+   pair_coeff 1 1 1.0 1.0
+   run 0 post no""")
+
+   # look up the neighbor list
+   nlidx = lmp.find_pair_neighlist('lj/cut')
+   nl = lmp.numpy.get_neighlist(nlidx)
+   tags = lmp.extract_atom('id')
+   print("half neighbor list with {} entries".format(nl.size))
+   # print neighbor list contents
+   for i in range(0,nl.size):
+       idx, nlist  = nl.get(i)
+       print("\natom {} with ID {} has {} neighbors:".format(idx,tags[idx],nlist.size))
+       if nlist.size > 0:
+           for n in np.nditer(nlist):
+               print("  atom {} with ID {}".format(n,tags[n]))
+
 **Methods:**
 
 * :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

doc/src/Tools.rst

@@ -93,6 +93,8 @@ Miscellaneous tools
    * :ref:`i-pi <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
+   * :ref:`LAMMPS magic patterns for file(1) <magic>`
+   * :ref:`Offline build tool <offline>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -641,6 +643,39 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 ----------
 
+.. _magic:
+
+Magic patterns for the "file" command
+-------------------------------------
+
+.. versionadded:: 10Mar2021
+
+The file ``magic`` contains patterns that are used by the
+`file program <https://en.wikipedia.org/wiki/File_(command)>`_
+available on most Unix-like operating systems which enables it
+to detect various LAMMPS files and print some useful information
+about them.  To enable these patterns, append or copy the contents
+of the file to either the file ``.magic`` in your home directory
+or (as administrator) to ``/etc/magic`` (for a system-wide
+installation).  Afterwards the ``file`` command should be able to
+detect most LAMMPS restarts, dump, data and log files. Examples:
+
+.. code-block:: bash
+
+   $ file *.*
+   dihedral-quadratic.restart:   LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
+   mol-pair-wf_cut.restart:      LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
+   atom.bin:                     LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
+   custom.bin:                   LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
+   bn1.lammpstrj:                LAMMPS text mode dump, First time step: 5000
+   data.fourmol:                 LAMMPS data file written by LAMMPS
+   pnc.data:                     LAMMPS data file written by msi2lmp
+   data.spce:                    LAMMPS data file written by TopoTools
+   B.data:                       LAMMPS data file written by OVITO
+   log.lammps:                   LAMMPS log file written by version 10 Feb 2021
+
+----------
+
 .. _matlab:
 
 matlab tool
@@ -722,6 +757,103 @@ See the README file in the tools/msi2lmp folder for more information.
 
 ----------
 
+.. _offline:
+
+Scripts for building LAMMPS when offline
+----------------------------------------
+
+In some situations it might be necessary to build LAMMPS on a system
+without direct internet access. The scripts in ``tools/offline`` folder
+allow you to pre-load external dependencies for both the documentation
+build and for building LAMMPS with CMake.
+
+It does so by
+
+ #. downloading necessary ``pip`` packages,
+ #. cloning ``git`` repositories
+ #. downloading tarballs
+
+to a designated cache folder.
+
+As of April 2021, all of these downloads make up around 600MB. By
+default, the offline scripts will download everything into the
+``$HOME/.cache/lammps`` folder, but this can be changed by setting the
+``LAMMPS_CACHING_DIR`` environment variable.
+
+Once the caches have been initialized, they can be used for building the
+LAMMPS documentation or compiling LAMMPS using CMake on an offline
+system.
+
+The ``use_caches.sh`` script must be sourced into the current shell
+to initialize the offline build environment. Note that it must use
+the same ``LAMMPS_CACHING_DIR``. This script does the following:
+
+ #. Set up environment variables that modify the behavior of both,
+    ``pip`` and ``git``
+ #. Start a simple local HTTP server using Python to host files for CMake
+
+Afterwards, it will print out instruction on how to modify the CMake
+command line to make sure it uses the local HTTP server.
+
+To undo the environment changes and shutdown the local HTTP server,
+run the ``deactivate_caches`` command.
+
+Examples
+^^^^^^^^
+
+For all of the examples below, you first need to create the cache, which
+requires an internet connection.
+
+.. code-block:: bash
+
+   ./tools/offline/init_caches.sh
+
+Afterwards, you can disconnect or copy the contents of the
+``LAMMPS_CACHING_DIR`` folder to an offline system.
+
+Documentation Build
+^^^^^^^^^^^^^^^^^^^
+
+The documentation build will create a new virtual environment that
+typically first installs dependencies from ``pip``. With the offline
+environment loaded, these installations will instead grab the necessary
+packages from your local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+   cd doc/
+   make html
+
+   deactivate_caches
+
+CMake Build
+^^^^^^^^^^^
+
+When compiling certain packages with external dependencies, the CMake
+build system will download necessary files or sources from the web. For
+more flexibility the CMake configuration allows users to specify the URL
+of each of these dependencies.  What the ``init_caches.sh`` script does
+is create a CMake "preset" file, which sets the URLs for all of the known
+dependencies and redirects the download to the local cache.
+
+.. code-block:: bash
+
+   # if LAMMPS_CACHING_DIR is different from default, make sure to set it first
+   # export LAMMPS_CACHING_DIR=path/to/folder
+   source tools/offline/use_caches.sh
+
+   mkdir build
+   cd build
+   cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
+   make -j 8
+
+   deactivate_caches
+
+----------
+
 .. _phonon:
 
 phonon tool

doc/src/angle_cosine_periodic.rst

@@ -24,20 +24,17 @@ Examples
 Description
 """""""""""
 
-The *cosine/periodic* angle style uses the following potential, which
-is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
-particularly for organometallic systems where :math:`n` = 4 might be used
+The *cosine/periodic* angle style uses the following potential, which may be
+particularly used for organometallic systems where :math:`n` = 4 might be used
 for an octahedral complex and :math:`n` = 3 might be used for a trigonal
 center:
 
 .. math::
 
-   E = C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
+   E = \frac{2.0}{n^2} * C \left[ 1 - B(-1)^n\cos\left( n\theta\right) \right]
 
 where :math:`C`, :math:`B` and :math:`n` are coefficients defined for each angle type.
 
-See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field
-
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above, or in
 the data file or restart files read by the :doc:`read_data <read_data>`
@@ -47,10 +44,9 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`B` = 1 or -1
 * :math:`n` = 1, 2, 3, 4, 5 or 6 for periodicity
 
-Note that the prefactor :math:`C` is specified and not the overall force
-constant :math:`K = \frac{C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
-linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear
-geometry.
+Note that the prefactor :math:`C` is specified as coefficient and not the overall force
+constant :math:`K = \frac{2 C}{n^2}`.  When :math:`B = 1`, it leads to a minimum for the
+linear geometry.  When :math:`B = -1`, it leads to a maximum for the linear geometry.
 
 ----------
 
@@ -75,9 +71,3 @@ Default
 
 none
 
-----------
-
-.. _cosine-Mayo:
-
-**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
-(1990).

doc/src/angle_cosine_squared.rst

@@ -30,8 +30,11 @@ The *cosine/squared* angle style uses the potential
 
    E = K [\cos(\theta) - \cos(\theta_0)]^2
 
-where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a
-prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+, which is commonly used in the :doc:`DREIDING <Howto_bioFF>` force field,
+where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K`
+is a prefactor.  Note that the usual 1/2 factor is included in :math:`K`.
+
+See :ref:`(Mayo) <cosine-Mayo>` for a description of the DREIDING force field.
 
 The following coefficients must be defined for each angle type via the
 :doc:`angle_coeff <angle_coeff>` command as in the example above, or in
@@ -66,3 +69,10 @@ Default
 """""""
 
 none
+
+----------
+
+.. _cosine-Mayo:
+
+**(Mayo)** Mayo, Olfason, Goddard III, J Phys Chem, 94, 8897-8909
+(1990).

doc/src/atom_style.rst

@@ -27,7 +27,7 @@ Syntax
            template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
          *hybrid* args = list of one or more sub-styles, each with their args
 
-* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk*
+* accelerated styles (with same args) = *angle/kk* or *atomic/kk* or *bond/kk* or *charge/kk* or *full/kk* or *molecular/kk* or *spin/kk*
 
 Examples
 """"""""

doc/src/balance.rst

@@ -257,7 +257,7 @@ factor, similar to how the :doc:`fix balance shift <fix_balance>`
 command operates.
 
 The *dimstr* argument is a string of characters, each of which must be
-an "x" or "y" or "z".  Eacn character can appear zero or one time,
+an "x" or "y" or "z". Each character can appear zero or one time,
 since there is no advantage to balancing on a dimension more than
 once.  You should normally only list dimensions where you expect there
 to be a density variation in the particles.
@@ -285,7 +285,7 @@ plane gets closer to the target value.
 
 After the balanced plane positions are determined, if any pair of
 adjacent planes are closer together than the neighbor skin distance
-(as specified by the :doc`neigh_modify <neigh_modify>` command), then
+(as specified by the :doc:`neigh_modify <neigh_modify>` command), then
 the plane positions are shifted to separate them by at least this
 amount.  This is to prevent particles being lost when dynamics are run
 with processor sub-domains that are too narrow in one or more

doc/src/comm_modify.rst

@@ -11,13 +11,17 @@ Syntax
    comm_modify keyword value ...
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
+* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
 
   .. parsed-literal::
 
-       *mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
+       *mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
        *cutoff* value = Rcut (distance units) = communicate atoms from this far away
-       *cutoff/multi* type value
+       *cutoff/multi* collection value
+          collection = atom collection or collection range (supports asterisk notation)
+          value = Rcut (distance units) = communicate atoms for selected types from this far away
+       *reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
+       *cutoff/multi/old* type value
           type = atom type or type range (supports asterisk notation)
           value = Rcut (distance units) = communicate atoms for selected types from this far away
        *group* value = group-ID = only communicate atoms in the group
@@ -28,9 +32,9 @@ Examples
 
 .. code-block:: LAMMPS
 
-   comm_modify mode multi
+   comm_modify mode multi reduce/multi
    comm_modify mode multi group solvent
-   comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
+   comm_modify mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
    comm_modify vel yes
    comm_modify mode single cutoff 5.0 vel yes
    comm_modify cutoff/multi * 0.0
@@ -62,12 +66,18 @@ sub-domain.  The distance is by default the maximum of the neighbor
 cutoff across all atom type pairs.
 
 For many systems this is an efficient algorithm, but for systems with
-widely varying cutoffs for different type pairs, the *multi* mode can
-be faster.  In this case, each atom type is assigned its own distance
+widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
+be faster.  In *multi*, each atom is assigned to a collection which should
+correspond to a set of atoms with similar interaction cutoffs.
+In this case, each atom collection is assigned its own distance
 cutoff for communication purposes, and fewer atoms will be
-communicated.  See the :doc:`neighbor multi <neighbor>` command for a
-neighbor list construction option that may also be beneficial for
-simulations of this kind.
+communicated. in *multi/old*, a similar technique is used but atoms
+are grouped by atom type. See the :doc:`neighbor multi <neighbor>`  and
+:doc:`neighbor multi/old <neighbor>` commands for
+neighbor list construction options that may also be beneficial for
+simulations of this kind. The *multi* communication mode is only compatible
+with the *multi* neighbor style. The *multi/old* communication mode is comparable
+with both the *multi* and *multi/old* neighbor styles.
 
 The *cutoff* keyword allows you to extend the ghost cutoff distance
 for communication mode *single*\ , which is the distance from the borders
@@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
 communication cutoff used.
 
 The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
-communication mode *multi* instead. Since in this case the communication
-cutoffs are determined per atom type, a type specifier is needed and
-cutoff for one or multiple types can be extended. Also ranges of types
-using the usual asterisk notation can be given. For granular pair styles,
-the default cutoff is set to the sum of the current maximum atomic radii
-for each type.
+communication mode *multi* instead. Since the communication cutoffs are
+determined per atom collections, a collection specifier is needed and
+cutoff for one or multiple collections can be extended. Also ranges of
+collections using the usual asterisk notation can be given.  Collections
+are indexed from 1 to N where N is the total number of collections.
+Note that the arguments for *cutoff/multi* are parsed right before each
+simulation to account for potential changes in the number of
+collections.  Custom cutoffs are preserved between runs but if
+collections are redefined, one may want to re-specify the communication
+cutoffs.  For granular pair styles,the default cutoff is set to the sum
+of the current maximum atomic radii for each collection.  The
+*cutoff/multi/old* option is similar to *cutoff/multi* except it
+operates on atom types as opposed to collections.
+
+The *reduce/multi* option applies to *multi* and sets the communication
+cutoff for a particle equal to the maximum interaction distance between particles
+in the same collection. This reduces the number of
+ghost atoms that need to be communicated. This method is only compatible with the
+*multi* neighbor style and requires a half neighbor list and Newton on.
+See the :doc:`neighbor multi <neighbor>` command for more information.
 
 These are simulation scenarios in which it may be useful or even
 necessary to set a ghost cutoff > neighbor cutoff:
@@ -123,7 +147,7 @@ ghost cutoff should be set.
 In the last scenario, a :doc:`fix <fix>` or :doc:`compute <compute>` or
 :doc:`pairwise potential <pair_style>` needs to calculate with ghost
 atoms beyond the normal pairwise cutoff for some computation it
-performs (e.g. locate neighbors of ghost atoms in a multibody pair
+performs (e.g. locate neighbors of ghost atoms in a manybody pair
 potential).  Setting the ghost cutoff appropriately can insure it will
 find the needed atoms.
 

doc/src/commands_list.rst

@@ -59,6 +59,7 @@ Commands
    lattice
    log
    mass
+   mdi_engine
    message
    min_modify
    min_spin
@@ -77,6 +78,7 @@ Commands
    pair_style
    pair_write
    partition
+   plugin
    prd
    print
    processors

doc/src/compute_fep.rst

@@ -48,6 +48,8 @@ Examples
    compute 1 all fep 298 pair lj/cut epsilon 1 * v_delta pair lj/cut sigma 1 * v_delta volume yes
    compute 1 all fep 300 atom charge 2 v_delta
 
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""
 

doc/src/compute_pressure.rst

@@ -46,13 +46,14 @@ system volume (or area in 2d).  The second term is the virial, equal to
 -dU/dV, computed for all pairwise as well as 2-body, 3-body, 4-body,
 many-body, and long-range interactions, where :math:`r_i` and
 :math:`f_i` are the position and force vector of atom *i*, and the black
-dot indicates a dot product.  When periodic boundary conditions are
-used, N' necessarily includes periodic image (ghost) atoms outside the
-central box, and the position and force vectors of ghost atoms are thus
-included in the summation.  When periodic boundary conditions are not
-used, N' = N = the number of atoms in the system.  :doc:`Fixes <fix>`
-that impose constraints (e.g. the :doc:`fix shake <fix_shake>` command)
-also contribute to the virial term.
+dot indicates a dot product.  This is computed in parallel for each
+sub-domain and then summed over all parallel processes. Thus N'
+necessarily includes atoms from neighboring sub-domains (so-called ghost
+atoms) and the position and force vectors of ghost atoms are thus
+included in the summation.  Only when running in serial and without
+periodic boundary conditions is N' = N = the number of atoms in the
+system.  :doc:`Fixes <fix>` that impose constraints (e.g. the :doc:`fix
+shake <fix_shake>` command) may also contribute to the virial term.
 
 A symmetric pressure tensor, stored as a 6-element vector, is also
 calculated by this compute.  The 6 components of the vector are

doc/src/compute_temp_drude.rst

@@ -20,6 +20,8 @@ Examples
 
    compute TDRUDE all temp/drude
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/dihedral_style.rst

@@ -113,7 +113,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`quadratic <dihedral_quadratic>` - dihedral with quadratic term in angle
 * :doc:`spherical <dihedral_spherical>` - dihedral which includes angle terms to avoid singularities
 * :doc:`table <dihedral_table>` - tabulated dihedral
-* :doc:`table/cut <dihedral_table_cut>` - tabulated dihedral with analytic cutoff
+* :doc:`table/cut <dihedral_table>` - tabulated dihedral with analytic cutoff
 
 ----------
 

doc/src/dihedral_table.rst

@@ -1,19 +1,24 @@
 .. index:: dihedral_style table
 .. index:: dihedral_style table/omp
+.. index:: dihedral_style table/cut
 
 dihedral_style table command
 ============================
 
 Accelerator Variants: *table/omp*
 
+dihedral_style table/cut command
+================================
+
 Syntax
 """"""
 
 .. code-block:: LAMMPS
 
-   dihedral_style table style Ntable
+   dihedral_style style interpolation Ntable
 
-* style = *linear* or *spline* = method of interpolation
+* style = *table* or *table/cut*
+* interpolation = *linear* or *spline* = method of interpolation
 * Ntable = size of the internal lookup table
 
 Examples
@@ -26,13 +31,21 @@ Examples
    dihedral_coeff 1 file.table DIH_TABLE1
    dihedral_coeff 2 file.table DIH_TABLE2
 
+   dihedral_style table/cut spline 400
+   dihedral_style table/cut linear 1000
+   dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
+   dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
+
 Description
 """""""""""
 
-The *table* dihedral style creates interpolation tables of length
-*Ntable* from dihedral potential and derivative values listed in a
-file(s) as a function of the dihedral angle "phi".  The files are read
-by the :doc:`dihedral_coeff <dihedral_coeff>` command.
+The *table* and *table/cut* dihedral styles create interpolation tables
+of length *Ntable* from dihedral potential and derivative values listed
+in a file(s) as a function of the dihedral angle "phi".  The files are
+read by the :doc:`dihedral_coeff <dihedral_coeff>` command.  For
+dihedral style *table/cut* additionally an analytic cutoff that is
+quadratic in the bond-angle (theta) is applied in order to regularize
+the dihedral interaction.
 
 The interpolation tables are created by fitting cubic splines to the
 file values and interpolating energy and derivative values at each of
@@ -51,16 +64,53 @@ interpolated table.  For a given dihedral angle (phi), the appropriate
 coefficients are chosen from this list, and a cubic polynomial is used
 to compute the energy and the derivative at this angle.
 
-The following coefficients must be defined for each dihedral type via
-the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
-above.
+For dihedral style *table* the following coefficients must be defined
+for each dihedral type via the :doc:`dihedral_coeff <dihedral_coeff>`
+command as in the example above.
 
 * filename
 * keyword
 
-The filename specifies a file containing tabulated energy and
-derivative values. The keyword specifies a section of the file.  The
-format of this file is described below.
+The filename specifies a file containing tabulated energy and derivative
+values. The keyword specifies which section of the file to read.  The
+format of this file is the same for both dihedral styles and described
+below.
+
+For dihedral style *table/cut* the following coefficients must be
+defined for each dihedral type via the :doc:`dihedral_coeff
+<dihedral_coeff>` command as in the example above.
+
+* style (aat)
+* cutoff prefactor
+* cutoff angle1
+* cutoff angle2
+* filename
+* keyword
+
+The cutoff dihedral style uses a tabulated dihedral interaction with a
+cutoff function:
+
+.. math::
+
+   f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
+   f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
+
+The cutoff specifies an prefactor to the cutoff function.  While this
+value would ordinarily equal 1 there may be situations where the value
+should change.
+
+The cutoff :math:`\theta_1` specifies the angle (in degrees) below which
+the dihedral interaction is unmodified, i.e. the cutoff function is 1.
+
+The cutoff function is applied between :math:`\theta_1` and
+:math:`\theta_2`, which is the angle at which the cutoff function drops
+to zero.  The value of zero effectively "turns off" the dihedral
+interaction.
+
+The filename specifies a file containing tabulated energy and derivative
+values. The keyword specifies which section of the file to read.  The
+format of this file is the same for both dihedral styles and described
+below.
 
 ----------
 
@@ -182,18 +232,19 @@ that matches the specified keyword.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This dihedral style writes the settings for the "dihedral_style table"
-command to :doc:`binary restart files <restart>`, so a dihedral_style
-command does not need to specified in an input script that reads a
-restart file.  However, the coefficient information is not stored in
-the restart file, since it is tabulated in the potential files.  Thus,
+These dihedral styles write the settings for the "dihedral_style table"
+or "dihedral_style table/cut" command to :doc:`binary restart files
+<restart>`, so a dihedral_style command does not need to specified in an
+input script that reads a restart file.  However, the coefficient
+information loaded from the table file(s) is not stored in the restart
+file, since it is tabulated in the potential files.  Thus, suitable
 dihedral_coeff commands do need to be specified in the restart input
-script.
+script after reading the restart file.
 
 Restrictions
 """"""""""""
 
-This dihedral style can only be used if LAMMPS was built with the
+These dihedral styles can only be used if LAMMPS was built with the
 USER-MISC package.  See the :doc:`Build package <Build_package>` doc
 page for more info.
 

doc/src/dihedral_table_cut.rst

@@ -1,229 +0,0 @@
-.. index:: dihedral_style table/cut
-
-dihedral_style table/cut command
-================================
-
-Syntax
-""""""
-
-.. code-block:: LAMMPS
-
-   dihedral_style table/cut style Ntable
-
-* style = *linear* or *spline* = method of interpolation
-* Ntable = size of the internal lookup table
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   dihedral_style table/cut spline 400
-   dihedral_style table/cut linear 1000
-   dihedral_coeff 1 aat 1.0 177 180 file.table DIH_TABLE1
-   dihedral_coeff 2 aat 0.5 170 180 file.table DIH_TABLE2
-
-Description
-"""""""""""
-
-The *table/cut* dihedral style creates interpolation tables of length
-*Ntable* from dihedral potential and derivative values listed in a
-file(s) as a function of the dihedral angle "phi".  In addition, an
-analytic cutoff that is quadratic in the bond-angle (theta) is applied
-in order to regularize the dihedral interaction.  The dihedral table
-files are read by the :doc:`dihedral_coeff <dihedral_coeff>` command.
-
-The interpolation tables are created by fitting cubic splines to the
-file values and interpolating energy and derivative values at each of
-*Ntable* dihedral angles. During a simulation, these tables are used
-to interpolate energy and force values on individual atoms as
-needed. The interpolation is done in one of 2 styles: *linear* or
-*spline*\ .
-
-For the *linear* style, the dihedral angle (phi) is used to find 2
-surrounding table values from which an energy or its derivative is
-computed by linear interpolation.
-
-For the *spline* style, cubic spline coefficients are computed and
-stored at each of the *Ntable* evenly-spaced values in the
-interpolated table.  For a given dihedral angle (phi), the appropriate
-coefficients are chosen from this list, and a cubic polynomial is used
-to compute the energy and the derivative at this angle.
-
-The following coefficients must be defined for each dihedral type via
-the :doc:`dihedral_coeff <dihedral_coeff>` command as in the example
-above.
-
-* style (aat)
-* cutoff prefactor
-* cutoff angle1
-* cutoff angle2
-* filename
-* keyword
-
-The cutoff dihedral style uses a tabulated dihedral interaction with a
-cutoff function:
-
-.. math::
-
-   f(\theta) & = K \qquad\qquad\qquad\qquad\qquad\qquad \theta < \theta_1 \\
-   f(\theta) & = K \left(1-\frac{(\theta - \theta_1)^2}{(\theta_2 - \theta_1)^2}\right) \qquad \theta_1 < \theta < \theta_2
-
-The cutoff specifies an prefactor to the cutoff function.  While this value
-would ordinarily equal 1 there may be situations where the value should change.
-
-The cutoff :math:`\theta_1` specifies the angle (in degrees) below which the dihedral
-interaction is unmodified, i.e. the cutoff function is 1.
-
-The cutoff function is applied between :math:`\theta_1` and :math:`\theta_2`, which is
-the angle at which the cutoff function drops to zero.  The value of zero effectively
-"turns off" the dihedral interaction.
-
-The filename specifies a file containing tabulated energy and
-derivative values. The keyword specifies a section of the file.  The
-format of this file is described below.
-
-----------
-
-The format of a tabulated file is as follows (without the
-parenthesized comments).  It can begin with one or more comment
-or blank lines.
-
-.. parsed-literal::
-
-   # Table of the potential and its negative derivative
-
-   DIH_TABLE1                   (keyword is the first text on line)
-   N 30 DEGREES                 (N, NOF, DEGREES, RADIANS, CHECKU/F)
-                                (blank line)
-   1 -168.0 -1.40351172223 0.0423346818422
-   2 -156.0 -1.70447981034 0.00811786522531
-   3 -144.0 -1.62956100432 -0.0184129719987
-   ...
-   30 180.0 -0.707106781187 0.0719306095245
-
-   # Example 2: table of the potential. Forces omitted
-
-   DIH_TABLE2
-   N 30 NOF CHECKU testU.dat CHECKF testF.dat
-
-   1 -168.0 -1.40351172223
-   2 -156.0 -1.70447981034
-   3 -144.0 -1.62956100432
-   ...
-   30 180.0 -0.707106781187
-
-A section begins with a non-blank line whose first character is not a
-"#"; blank lines or lines starting with "#" can be used as comments
-between sections. The first line begins with a keyword which
-identifies the section. The line can contain additional text, but the
-initial text must match the argument specified in the
-:doc:`dihedral_coeff <dihedral_coeff>` command. The next line lists (in
-any order) one or more parameters for the table. Each parameter is a
-keyword followed by one or more numeric values.
-
-Following a blank line, the next N lines list the tabulated values. On
-each line, the first value is the index from 1 to N, the second value is
-the angle value, the third value is the energy (in energy units), and
-the fourth is -dE/d(phi) also in energy units). The third term is the
-energy of the 4-atom configuration for the specified angle.  The fourth
-term (when present) is the negative derivative of the energy with
-respect to the angle (in degrees, or radians depending on whether the
-user selected DEGREES or RADIANS).  Thus the units of the last term
-are still energy, not force. The dihedral angle values must increase
-from one line to the next.
-
-Dihedral table splines are cyclic.  There is no discontinuity at 180
-degrees (or at any other angle).  Although in the examples above, the
-angles range from -180 to 180 degrees, in general, the first angle in
-the list can have any value (positive, zero, or negative).  However
-the *range* of angles represented in the table must be *strictly* less
-than 360 degrees (2pi radians) to avoid angle overlap.  (You may not
-supply entries in the table for both 180 and -180, for example.)  If
-the user's table covers only a narrow range of dihedral angles,
-strange numerical behavior can occur in the large remaining gap.
-
-**Parameters:**
-
-The parameter "N" is required and its value is the number of table
-entries that follow. Note that this may be different than the N
-specified in the :doc:`dihedral_style table <dihedral_style>` command.
-Let *Ntable* is the number of table entries requested dihedral_style
-command, and let *Nfile* be the parameter following "N" in the
-tabulated file ("30" in the sparse example above).  What LAMMPS does
-is a preliminary interpolation by creating splines using the *Nfile*
-tabulated values as nodal points.  It uses these to interpolate as
-needed to generate energy and derivative values at *Ntable* different
-points (which are evenly spaced over a 360 degree range, even if the
-angles in the file are not).  The resulting tables of length *Ntable*
-are then used as described above, when computing energy and force for
-individual dihedral angles and their atoms.  This means that if you
-want the interpolation tables of length *Ntable* to match exactly what
-is in the tabulated file (with effectively nopreliminary
-interpolation), you should set *Ntable* = *Nfile*\ .  To insure the
-nodal points in the user's file are aligned with the interpolated
-table entries, the angles in the table should be integer multiples of
-360/\ *Ntable* degrees, or 2\*PI/\ *Ntable* radians (depending on your
-choice of angle units).
-
-The optional "NOF" keyword allows the user to omit the forces
-(negative energy derivatives) from the table file (normally located in
-the fourth column).  In their place, forces will be calculated
-automatically by differentiating the potential energy function
-indicated by the third column of the table (using either linear or
-spline interpolation).
-
-The optional "DEGREES" keyword allows the user to specify angles in
-degrees instead of radians (default).
-
-The optional "RADIANS" keyword allows the user to specify angles in
-radians instead of degrees.  (Note: This changes the way the forces
-are scaled in the fourth column of the data file.)
-
-The optional "CHECKU" keyword is followed by a filename.  This allows
-the user to save all of the *Ntable* different entries in the
-interpolated energy table to a file to make sure that the interpolated
-function agrees with the user's expectations.  (Note: You can
-temporarily increase the *Ntable* parameter to a high value for this
-purpose.  "\ *Ntable*\ " is explained above.)
-
-The optional "CHECKF" keyword is analogous to the "CHECKU" keyword.
-It is followed by a filename, and it allows the user to check the
-interpolated force table.  This option is available even if the user
-selected the "NOF" option.
-
-Note that one file can contain many sections, each with a tabulated
-potential. LAMMPS reads the file section by section until it finds one
-that matches the specified keyword.
-
-Restart, fix_modify, output, run start/stop, minimize info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
-
-This dihedral style writes the settings for the "dihedral_style table/cut"
-command to :doc:`binary restart files <restart>`, so a dihedral_style
-command does not need to specified in an input script that reads a
-restart file.  However, the coefficient information is not stored in
-the restart file, since it is tabulated in the potential files.  Thus,
-dihedral_coeff commands do need to be specified in the restart input
-script.
-
-Restrictions
-""""""""""""
-
-This dihedral style can only be used if LAMMPS was built with the
-USER-MISC package.  See the :doc:`Build package <Build_package>` doc
-page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`dihedral_coeff <dihedral_coeff>`, :doc:`dihedral_style table <dihedral_table>`
-
-Default
-"""""""
-
-none
-
-.. _dihedralcut-Salerno:
-
-**(Salerno)** Salerno, Bernstein, J Chem Theory Comput, --, ---- (2018).

doc/src/dump.rst

@@ -349,7 +349,7 @@ the box size stored with the snapshot.
 
 The *xtc* style writes XTC files, a compressed trajectory format used
 by the GROMACS molecular dynamics package, and described
-`here <http://manual.gromacs.org/current/online/xtc.html>`_.
+`here <https://manual.gromacs.org/current/reference-manual/file-formats.html#xtc>`_.
 The precision used in XTC files can be adjusted via the
 :doc:`dump_modify <dump_modify>` command.  The default value of 1000
 means that coordinates are stored to 1/1000 nanometer accuracy.  XTC

doc/src/dump_modify.rst

@@ -308,9 +308,9 @@ performed with dump style *xtc*\ .
 
 ----------
 
-The *format* keyword can be used to change the default numeric format
-output by the text-based dump styles: *atom*\ , *custom*\ , *cfg*\ , and
-*xyz* styles, and their MPIIO variants.  Only the *line* or *none*
+The *format* keyword can be used to change the default numeric format output
+by the text-based dump styles: *atom*\ , *local*\ , *custom*\ , *cfg*\ , and
+*xyz* styles, and their MPIIO variants. Only the *line* or *none*
 options can be used with the *atom* and *xyz* styles.
 
 All the specified format strings are C-style formats, e.g. as used by
@@ -362,7 +362,7 @@ settings, reverting all values to their default format.
 
    compute     1 all property/local batom1 batom2
    dump        1 all local 100 tmp.bonds index c_1[1] c_1[2]
-   dump_modify 1 format "%d %0.0f %0.0f"
+   dump_modify 1 format line "%d %0.0f %0.0f"
 
 will output the two atom IDs for atoms in each bond as integers.  If
 the dump_modify command were omitted, they would appear as

doc/src/fix.rst

@@ -182,6 +182,9 @@ accelerated styles exist.
 * :doc:`ave/time <fix_ave_time>` - compute/output global time-averaged quantities
 * :doc:`aveforce <fix_aveforce>` - add an averaged force to each atom
 * :doc:`balance <fix_balance>` - perform dynamic load-balancing
+* :doc:`brownian <fix_brownian>` - overdamped translational brownian motion
+* :doc:`brownian/asphere <fix_brownian>` - overdamped translational and rotational brownian motion for ellipsoids
+* :doc:`brownian/sphere <fix_brownian>` - overdamped translational and rotational brownian motion for spheres
 * :doc:`bocs <fix_bocs>` - NPT style time integration with pressure correction
 * :doc:`bond/break <fix_bond_break>` - break bonds on the fly
 * :doc:`bond/create <fix_bond_create>` - create bonds on the fly
@@ -189,6 +192,7 @@ accelerated styles exist.
 * :doc:`bond/react <fix_bond_react>` - apply topology changes to model reactions
 * :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
 * :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
+* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
 * :doc:`client/md <fix_client_md>` - MD client for client/server simulations
 * :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
 * :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
@@ -240,6 +244,7 @@ accelerated styles exist.
 * :doc:`lb/viscous <fix_lb_viscous>` -
 * :doc:`lineforce <fix_lineforce>` - constrain atoms to move in a line
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
+* :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms

doc/src/fix_adapt_fep.rst

@@ -56,6 +56,9 @@ Examples
    fix 1 all adapt/fep 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
    fix 1 all adapt/fep 10 atom diameter 1 v_size
 
+
+Example input scripts available: examples/USER/fep
+
 Description
 """""""""""
 

doc/src/fix_ave_chunk.rst

@@ -307,7 +307,9 @@ atoms in the chunk.  The averaged output value for the chunk on the
 average over atoms across the entire *Nfreq* timescale.  For the
 *density/number* and *density/mass* values, the volume (bin volume or
 system volume) used in the final normalization will be the volume at
-the final *Nfreq* timestep.
+the final *Nfreq* timestep. For the *temp* values, degrees of freedom and
+kinetic energy are summed separately across the entire *Nfreq* timescale, and
+the output value is calculated by dividing those two sums.
 
 If the *norm* setting is *sample*\ , the chunk value is summed over
 atoms for each sample, as is the count, and an "average sample value"

doc/src/fix_ave_histo.rst

@@ -138,8 +138,8 @@ vector or columns of the array had been listed one by one.  E.g. these
 .. code-block:: LAMMPS
 
    compute myCOM all com/chunk
-   fix 1 all ave/histo 100 1 100 c_myCOM[*] file tmp1.com mode vector
-   fix 2 all ave/histo 100 1 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
+   fix 1 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[*] file tmp1.com mode vector
+   fix 2 all ave/histo 100 1 100 -10.0 10.0 100 c_myCOM[1] c_myCOM[2] c_myCOM[3] file tmp2.com mode vector
 
 If the fix ave/histo/weight command is used, exactly two values must
 be specified.  If the values are vectors, they must be the same

doc/src/fix_balance.rst

@@ -216,7 +216,7 @@ above.  It changes the positions of cutting planes between processors
 in an iterative fashion, seeking to reduce the imbalance factor.
 
 The *dimstr* argument is a string of characters, each of which must be
-an "x" or "y" or "z".  Eacn character can appear zero or one time,
+an "x" or "y" or "z".  Each character can appear zero or one time,
 since there is no advantage to balancing on a dimension more than
 once.  You should normally only list dimensions where you expect there
 to be a density variation in the particles.

doc/src/fix_bond_react.rst

@@ -328,8 +328,8 @@ keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
 handedness should be enforced. The fifth optional section begins with
 the keyword 'Constraints' and lists additional criteria that must be
 satisfied in order for the reaction to occur. Currently, there are
-five types of constraints available, as discussed below: 'distance',
-'angle', 'dihedral', 'arrhenius', and 'rmsd'.
+six types of constraints available, as discussed below: 'distance',
+'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
 
 A sample map file is given below:
 
@@ -500,6 +500,45 @@ example, the molecule fragment could consist of only the backbone
 atoms of a polymer chain. This constraint can be used to enforce a
 specific relative position and orientation between reacting molecules.
 
+The constraint of type 'custom' has the following syntax:
+
+.. parsed-literal::
+
+   custom *varstring*
+
+where 'custom' is the required keyword, and *varstring* is a
+variable expression. The expression must be a valid equal-style
+variable formula that can be read by the :doc:`variable <variable>` command,
+after any special reaction functions are evaluated. If the resulting
+expression is zero, the reaction is prevented from occurring;
+otherwise, it is permitted to occur. There are two special reaction
+functions available, 'rxnsum' and 'rxnave'. These functions operate
+over the atoms in a given reaction site, and have one mandatory
+argument and one optional argument. The mandatory argument is the
+identifier for an atom-style variable. The second, optional argument
+is the name of a molecule fragment in the pre-reaction template, and
+can be used to operate over a subset of atoms in the reaction site.
+The 'rxnsum' function sums the atom-style variable over the reaction
+site, while the 'rxnave' returns the average value. For example, a
+constraint on the total potential energy of atoms involved in the
+reaction can be imposed as follows:
+
+.. code-block:: LAMMPS
+
+compute 1 all pe/atom # in LAMMPS input script
+variable my_pe atom c_1 # in LAMMPS input script
+
+.. code-block:: LAMMPS
+
+custom "rxnsum(v_my_pe) > 100" # in Constraints section of map file
+
+The above example prevents the reaction from occurring unless the
+total potential energy of the reaction site is above 100. The variable
+expression can be interpreted as the probability of the reaction
+occurring by using an inequality and the 'random(x,y,z)' function
+available as an equal-style variable input, similar to the 'arrhenius'
+constraint above.
+
 By default, all constraints must be satisfied for the reaction to
 occur. In other words, constraints are evaluated as a series of
 logical values using the logical AND operator "&&". More complex logic

doc/src/fix_brownian.rst

@@ -0,0 +1,216 @@
+.. index:: fix brownian
+.. index:: fix brownian/sphere
+.. index:: fix brownian/asphere
+
+fix brownian command
+===========================
+
+fix brownian/sphere command
+===========================
+
+fix brownian/sphere command
+===========================
+
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+   fix ID group-ID style_name temp seed keyword args
+
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* style_name = *brownian* or *brownian/sphere* or *brownian/asphere*
+* temp = temperature
+* seed = random number generator seed
+* one or more keyword/value pairs may be appended
+* keyword = *rng* or *dipole* or *gamma_r_eigen* or *gamma_t_eigen* or *gamma_r* or *gamma_t*
+
+  .. parsed-literal::
+
+        *rng* value = *uniform* or *gaussian* or *none*
+         *uniform* = use uniform random number generator
+         *gaussian* = use gaussian random number generator
+         *none* = turn off noise
+        *dipole* value = *mux* and *muy* and *muz* for *brownian/asphere*
+         *mux*, *muy*, and *muz* = update orientation of dipole having direction (*mux*,*muy*,*muz*) in body frame of rigid body
+        *gamma_r_eigen* values = *gr1* and *gr2* and *gr3* for *brownian/asphere*
+         *gr1*, *gr2*, and *gr3* = diagonal entries of body frame rotational friction tensor
+        *gamma_r* values = *gr* for *brownian/sphere*
+         *gr* = magnitude of the (isotropic) rotational friction tensor
+        *gamma_t_eigen* values = *gt1* and *gt2* and *gt3* for *brownian/asphere*
+         *gt1*, *gt2*, and *gt3* = diagonal entries of body frame translational friction tensor
+        *gamma_t* values = *gt* for *brownian* and *brownian/sphere*
+         *gt* = magnitude of the (isotropic) translational friction tensor
+
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   fix 1 all brownian 1.0 12908410 gamma_t 1.0
+   fix 1 all brownian 1.0 12908410 gamma_t 3.0 rng gaussian
+   fix 1 all brownian/sphere 1.0 1294019 gamma_t 3.0 gamma_r 1.0
+   fix 1 all brownian/sphere 1.0 19581092 gamma_t 1.0 gamma_r 0.3  rng none
+   fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 rng gaussian
+   fix 1 all brownian/asphere 1.0 1294019 gamma_t_eigen 1.0 2.0 3.0 gamma_r_eigen 4.0 7.0 8.0 dipole 1.0 0.0 0.0
+
+
+Description
+"""""""""""
+
+Perform Brownian Dynamics time integration to update position, velocity,
+dipole orientation (for spheres) and quaternion orientation (for
+ellipsoids, with optional dipole update as well) of all particles in the
+fix group in each timestep.  Brownian Dynamics uses Newton's laws of
+motion in the limit that inertial forces are negligible compared to
+viscous forces. The stochastic equation of motion for the center of mass
+positions is
+
+.. math::
+
+   d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
+
+in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
+only depends on orientation and so the noise is still additive).
+
+The rotational motion for the spherical and ellipsoidal particles is not
+as simple an expression, but is chosen to replicate the Boltzmann
+distribution for the case of conservative torques (see :ref:`(Ilie)
+<Ilie1>` or :ref:`(Delong) <Delong1>`).
+
+For the style *brownian*, only the positions of the particles are
+updated. This is therefore suitable for point particle simulations.
+
+For the style *brownian/sphere*, the positions of the particles are
+updated, and a dipole slaved to the spherical orientation is also
+updated. This style therefore requires the hybrid atom style
+:doc:`atom_style dipole <atom_style>` and :doc:`atom_style sphere
+<atom_style>`.
+
+For the style *brownian/asphere*, the center of mass positions and the
+quaternions of ellipsoidal particles are updated. This fix style is
+suitable for equations of motion where the rotational and translational
+friction tensors can be diagonalized in a certain (body) reference frame.
+
+
+---------
+
+.. note::
+
+   This integrator does not by default assume a relationship between the
+   rotational and translational friction tensors, though such a relationship
+   should exist in the case of no-slip boundary conditions between the particles and
+   the surrounding (implicit) solvent. E.g. in the case of spherical particles,
+   the condition :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly
+   accounted for by setting *gamma_t* to 3x and *gamma_r* to x (where
+   :math:`\sigma` is the spherical diameter). A similar (though more complex)
+   relationship holds for ellipsoids and rod-like particles.
+
+---------
+
+.. note::
+
+   Temperature computation using the :doc:`compute temp <compute_temp>`
+   will not correctly compute temperature of these overdamped dynamics
+   since we are explicitly neglecting inertial effects.
+   Furthermore, this time integrator does not add the stochastic terms or
+   viscous terms to the force and/or torques.  Rather, they are just added
+   in to the equations of motion to update the degrees of freedom.
+
+---------
+
+
+If the *rng* keyword is used with the *uniform* value, then the noise
+is generated from a uniform distribution (see
+:ref:`(Dunweg) <Dunweg7>` for why this works). This is the same method
+of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
+
+If the *rng* keyword is used with the *gaussian* value, then the noise
+is generated from a gaussian distribution. Typically this added
+complexity is unnecessary, and one should be fine using the *uniform*
+value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
+
+If the *rng* keyword is used with the *none* value, then the noise
+terms are set to zero.
+
+The *gamma_t* keyword sets the (isotropic) translational viscous damping.
+Required for (and only compatible with) *brownian* and *brownian/sphere*.
+The units of *gamma_t* are mass/time.
+
+The *gamma_r* keyword sets the (isotropic) rotational viscous damping.
+Required for (and only compatible with) *brownian/sphere*.
+The units of *gamma_r* are mass*length**2/time.
+
+The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
+the rotational and viscous damping tensors (having the same units as
+their isotropic counterparts). Required for (and only compatible with)
+*brownian/asphere*. For a 2D system, the first two values of *gamma_r_eigen*
+must be inf (only rotation in xy plane), and the third value of *gamma_t_eigen*
+must be inf (only diffusion in xy plane).
+
+If the *dipole* keyword is used, then the dipole moments of the particles
+are updated as described above. Only compatible with *brownian/asphere*
+(as *brownian/sphere* updates dipoles automatically).
+
+----------
+
+.. note::
+   For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
+   *gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
+   *brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
+
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+No information about this fix is written to :doc:`binary restart files <restart>`.
+No global or per-atom quantities are stored
+by this fix for access by various :doc:`output commands <Howto_output>`.
+
+
+No parameter of this fix can be used with the *start/stop* keywords of
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
+
+Restrictions
+""""""""""""
+
+The style *brownian/sphere* fix requires that atoms store torque and angular velocity (omega)
+as defined by the :doc:`atom_style sphere <atom_style>` command.
+The style *brownian/asphere* fix requires that atoms store torque and quaternions
+as defined by the :doc:`atom_style ellipsoid <atom_style>` command.
+If the *dipole* keyword is used, they must also store a dipole moment
+as defined by the :doc:`atom_style dipole <atom_style>` command.
+
+This fix is part of the USER-BROWNIAN package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package <Build_package>`
+doc page for more info.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix propel/self <fix_propel_self>`,
+:doc:`fix langevin <fix_langevin>`, :doc:`fix nve/sphere <fix_nve_sphere>`,
+
+Default
+"""""""
+
+The default for *rng* is *uniform*. The default for the rotational and translational friction
+tensors are the identity tensor.
+
+----------
+
+.. _Ilie1:
+
+**(Ilie)** Ilie, Briels, den Otter, Journal of Chemical Physics, 142, 114103 (2015).
+
+.. _Delong1:
+
+**(Delong)** Delong, Usabiaga, Donev, Journal of Chemical Physics. 143, 144107 (2015)
+
+.. _Dunweg7:
+
+**(Dunweg)** Dunweg and Paul, Int J of Modern Physics C, 2, 817-27 (1991).

doc/src/fix_charge_regulation.rst

@@ -0,0 +1,276 @@
+
+.. index:: fix charge/regulation
+
+fix charge/regulation command
+=============================
+
+Syntax
+""""""
+
+.. parsed-literal::
+
+    fix ID group-ID charge/regulation cation_type anion_type keyword value(s)
+
+* ID, group-ID are documented in fix command
+* charge/regulation = style name of this fix command
+* cation_type = atom type of free cations
+* anion_type = atom type of free anions
+
+* zero or more keyword/value pairs may be appended
+
+  .. parsed-literal::
+
+     keyword = *pH*, *pKa*, *pKb*, *pIp*, *pIm*, *pKs*, *acid_type*, *base_type*, *lunit_nm*, *temp*, *tempfixid*, *nevery*, *nmc*, *xrd*, *seed*, *tag*, *group*, *onlysalt*, *pmcmoves*
+     *pH* value = pH of the solution
+     *pKa* value = acid dissociation constant
+     *pKb* value = base dissociation constant
+     *pIp* value = chemical potential of free cations
+     *pIm* value = chemical potential of free anions
+     *pKs* value = solution self-dissociation constant
+     *acid_type* = atom type of acid groups
+     *base_type*  = atom type of base groups
+     *lunit_nm* value = unit length used by LAMMPS (# in the units of nanometers)
+     *temp* value = temperature
+     *tempfixid* value = fix ID of temperature thermostat
+     *nevery* value = invoke this fix every nevery steps
+     *nmc* value = number of charge regulation MC moves to attempt every nevery steps
+     *xrd* value = cutoff distance for acid/base reaction
+     *seed* value = random # seed (positive integer)
+     *tag* value = yes or no (yes: The code assign unique tags to inserted ions; no: The tag of all inserted ions is "0")
+     *group* value = group-ID, inserted ions are assigned to group group-ID. Can be used multiple times to assign inserted ions to multiple groups.
+     *onlysalt* values = flag charge_cation charge_anion.
+        flag = yes or no (yes: the fix performs only ion insertion/deletion, no: perform acid/base dissociation and ion insertion/deletion)
+        charge_cation, charge_anion = value of cation/anion charge, must be an integer (only specify if flag = yes)
+     *pmcmoves* values = pmcA pmcB pmcI -  MC move fractions for acid ionization (pmcA), base ionization (pmcB) and free ion exchange (pmcI)
+
+Examples
+""""""""
+.. code-block:: LAMMPS
+
+    fix chareg all charge/regulation 1 2 acid_type 3 base_type 4 pKa 5 pKb 7 lb 1.0 nevery 200 nexchange 200 seed 123 tempfixid fT
+
+    fix chareg all charge/regulation 1 2 pIp 3 pIm 3 onlysalt yes 2 -1 seed 123 tag yes temp 1.0
+
+Description
+"""""""""""
+
+This fix performs Monte Carlo (MC) sampling of charge regulation and
+exchange of ions with a reservoir as discussed in :ref:`(Curk1) <Curk1>`
+and :ref:`(Curk2) <Curk2>`.  The implemented method is largely analogous
+to the grand-reaction ensemble method in :ref:`(Landsgesell)
+<Landsgesell>`.  The implementation is parallelized, compatible with
+existing LAMMPS functionalities, and applicable to any system utilizing
+discrete, ionizable groups or surface sites.
+
+Specifically, the fix implements the following three types of MC moves,
+which discretely change the charge state of individual particles and
+insert ions into the systems: :math:`\mathrm{A} \rightleftharpoons
+\mathrm{A}^-+\mathrm{X}^+`, :math:`\mathrm{B} \rightleftharpoons
+\mathrm{B}^++\mathrm{X}^-`, and :math:`\emptyset \rightleftharpoons
+Z^-\mathrm{X}^{Z^+}+Z^+\mathrm{X}^{-Z^-}`.  In the former two types of
+reactions, Monte Carlo moves alter the charge value of specific atoms
+(:math:`\mathrm{A}`, :math:`\mathrm{B}`) and simultaneously insert a
+counterion to preserve the charge neutrality of the system, modeling the
+dissociation/association process.  The last type of reaction performs
+grand canonical MC exchange of ion pairs with a (fictitious) reservoir.
+
+In our implementation "acid" refers to particles that can attain charge
+:math:`q=\{0,-1\}` and "base" to particles with :math:`q=\{0,1\}`,
+whereas the MC exchange of free ions allows any integer charge values of
+:math:`{Z^+}` and :math:`{Z^-}`.
+
+Here we provide several practical examples for modeling charge
+regulation effects in solvated systems.  An acid ionization reaction
+(:math:`\mathrm{A} \rightleftharpoons \mathrm{A}^-+\mathrm{H}^+`) can be
+defined via a single line in the input file
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 2 3 acid_type 1 pH 7.0 pKa 5.0 pIp 7.0 pIm 7.0
+
+where the fix attempts to charge :math:`\mathrm{A}` (discharge
+:math:`\mathrm{A}^-`) to :math:`\mathrm{A}^-` (:math:`\mathrm{A}`) and
+insert (delete) a proton (atom type 2). Besides, the fix implements
+self-ionization reaction of water :math:`\emptyset \rightleftharpoons
+\mathrm{H}^++\mathrm{OH}^-`.  However, this approach is highly
+inefficient at :math:`\mathrm{pH} \approx 7` when the concentration of
+both protons and hydroxyl ions is low, resulting in a relatively low
+acceptance rate of MC moves.
+
+A more efficient way is to allow salt ions to participate in ionization
+reactions, which can be easily achieved via
+
+.. code-block:: LAMMPS
+
+    fix acid_reaction all charge/regulation 4 5 acid_type 1 pH 7.0 pKa 5.0 pIp 2.0 pIm 2.0
+
+where particles of atom type 4 and 5 are the salt cations and anions,
+both at chemical potential pI=2.0, see :ref:`(Curk1) <Curk1>` and
+:ref:`(Landsgesell) <Landsgesell>` for more details.
+
+
+ Similarly, we could have simultaneously added a base ionization reaction
+ (:math:`\mathrm{B} \rightleftharpoons \mathrm{B}^++\mathrm{OH}^-`)
+
+.. code-block:: LAMMPS
+
+    fix base_reaction all charge/regulation 2 3 base_type 6 pH 7.0 pKb 6.0 pIp 7.0 pIm 7.0
+
+where the fix will attempt to charge :math:`\mathrm{B}` (discharge
+:math:`\mathrm{B}^+`) to :math:`\mathrm{B}^+` (:math:`\mathrm{B}`) and
+insert (delete) a hydroxyl ion :math:`\mathrm{OH}^-` of atom type 3.  If
+neither the acid or the base type is specified, for example,
+
+.. code-block:: LAMMPS
+
+    fix salt_reaction all charge/regulation 4 5 pIp 2.0 pIm 2.0
+
+the fix simply inserts or deletes an ion pair of a free cation (atom
+type 4) and a free anion (atom type 5) as done in a conventional
+grand-canonical MC simulation.
+
+
+The fix is compatible with LAMMPS sub-packages such as *molecule* or
+*rigid*. That said, the acid and base particles can be part of larger
+molecules or rigid bodies. Free ions that are inserted to or deleted
+from the system must be defined as single particles (no bonded
+interactions allowed) and cannot be part of larger molecules or rigid
+bodies. If *molecule* package is used, all inserted ions have a molecule
+ID equal to zero.
+
+Note that LAMMPS implicitly assumes a constant number of particles
+(degrees of freedom). Since using this fix alters the total number of
+particles during the simulation, any thermostat used by LAMMPS, such as
+NVT or Langevin, must use a dynamic calculation of system
+temperature. This can be achieved by specifying a dynamic temperature
+compute (e.g. dtemp) and using it with the desired thermostat, e.g. a
+Langevin thermostat:
+
+.. code-block:: LAMMPS
+
+    compute dtemp all temp
+    compute_modify dtemp dynamic yes
+    fix fT all langevin 1.0 1.0 1.0 123
+    fix_modify fT temp dtemp
+
+The chemical potential units (e.g. pH) are in the standard log10
+representation assuming reference concentration :math:`\rho_0 =
+\mathrm{mol}/\mathrm{l}`.  Therefore, to perform the internal unit
+conversion, the length (in nanometers) of the LAMMPS unit length must be
+specified via *lunit_nm* (default is set to the Bjerrum length in water
+at room temperature *lunit_nm* = 0.71nm). For example, in the dilute
+ideal solution limit, the concentration of free ions will be
+:math:`c_\mathrm{I} = 10^{-\mathrm{pIp}}\mathrm{mol}/\mathrm{l}`.
+
+The temperature used in MC acceptance probability is set by *temp*. This
+temperature should be the same as the temperature set by the molecular
+dynamics thermostat. For most purposes, it is probably best to use
+*tempfixid* keyword which dynamically sets the temperature equal to the
+chosen MD thermostat temperature, in the example above we assumed the
+thermostat fix-ID is *fT*. The inserted particles attain a random
+velocity corresponding to the specified temperature. Using *tempfixid*
+overrides any fixed temperature set by *temp*.
+
+The *xrd* keyword can be used to restrict the inserted/deleted
+counterions to a specific radial distance from an acid or base particle
+that is currently participating in a reaction. This can be used to
+simulate more realist reaction dynamics. If *xrd* = 0 or *xrd* > *L* /
+2, where *L* is the smallest box dimension, the radial restriction is
+automatically turned off and free ion can be inserted or deleted
+anywhere in the simulation box.
+
+If the *tag yes* is used, every inserted atom gets a unique tag ID,
+otherwise, the tag of every inserted atom is set to 0. *tag yes* might
+cause an integer overflow in very long simulations since the tags are
+unique to every particle and thus increase with every successful
+particle insertion.
+
+The *pmcmoves* keyword sets the relative probability of attempting the
+three types of MC moves (reactions): acid charging, base charging, and
+ion pair exchange.  The fix only attempts to perform particle charging
+MC moves if *acid_type* or *base_type* is defined. Otherwise fix only
+performs free ion insertion/deletion. For example, if *acid_type* is not
+defined, *pmcA* is automatically set to 0. The vector *pmcmoves* is
+automatically normalized, for example, if set to *pmcmoves* 0 0.33 0.33,
+the vector would be normalized to [0,0.5,0.5].
+
+The *only_salt* option can be used to perform multivalent
+grand-canonical ion-exchange moves. If *only_salt yes* is used, no
+charge exchange is performed, only ion insertion/deletion (*pmcmoves* is
+set to [0,0,1]), but ions can be multivalent. In the example above, an
+MC move would consist of three ion insertion/deletion to preserve the
+charge neutrality of the system.
+
+The *group* keyword can be used to add inserted particles to a specific
+group-ID. All inserted particles are automatically added to group *all*.
+
+
+Output
+""""""
+
+This fix computes a global vector of length 8, which can be accessed by
+various output commands. The vector values are the following global
+quantities:
+
+* 1 = cumulative MC attempts
+* 2 = cumulative MC successes
+* 3 = current # of neutral acid atoms
+* 4 = current # of -1 charged acid atoms
+* 5 = current # of neutral base atoms
+* 6 = current # of +1 charged base atoms
+* 7 = current # of free cations
+* 8 = current # of free anions
+
+
+Restrictions
+""""""""""""
+
+This fix is part of the MC package. It is only enabled if LAMMPS
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
+
+The :doc:`atom_style <atom_style>`, used must contain the charge
+property, for example, the style could be *charge* or *full*. Only
+usable for 3D simulations. Atoms specified as free ions cannot be part
+of rigid bodies or molecules and cannot have bonding interactions. The
+scheme is limited to integer charges, any atoms with non-integer charges
+will not be considered by the fix.
+
+All interaction potentials used must be continuous, otherwise the MD
+integration and the particle exchange MC moves do not correspond to the
+same equilibrium ensemble. For example, if an lj/cut pair style is used,
+the LJ potential must be shifted so that it vanishes at the cutoff. This
+can be easily achieved using the :doc:`pair_modify <pair_modify>`
+command, i.e., by using: *pair_modify shift yes*.
+
+.. note::
+
+   Region restrictions are not yet implemented.
+
+Related commands
+""""""""""""""""
+
+:doc:`fix gcmc <fix_gcmc>`,
+:doc:`fix atom/swap <fix_atom_swap>`
+
+Default
+"""""""
+
+pH = 7.0; pKa = 100.0; pKb = 100.0; pIp = 5.0; pIm = 5.0; pKs = 14.0;
+acid_type = -1; base_type = -1; lunit_nm = 0.71; temp = 1.0; nevery =
+100; nmc = 100; xrd = 0; seed = 0; tag = no; onlysalt = no, pmcmoves =
+[1/3, 1/3, 1/3], group-ID = all
+
+----------
+
+.. _Curk1:
+
+**(Curk1)** T. Curk, J. Yuan, and E. Luijten, "Coarse-grained simulation of charge regulation using LAMMPS", preprint (2021).
+
+.. _Curk2:
+
+**(Curk2)** T. Curk and E. Luijten, "Charge-regulation effects in nanoparticle self-assembly", PRL (2021)
+
+.. _Landsgesell:
+
+**(Landsgesell)** J. Landsgesell, P. Hebbeker, O. Rud, R. Lunkad, P. Kosovan, and C. Holm, "Grand-reaction method for simulations of ionization equilibria coupled to ion partitioning", Macromolecules 53, 3007-3020 (2020).

doc/src/fix_cmap.rst

@@ -127,6 +127,11 @@ the :doc:`run <run>` command.
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.
 
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
+fix. This allows to set at which level of the :doc:`r-RESPA
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
+
 .. note::
 
    If you want the potential energy associated with the CMAP terms

doc/src/fix_drude.rst

@@ -22,6 +22,8 @@ Examples
    fix 1 all drude 1 1 0 1 0 2 2 2
    fix 1 all drude C C N C N D D D
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_drude_transform.rst

@@ -25,6 +25,8 @@ Examples
    fix 3 all drude/transform/direct
    fix 1 all drude/transform/inverse
 
+Example input scripts available: examples/USER/drude
+
 Description
 """""""""""
 

doc/src/fix_grem.rst

@@ -92,6 +92,11 @@ The :doc:`thermo_modify <thermo_modify>` *press* option is supported
 by this fix to add the rescaled kinetic pressure as part of
 :doc:`thermodynamic output <thermo_style>`.
 
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the effective
+temperature :math:`T_{eff}`.  The scalar value calculated by this
+fix is "intensive".
+
 Restrictions
 """"""""""""