Merge pull request #2701 from akohlmey/next_lammps_version

Step version strings for next patch release

.github/CONTRIBUTING.md

@@ -108,7 +108,7 @@ For bug reports, the next step is that one of the core LAMMPS developers will se
 
 For submitting pull requests, there is a [detailed tutorial](https://lammps.sandia.gov/doc/Howto_github.html) in the LAMMPS manual. Thus only a brief breakdown of the steps is presented here. Please note, that the LAMMPS developers are still reviewing and trying to improve the process. If you are unsure about something, do not hesitate to post a question on the lammps-users mailing list or contact one fo the core LAMMPS developers.
 Immediately after the submission, the LAMMPS continuing integration server at ci.lammps.org will download your submitted branch and perform a simple compilation test, i.e. will test whether your submitted code can be compiled under various conditions. It will also do a check on whether your included documentation translates cleanly. Whether these tests are successful or fail will be recorded. If a test fails, please inspect the corresponding output on the CI server and take the necessary steps, if needed, so that the code can compile cleanly again. The test will be re-run each the pull request is updated with a push to the remote branch on GitHub.
-Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assesment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
+Next a LAMMPS core developer will self-assign and do an overall technical assessment of the submission. If you are not yet registered as a LAMMPS collaborator, you will receive an invitation for that. As part of the assessment, the pull request will be categorized with labels. There are two special labels: `needs_work` (indicates that work from the submitter of the pull request is needed) and `work_in_progress` (indicates, that the assigned LAMMPS developer will make changes, if not done by the contributor who made the submit). 
 You may also receive comments and suggestions on the overall submission or specific details and on occasion specific requests for changes as part of the review. If permitted, also additional changes may be pushed into your pull request branch or a pull request may be filed in your LAMMPS fork on GitHub to include those changes.
 The LAMMPS developer may then decide to assign the pull request to another developer (e.g. when that developer is more knowledgeable about the submitted feature or enhancement or has written the modified code). It may also happen, that additional developers are requested to provide a review and approve the changes. For submissions, that may change the general behavior of LAMMPS, or where a possibility of unwanted side effects exists, additional tests may be requested by the assigned developer.
 If the assigned developer is satisfied and considers the submission ready for inclusion into LAMMPS, the pull request will receive approvals and be merged into the master branch by one of the core LAMMPS developers. After the pull request is merged, you may delete the feature branch used for the pull request in your personal LAMMPS fork.

.github/workflows/codeql-analysis.yml

@@ -0,0 +1,47 @@
+# GitHub action to run static code analysis on C++ and Python code
+name: "CodeQL Code Analysis"
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  analyze:
+    name: Analyze
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        language: ['cpp', 'python']
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 2
+
+    - name: Setup Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.x'
+
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v1
+      with:
+        languages: ${{ matrix.language }}
+
+    - name: Create Build Environment
+      run: cmake -E make_directory ${{github.workspace}}/build
+
+    - name: Building LAMMPS via CMake
+      if: ${{ matrix.language == 'cpp' }}
+      shell: bash
+      working-directory: ${{github.workspace}}/build
+      run: |
+        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake
+        cmake --build . --parallel 2
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v1

.github/workflows/unittest-macos.yml

@@ -0,0 +1,36 @@
+# GitHub action to build LAMMPS on MacOS and run unit tests
+name: "Unittest for MacOS"
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  build:
+    name: MacOS Unit Test
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: macos-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 2
+
+    - name: Create Build Environment
+      run: cmake -E make_directory ${{github.workspace}}/build
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      working-directory: ${{github.workspace}}/build
+      run: |
+        cmake -C $GITHUB_WORKSPACE/cmake/presets/clang.cmake \
+              -C $GITHUB_WORKSPACE/cmake/presets/most.cmake \
+                 $GITHUB_WORKSPACE/cmake \
+              -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
+        cmake --build . --parallel 2
+
+    - name: Run Tests
+      working-directory: ${{github.workspace}}/build
+      shell: bash
+      run: ctest -V

LICENSE

@@ -1,6 +1,6 @@
 GNU GENERAL PUBLIC LICENSE
 
-Version 2, June 1991 
+Version 2, June 1991
 
 Copyright (C) 1989, 1991 Free Software Foundation, Inc.  
 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
@@ -301,9 +301,8 @@ one line to give the program's name and an idea of what it does.
 Copyright (C) yyyy  name of author
 
 This program is free software; you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation; either version 2 of the License, or (at
-your option) any later version.
+it under the terms of the GNU General Public License version 2 as
+published by the Free Software Foundation.
 
 This program is distributed in the hope that it will be useful, but
 WITHOUT ANY WARRANTY; without even the implied warranty of

README

@@ -37,14 +37,14 @@ tools                      pre- and post-processing tools
 
 Point your browser at any of these files to get started:
 
-https://lammps.sandia.gov/doc/Manual.html         LAMMPS user manual
+https://lammps.sandia.gov/doc/Manual.html         LAMMPS manual
 https://lammps.sandia.gov/doc/Intro.html          hi-level introduction
 https://lammps.sandia.gov/doc/Build.html          how to build LAMMPS
 https://lammps.sandia.gov/doc/Run_head.html       how to run LAMMPS
 https://lammps.sandia.gov/doc/Commands_all.html   Table of available commands
-https://lammps.sandia.gov/doc/pg_library.html     LAMMPS programmer guide
+https://lammps.sandia.gov/doc/Library.html        LAMMPS library interfaces
 https://lammps.sandia.gov/doc/Modify.html         how to modify and extend LAMMPS
-https://lammps.sandia.gov/doc/pg_developer.html   LAMMPS developer guide
+https://lammps.sandia.gov/doc/Developer.html      LAMMPS developer info
 
 You can also create these doc pages locally:
 

cmake/CMakeLists.txt

@@ -22,18 +22,30 @@ 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 $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
-if (CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+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)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
 set(CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/Modules)
 
 # make sure LIBRARY_PATH is set if environment variable is set
-if (DEFINED ENV{LIBRARY_PATH})
+if(DEFINED ENV{LIBRARY_PATH})
   list(APPEND CMAKE_LIBRARY_PATH "$ENV{LIBRARY_PATH}")
   message(STATUS "Appending $ENV{LIBRARY_PATH} to CMAKE_LIBRARY_PATH: ${CMAKE_LIBRARY_PATH}")
 endif()
@@ -106,14 +118,16 @@ 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
-  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-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-ADIOS)
-set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
+  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-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)
+
+set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
+
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
@@ -154,8 +168,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
@@ -220,6 +233,7 @@ if(BUILD_OMP)
   endif()
 
   if (((CMAKE_CXX_COMPILER_ID STREQUAL "GNU") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.0)) OR
+      (CMAKE_CXX_COMPILER_ID STREQUAL "PGI") OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Clang") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 10.0)) OR
       ((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") AND (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 19.0)))
     # GCC 9.x and later plus Clang 10.x and later implement strict OpenMP 4.0 semantics for consts.
@@ -372,7 +386,7 @@ else()
   set(CUDA_REQUEST_PIC)
 endif()
 
-foreach(PKG_WITH_INCL KSPACE PYTHON VORONOI USER-COLVARS USER-MOLFILE USER-NETCDF USER-PLUMED USER-QMMM
+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)
   if(PKG_${PKG_WITH_INCL})
     include(Packages/${PKG_WITH_INCL})
@@ -524,6 +538,18 @@ 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 ${CMAKE_DL_LIBS})
+  endif()
+endif()
+
 ######################################################################
 # the windows version of LAMMPS requires a couple extra libraries
 # and the MPI library - if use - has to be linked right before those
@@ -579,7 +605,7 @@ add_dependencies(lammps gitversion)
 ############################################
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
-if (${_index} GREATER -1)
+if(${_index} GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
 set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
@@ -649,7 +675,7 @@ install(
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
     # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
+    set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -659,10 +685,10 @@ if(BUILD_SHARED_LIBS)
   endif()
   if (Python_EXECUTABLE)
     add_custom_target(
-      install-python
-      ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
-      -m ${LAMMPS_PYTHON_DIR}/lammps.py
-      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      install-python ${CMAKE_COMMAND} -E remove_directory build
+      COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      -p ${LAMMPS_PYTHON_DIR}/lammps
+      -l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()
@@ -691,11 +717,8 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if (Python_EXECUTABLE)
-    execute_process(COMMAND ${Python_EXECUTABLE}
-      -c "import distutils.sysconfig as cg; print(cg.get_python_lib(1,0,prefix='${CMAKE_INSTALL_PREFIX}'))"
-      OUTPUT_VARIABLE PYTHON_DEFAULT_INSTDIR OUTPUT_STRIP_TRAILING_WHITESPACE)
-    set(PYTHON_INSTDIR ${PYTHON_DEFAULT_INSTDIR} CACHE PATH "Installation folder for LAMMPS Python module")
-    install(FILES ${LAMMPS_PYTHON_DIR}/lammps.py DESTINATION ${PYTHON_INSTDIR})
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
+    install(CODE "execute_process(COMMAND ${Python_EXECUTABLE} setup.py build -b ${CMAKE_BINARY_DIR}/python install --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR}/ WORKING_DIRECTORY ${LAMMPS_PYTHON_DIR})")
   endif()
 endif()
 
@@ -739,14 +762,14 @@ if(OPTIONS)
 endif()
 get_property(LANGUAGES GLOBAL PROPERTY ENABLED_LANGUAGES)
 list (FIND LANGUAGES "Fortran" _index)
-if (${_index} GREATER -1)
+if(${_index} GREATER -1)
   message(STATUS "Fortran Compiler: ${CMAKE_Fortran_COMPILER}
       Type:          ${CMAKE_Fortran_COMPILER_ID}
       Version:       ${CMAKE_Fortran_COMPILER_VERSION}
       Fortran Flags:${CMAKE_Fortran_FLAGS} ${CMAKE_Fortran_FLAGS_${BTYPE}}")
 endif()
 list (FIND LANGUAGES "C" _index)
-if (${_index} GREATER -1)
+if(${_index} GREATER -1)
   message(STATUS "C compiler:       ${CMAKE_C_COMPILER}
       Type:          ${CMAKE_C_COMPILER_ID}
       Version:       ${CMAKE_C_COMPILER_VERSION}
@@ -778,9 +801,7 @@ if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
 -- GPU API:          ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU architecture: ${GPU_ARCH}")
-  elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
+    message(STATUS "GPU default architecture: ${GPU_ARCH}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")

cmake/Modules/CodingStandard.cmake

@@ -8,7 +8,7 @@ else()
     find_package(Python3 COMPONENTS Interpreter QUIET)
 endif()
 
-if (Python3_EXECUTABLE)
+if(Python3_EXECUTABLE)
     if(Python3_VERSION VERSION_GREATER_EQUAL 3.5)
         add_custom_target(
           check-whitespace

cmake/Modules/Documentation.cmake

@@ -50,27 +50,25 @@ if(BUILD_DOC)
     OUTPUT ${DOC_BUILD_DIR}/requirements.txt
     DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
     COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    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/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" 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/3.0.5.tar.gz"
+    file(DOWNLOAD ${MATHJAX_URL}
       "${CMAKE_CURRENT_BINARY_DIR}/mathjax.tar.gz"
-      EXPECTED_MD5 5d9d3799cce77a1a95eee6be04eb68e7)
+      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)
   endif()
 
-  # for increased browser compatibility
-  if(NOT EXISTS ${DOC_BUILD_STATIC_DIR}/polyfill.js)
-    file(DOWNLOAD "https://polyfill.io/v3/polyfill.min.js?features=es6"
-      "${DOC_BUILD_STATIC_DIR}/polyfill.js")
-  endif()
-
   # set up doxygen and add targets to run it
   file(MAKE_DIRECTORY ${DOXYGEN_BUILD_DIR})
   file(COPY ${LAMMPS_DOC_DIR}/doxygen/lammps-logo.png DESTINATION ${DOXYGEN_BUILD_DIR}/lammps-logo.png)

cmake/Modules/FindCythonize.cmake

@@ -0,0 +1,30 @@
+# Find the Cythonize tool.
+#
+# This code sets the following variables:
+#
+#  Cythonize_EXECUTABLE
+#
+# adapted from https://github.com/cmarshall108/cython-cmake-example/blob/master/cmake/FindCython.cmake
+#=============================================================================
+
+if(CMAKE_VERSION VERSION_LESS 3.12)
+    find_package(PythonInterp 3.6 QUIET) # Deprecated since version 3.12
+    if(PYTHONINTERP_FOUND)
+        set(Python3_EXECUTABLE ${PYTHON_EXECUTABLE})
+    endif()
+else()
+    find_package(Python3 3.6 COMPONENTS Interpreter QUIET)
+endif()
+
+# Use the Cython executable that lives next to the Python executable
+# if it is a local installation.
+if(Python3_EXECUTABLE)
+  get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
+  find_program(Cythonize_EXECUTABLE
+    NAMES cythonize3 cythonize cythonize.bat
+    HINTS ${_python_path})
+endif()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Cythonize REQUIRED_VARS Cythonize_EXECUTABLE)
+mark_as_advanced(Cythonize_EXECUTABLE)

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} ${CMAKE_EXTRA_GTEST_OPTS}
@@ -20,10 +22,10 @@ ExternalProject_Add(googletest
                                     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
                                     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
                                     -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
-                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a
-                                     <BINARY_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a
+                    BUILD_BYPRODUCTS <BINARY_DIR>/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
+                                     <BINARY_DIR>/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX}
                     LOG_DOWNLOAD ON
                     LOG_CONFIGURE ON
                     LOG_BUILD ON
@@ -39,10 +41,10 @@ file(MAKE_DIRECTORY ${GTEST_INCLUDE_DIR})
 file(MAKE_DIRECTORY ${GMOCK_INCLUDE_DIR})
 
 ExternalProject_Get_Property(googletest BINARY_DIR)
-set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock${GTEST_LIB_POSTFIX}.a)
-set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gtest_main${GTEST_LIB_POSTFIX}.a)
-set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}gmock_main${GTEST_LIB_POSTFIX}.a)
+set(GTEST_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GTEST_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgtest_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
+set(GMOCK_MAIN_LIBRARY_PATH ${BINARY_DIR}/lib/libgmock_main${GTEST_LIB_POSTFIX}${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 # Prevent GoogleTest from overriding our compiler/linker options
 # when building with Visual Studio

cmake/Modules/LAMMPSUtils.cmake

@@ -50,6 +50,7 @@ function(check_for_autogen_files source_dir)
     file(GLOB SRC_AUTOGEN_FILES ${source_dir}/style_*.h)
     file(GLOB SRC_AUTOGEN_PACKAGES ${source_dir}/packages_*.h)
     list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/lmpinstalledpkgs.h ${source_dir}/lmpgitversion.h)
+    list(APPEND SRC_AUTOGEN_FILES ${SRC_AUTOGEN_PACKAGES} ${source_dir}/mliap_model_python_couple.h ${source_dir}/mliap_model_python_couple.cpp)
     foreach(_SRC ${SRC_AUTOGEN_FILES})
       get_filename_component(FILENAME "${_SRC}" NAME)
       if(EXISTS ${source_dir}/${FILENAME})
@@ -85,7 +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)

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")
+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

@@ -0,0 +1,50 @@
+message(STATUS "Downloading and building OpenCL loader library")
+set(OPENCL_LOADER_URL "${LAMMPS_THIRDPARTY_URL}/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+set(OPENCL_LOADER_MD5 "011cdcbd41030be94f3fced6d763a52a" CACHE STRING "MD5 checksum of OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+mark_as_advanced(OPENCL_LOADER_MD5)
+
+include(ExternalProject)
+ExternalProject_Add(opencl_loader
+                    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} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
+set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
+
+ExternalProject_Get_Property(opencl_loader BINARY_DIR)
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
+
+find_package(Threads QUIET)
+if(NOT WIN32)
+  set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
+else()
+  set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
+endif()
+
+add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+add_dependencies(OpenCL::OpenCL opencl_loader)
+
+set_target_properties(OpenCL::OpenCL PROPERTIES
+  IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
+  INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
+  INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
+
+

cmake/Modules/Packages/GPU.cmake

@@ -1,7 +1,10 @@
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
-                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.h
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.cpp)
+target_compile_definitions(lammps PRIVATE -DLMP_GPU)
 
 set(GPU_API "opencl" CACHE STRING "API used by GPU package")
 set(GPU_API_VALUES opencl cuda hip)
@@ -32,9 +35,12 @@ 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)
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+    endif()
     set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
   endif()
 
@@ -97,6 +103,10 @@ if(GPU_API STREQUAL "CUDA")
   if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
     string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
   endif()
+  # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+  endif()
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
     message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
@@ -121,7 +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)
@@ -135,27 +145,13 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-    # download and unpack support binaries for compilation of windows binaries.
-    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
-    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
-            EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
-    if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
-    elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
-    endif()
-    set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
+  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
+  mark_as_advanced(USE_STATIC_OPENCL_LOADER)
+  if (USE_STATIC_OPENCL_LOADER)
+    include(OpenCLLoader)
   else()
     find_package(OpenCL REQUIRED)
   endif()
-  set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-  set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-  set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-  validate_option(OCL_TUNE OCL_TUNE_VALUES)
-  string(TOUPPER ${OCL_TUNE} OCL_TUNE)
 
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@@ -199,7 +195,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
   target_link_libraries(lammps PRIVATE gpu)
@@ -207,6 +203,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
+  add_dependencies(ocl_get_devices OpenCL::OpenCL)
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
@@ -221,7 +218,7 @@ 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()
@@ -229,7 +226,7 @@ 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)
@@ -287,7 +284,7 @@ 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")
@@ -341,11 +338,16 @@ 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 ""
@@ -357,7 +359,7 @@ 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()
 
@@ -384,18 +386,21 @@ 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)
 endif()
 
-# GPU package
-FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
-# detects styles which have GPU version
+# detect styles which have a GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 

cmake/Modules/Packages/KIM.cmake

@@ -19,6 +19,8 @@ if(CURL_FOUND)
     target_compile_definitions(lammps PRIVATE -DLMP_NO_SSL_CHECK)
   endif()
 endif()
+set(KIM_EXTRA_UNITTESTS OFF CACHE STRING "Set extra unit tests verbose mode on/off. If on, extra tests are included.")
+mark_as_advanced(KIM_EXTRA_UNITTESTS)
 find_package(PkgConfig QUIET)
 set(DOWNLOAD_KIM_DEFAULT ON)
 if(PKG_CONFIG_FOUND)
@@ -33,9 +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-2.1.3.txz
-    URL_MD5 6ee829a1bbba5f8b9874c88c4c4ebff8
+    URL     ${KIM_URL}
+    URL_MD5 ${KIM_MD5}
     BINARY_DIR build
     CMAKE_ARGS ${CMAKE_REQUEST_PIC}
                -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
@@ -53,11 +59,28 @@ if(DOWNLOAD_KIM)
   add_library(LAMMPS::KIM UNKNOWN IMPORTED)
   set_target_properties(LAMMPS::KIM PROPERTIES
     IMPORTED_LOCATION "${INSTALL_DIR}/lib/libkim-api${CMAKE_SHARED_LIBRARY_SUFFIX}"
-    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api")
-  target_link_libraries(lammps PRIVATE LAMMPS::KIM)
+    INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include/kim-api"
+    )
   add_dependencies(LAMMPS::KIM kim_build)
+  target_link_libraries(lammps PRIVATE LAMMPS::KIM)
+  # Set rpath so lammps build directory is relocatable
+  if("${CMAKE_SYSTEM_NAME}" STREQUAL "Darwin")
+    set(_rpath_prefix "@loader_path")
+  else()
+    set(_rpath_prefix "$ORIGIN")
+  endif()
+  set_target_properties(lmp PROPERTIES
+    BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
+    )
 else()
-  find_package(PkgConfig REQUIRED)
-  pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
-  target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
+  if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
+    # For kim-api >= 2.2.0
+    find_package(KIM-API 2.2.0 CONFIG REQUIRED)
+    target_link_libraries(lammps PRIVATE KIM-API::kim-api)
+  else()
+    # For kim-api 2.1.3 (consistent with previous version of this file)
+    find_package(PkgConfig REQUIRED)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
+    target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
+  endif()
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,4 +1,7 @@
 ########################################################################
+# As of version 3.3.0 Kokkos requires C++14
+set(CMAKE_CXX_STANDARD 14)
+########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
   message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
@@ -34,9 +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/3.3.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_MD5 "08201d1c7cf5bc458ce0f5b44a629d5a" 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/3.2.00.tar.gz
-    URL_MD5 81569170fe232e5e64ab074f7cca5e50
+    URL     ${KOKKOS_URL}
+    URL_MD5 ${KOKKOS_MD5}
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -48,10 +55,12 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_INCLUDE_DIRECTORIES "${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 3.2.00 REQUIRED CONFIG)
+  find_package(Kokkos 3.3.01 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)
@@ -63,6 +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/MESSAGE.cmake

@@ -2,9 +2,8 @@ if(LAMMPS_SIZES STREQUAL BIGBIG)
   message(FATAL_ERROR "The MESSAGE Package is not compatible with -DLAMMPS_BIGBIG")
 endif()
 option(MESSAGE_ZMQ "Use ZeroMQ in MESSAGE package" OFF)
-file(GLOB_RECURSE cslib_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.F
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.c
-    ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
+file(GLOB_RECURSE cslib_SOURCES
+        ${LAMMPS_LIB_SOURCE_DIR}/message/cslib/[^.]*.cpp)
 
 add_library(cslib STATIC ${cslib_SOURCES})
 target_compile_definitions(cslib PRIVATE -DLAMMPS_${LAMMPS_SIZES})

cmake/Modules/Packages/MLIAP.cmake

@@ -0,0 +1,40 @@
+# if PYTHON package is included we may also include Python support in MLIAP
+set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
+if(PKG_PYTHON)
+  find_package(Cythonize QUIET)
+  if(Cythonize_FOUND)
+    set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
+  endif()
+endif()
+
+option(MLIAP_ENABLE_PYTHON "Build MLIAP package with Python support" ${MLIAP_ENABLE_PYTHON_DEFAULT})
+
+if(MLIAP_ENABLE_PYTHON)
+  find_package(Cythonize REQUIRED)
+  if(NOT PKG_PYTHON)
+    message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
+  endif()
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  else()
+    if(Python_VERSION VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  endif()
+
+  set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
+  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)
+  get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_SRC} NAME_WE)
+  file(MAKE_DIRECTORY ${MLIAP_BINARY_DIR})
+  add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
+          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+          COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+          COMMENT "Generating C++ sources with cythonize...")
+  target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
+  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
+endif()

cmake/Modules/Packages/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")

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-PLUMED.cmake

@@ -53,10 +53,16 @@ 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/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" 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/v2.6.1/plumed-src-2.6.1.tgz
-    URL_MD5 89a9a450fc6025299fe16af235957163
+    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/Tools.cmake

@@ -34,13 +34,24 @@ if(BUILD_LAMMPS_SHELL)
   if(NOT LAMMPS_EXCEPTIONS)
     message(WARNING "The LAMMPS shell needs LAMMPS_EXCEPTIONS enabled for full functionality")
   endif()
-  add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp)
+
+  # include resource compiler to embed icons into the executable on Windows
+  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    enable_language(RC)
+    set(ICON_RC_FILE ${LAMMPS_TOOLS_DIR}/lammps-shell/lmpicons.rc)
+  endif()
+
+  add_executable(lammps-shell ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.cpp ${ICON_RC_FILE})
+  target_include_directories(lammps-shell PRIVATE ${LAMMPS_TOOLS_DIR}/lammps-shell)
+
   # workaround for broken readline pkg-config file on FreeBSD
   if(CMAKE_SYSTEM_NAME STREQUAL FreeBSD)
     target_include_directories(lammps-shell PRIVATE /usr/local/include)
   endif()
   target_link_libraries(lammps-shell PRIVATE lammps PkgConfig::READLINE)
   install(TARGETS lammps-shell EXPORT LAMMPS_Targets DESTINATION ${CMAKE_INSTALL_BINDIR})
+  install(DIRECTORY ${LAMMPS_TOOLS_DIR}/lammps-shell/icons DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/)
+  install(FILES ${LAMMPS_TOOLS_DIR}/lammps-shell/lammps-shell.desktop DESTINATION ${CMAKE_INSTALL_DATAROOTDIR}/applications/)
 endif()
 
 

cmake/Modules/YAML.cmake

@@ -0,0 +1,35 @@
+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           ${YAML_MD5}
+                    SOURCE_DIR        "${CMAKE_BINARY_DIR}/yaml-src"
+                    BINARY_DIR        "${CMAKE_BINARY_DIR}/yaml-build"
+                    CONFIGURE_COMMAND <SOURCE_DIR>/configure ${CONFIGURE_REQUEST_PIC}
+                                      CXX=${CMAKE_CXX_COMPILER}
+                                      CC=${CMAKE_C_COMPILER}
+                                      --prefix=<INSTALL_DIR> --disable-shared
+                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    TEST_COMMAND      "")
+
+ExternalProject_Get_Property(libyaml INSTALL_DIR)
+set(YAML_INCLUDE_DIR ${INSTALL_DIR}/include)
+set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
+file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
+
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
+
+add_library(Yaml::Yaml UNKNOWN IMPORTED)
+set_target_properties(Yaml::Yaml PROPERTIES
+        IMPORTED_LOCATION ${YAML_LIBRARY_PATH}
+        INTERFACE_INCLUDE_DIRECTORIES ${YAML_INCLUDE_DIR})
+add_dependencies(Yaml::Yaml libyaml)

cmake/Modules/generate_lmpgitversion.cmake

@@ -7,17 +7,20 @@ set(temp_git_info "false")
 message(STATUS "Git Directory: ${LAMMPS_DIR}/.git")
 if(GIT_FOUND AND EXISTS ${LAMMPS_DIR}/.git)
   set(temp_git_info "true")
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse HEAD
     OUTPUT_VARIABLE temp_git_commit
     ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} rev-parse --abbrev-ref HEAD
+  execute_process(COMMAND ${GIT_EXECUTABLE} rev-parse --abbrev-ref HEAD
     OUTPUT_VARIABLE temp_git_branch
     ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
-  execute_process(COMMAND ${GIT_EXECUTABLE} -C ${LAMMPS_DIR} describe --dirty=-modified
+  execute_process(COMMAND ${GIT_EXECUTABLE} describe --dirty=-modified
     OUTPUT_VARIABLE temp_git_describe
     ERROR_QUIET
+    WORKING_DIRECTORY ${LAMMPS_DIR}
     OUTPUT_STRIP_TRAILING_WHITESPACE)
 endif()
 

cmake/presets/most.cmake

@@ -4,7 +4,7 @@
 
 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
+        PLUGIN 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

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)
+

cmake/presets/pgi.cmake

@@ -0,0 +1,16 @@
+# preset that will enable clang/clang++ with support for MPI and OpenMP (on Linux boxes)
+
+set(CMAKE_CXX_COMPILER "pgc++" CACHE STRING "" FORCE)
+set(CMAKE_C_COMPILER "pgcc" CACHE STRING "" FORCE)
+set(CMAKE_Fortran_COMPILER "pgfortran" CACHE STRING "" FORCE)
+set(MPI_CXX "pgc++" CACHE STRING "" FORCE)
+set(MPI_CXX_COMPILER "mpicxx" CACHE STRING "" FORCE)
+unset(HAVE_OMP_H_INCLUDE CACHE)
+
+set(OpenMP_C "pgcc" CACHE STRING "" FORCE)
+set(OpenMP_C_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_C_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_CXX "pgc++" CACHE STRING "" FORCE)
+set(OpenMP_CXX_FLAGS "-mp" CACHE STRING "" FORCE)
+set(OpenMP_CXX_LIB_NAMES "omp" CACHE STRING "" FORCE)
+set(OpenMP_omp_LIBRARY "libomp.so" CACHE PATH "" FORCE)

doc/Makefile

@@ -14,7 +14,6 @@ TXT2RST        = $(VENV)/bin/txt2rst
 ANCHORCHECK    = $(VENV)/bin/rst_anchor_check
 SPHINXCONFIG   = $(BUILDDIR)/utils/sphinx-config
 MATHJAX        = $(SPHINXCONFIG)/_static/mathjax
-POLYFILL       = $(SPHINXCONFIG)/_static/polyfill.js
 
 PYTHON         = $(shell which python3)
 DOXYGEN        = $(shell which doxygen)
@@ -48,6 +47,8 @@ HAS_PDFLATEX = YES
 endif
 endif
 
+# override settings for PIP commands
+# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
 #SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
 
@@ -81,7 +82,7 @@ help:
 # ------------------------------------------
 
 clean-all: clean
-	rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(POLYFILL) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
+	rm -rf $(BUILDDIR)/docenv $(MATHJAX) $(BUILDDIR)/LAMMPS.mobi $(BUILDDIR)/LAMMPS.epub $(BUILDDIR)/Manual.pdf
 
 clean: clean-spelling
 	rm -rf $(BUILDDIR)/html $(BUILDDIR)/epub $(BUILDDIR)/latex $(BUILDDIR)/doctrees $(BUILDDIR)/doxygen/xml $(BUILDDIR)/doxygen-warn.log $(BUILDDIR)/doxygen/Doxyfile $(SPHINXCONFIG)/conf.py
@@ -95,7 +96,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
+html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -119,7 +120,7 @@ html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX) $(POLYFILL)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
@@ -229,20 +230,13 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install --upgrade pip; \
-		pip install --use-feature=2020-resolver -r $(BUILDDIR)/utils/requirements.txt; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
+		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
-
-# fall back to using wget and/or unencrypted download, if curl fails
-$(POLYFILL): $(MATHJAX)
-	@curl -s -o $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		curl -s -o $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		wget -O $@ "https://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1  || \
-		wget -O $@ "http://polyfill.io/v3/polyfill.min.js?features=es6" > /dev/null 2>&1
+	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/doxygen/Doxyfile.in

@@ -424,6 +424,8 @@ INPUT                  = @LAMMPS_SOURCE_DIR@/utils.cpp                 \
                          @LAMMPS_SOURCE_DIR@/input.h                   \
                          @LAMMPS_SOURCE_DIR@/tokenizer.cpp             \
                          @LAMMPS_SOURCE_DIR@/tokenizer.h               \
+                         @LAMMPS_SOURCE_DIR@/arg_info.cpp              \
+                         @LAMMPS_SOURCE_DIR@/arg_info.h                \
                          @LAMMPS_SOURCE_DIR@/text_file_reader.cpp      \
                          @LAMMPS_SOURCE_DIR@/text_file_reader.h        \
                          @LAMMPS_SOURCE_DIR@/potential_file_reader.cpp \

doc/github-development-workflow.md

@@ -95,7 +95,7 @@ on the pull request discussion page on GitHub, so that other developers
 can later review the entire discussion after the fact and understand the
 rationale behind choices made.  Exceptions to this policy are technical
 discussions, that are centered on tools or policies themselves
-(git, github, c++) rather than on the content of the pull request.
+(git, GitHub, c++) rather than on the content of the pull request.
 
 ### Checklist for Pull Requests
 

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "22 October 2020" "2020-10-22"
+.TH LAMMPS "8 April 2021" "2021-04-08"
 .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>`
@@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
 
       .. note::
 
-         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
          called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
          operating system does not support ``gettimeofday()``, you will
          need to insert code to call another timer.  Note that the
@@ -234,14 +234,21 @@ 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:
+         cmake ../cmake -DCMAKE_C_COMPILER=pgcc -DCMAKE_CXX_COMPILER=pgc++ -DCMAKE_Fortran_COMPILER=pgfortran
 
       For compiling with the Clang/LLVM compilers a CMake preset is
       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.
+      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
@@ -523,6 +530,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

doc/src/Build_development.rst

@@ -108,11 +108,18 @@ results over a given number of steps and operations within a given
 error margin).  The status of this automated testing can be viewed on
 `https://ci.lammps.org <https://ci.lammps.org>`_.
 
+The scripts and inputs for integration, run, and regression testing
+are maintained in a
+`separate repository <https://github.com/lammps/lammps-testing>`_
+of the LAMMPS project on GitHub.
+
 The unit testing facility is integrated into the CMake build process
 of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `PyYAML <http://pyyaml.org/>`_ library and development
-headers to compile and will download and compile a recent version of the
+It requires the `YAML <http://pyyaml.org/>`_ library and development
+headers (if those are not found locally a recent version will be
+downloaded and compiled along with LAMMPS and the test program) to
+compile and will download and compile a specific recent version of the
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
@@ -162,22 +169,21 @@ The ``ctest`` command has many options, the most important ones are:
 In its full implementation, the unit test framework will consist of multiple
 kinds of tests implemented in different programming languages (C++, C, Python,
 Fortran) and testing different aspects of the LAMMPS software and its features.
-At the moment only tests for "force styles" are implemented. More on those
-in the next section.
+The tests will adapt to the compilation settings of LAMMPS, so that tests
+will be skipped if prerequisite features are not available in LAMMPS.
 
 .. note::
 
-   The unit test framework is new and still under development.
-   The coverage is only minimal and will be expanded over time.
-   Tests styles of the same kind of style (e.g. pair styles or
-   bond styles) are performed with the same executable using
-   different input files in YAML format.  So to add a test for
-   another pair style can be done by copying the YAML file and
-   editing the style settings and then running the individual test
-   program with a flag to update the computed reference data.
-   Detailed documentation about how to add new test program and
-   the contents of the YAML files for existing test programs
-   will be provided in time as well.
+   The unit test framework was added in spring 2020 and is under active
+   development.  The coverage is not complete and will be expanded over
+   time.
+
+Tests for styles of the same kind of style (e.g. pair styles or bond
+styles) are performed with the same test executable using different
+input files in YAML format.  So to add a test for another style of the
+same kind it may be sufficient to add a suitable YAML file.
+:doc:`Detailed instructions for adding tests <Developer_unittest>` are
+provided in the Programmer Guide part of the manual.
 
 Unit tests for force styles
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Build_extras.rst

@@ -37,6 +37,7 @@ This is the list of packages that may require additional steps.
    * :ref:`KOKKOS <kokkos>`
    * :ref:`LATTE <latte>`
    * :ref:`MESSAGE <message>`
+   * :ref:`MLIAP <mliap>`
    * :ref:`MSCG <mscg>`
    * :ref:`OPT <opt>`
    * :ref:`POEMS <poems>`
@@ -119,21 +120,21 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D OCL_TUNE=value            # hardware choice for GPU_API=opencl
-                                # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
    -D HIP_ARCH=value            # primary GPU hardware choice for GPU_API=hip
                                 # value depends on selected HIP_PLATFORM
-                                # default is 'gfx906' for HIP_PLATFORM=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
-                                # 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
+                                      # value = yes (default) or no
 
 :code:`GPU_ARCH` settings for different GPU hardware is as follows:
 
@@ -160,19 +161,32 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
 using the traditional build procedure. CMake will detect files generated by that
 process and will terminate with an error and a suggestion for how to remove them.
 
+If you are compiling for OpenCL, the default setting is to download, build, and
+link with a static OpenCL ICD loader library and standard OpenCL headers.  This
+way no local OpenCL development headers or library needs to be present and only
+OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
+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)
@@ -218,11 +232,20 @@ Makefile if desired:
 * ``CUDA_PRECISION`` = precision (double, mixed, single)
 * ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
 
-The file Makefile.linux_multi is set up to include support for multiple
+The file Makefile.cuda is set up to include support for multiple
 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 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 must **not** use
+the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
+to empty.
+
 If the library build is successful, 3 files should be created:
 ``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
 ``lib/gpu/Makefile.lammps``\ .  The latter has settings that enable LAMMPS
@@ -249,18 +272,18 @@ To build with this package, the KIM library with API v2 must be downloaded
 and built on your system. It must include the KIM models that you want to
 use with LAMMPS.
 
-If you would like to use the :doc:`kim_query <kim_commands>`
+If you would like to use the :doc:`kim query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-If you would like to use the :doc:`kim_property <kim_commands>`
+If you would like to use the :doc:`kim property <kim_commands>`
 command, you need to build LAMMPS with the PYTHON package installed
 and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
 for more details on this. After successfully building LAMMPS with Python, you
-also need to install the kim-property Python package, which can be easily done using
-*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
-``conda install kim-property`` if LAMMPS is built in Conda. More detailed
-information is available at:
+also need to install the ``kim-property`` Python package, which can be easily
+done using *pip* as ``pip install kim-property``, or from the *conda-forge*
+channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
+detailed information is available at:
 `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 
 In addition to installing the KIM API, it is also necessary to install the
@@ -282,6 +305,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
          -D DOWNLOAD_KIM=value           # download OpenKIM API v2 for build, value = no (default) or yes
          -D LMP_DEBUG_CURL=value         # set libcurl verbose mode on/off, value = off (default) or on
          -D LMP_NO_SSL_CHECK=value       # tell libcurl to not verify the peer, value = no (default) or yes
+         -D KIM_EXTRA_UNITTESTS=value    # enables extra unit tests, value = no (default) or yes
 
       If ``DOWNLOAD_KIM`` is set to *yes* (or *on*), the KIM API library
       will be downloaded and built inside the CMake build directory.  If
@@ -290,11 +314,16 @@ minutes to hours) to build.  Of course you only need to do that once.)
       ``PKG_CONFIG_PATH`` environment variable so that libkim-api can be
       found, or run the command ``source kim-api-activate``.
 
+      Extra unit tests can only be available if they are explicitly requested
+      (``KIM_EXTRA_UNITTESTS`` is set to *yes* (or *on*)) and the prerequisites
+      are met. See :ref:`KIM Extra unit tests <kim_extra_unittests>` for
+      more details on this.
+
    .. tab:: Traditional make
 
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
-      this in one step from the lammps/src dir, using a command like
+      this in one step from the lammps/src directory, using a command like
       these, which simply invoke the ``lib/kim/Install.py`` script with
       the specified args.
 
@@ -314,7 +343,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: make
 
-         LMP_INC =       -DLMP_NO_SSL_CHECK
+         LMP_INC = -DLMP_NO_SSL_CHECK
 
 Debugging OpenKIM web queries in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -338,6 +367,39 @@ specify your own CA cert path by setting the environment variable
 ``CURL_CA_BUNDLE`` to the path of your choice.  A call to the KIM web
 query would get this value from the environment variable.
 
+.. _kim_extra_unittests:
+
+KIM Extra unit tests (CMake only)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+During development, testing, or debugging, if
+:doc:`unit testing <Build_development>` is enabled in LAMMPS, one can also
+enable extra tests on :doc:`KIM commands <kim_commands>` by setting the
+``KIM_EXTRA_UNITTESTS`` to *yes* (or *on*).
+
+Enabling the extra unit tests have some requirements,
+
+* It requires to have internet access.
+* It requires to have libcurl installed with the matching development headers
+  and the curl-config tool.
+* It requires to build LAMMPS with the PYTHON package installed and linked to
+  Python 3.6 or later. See the :ref:`PYTHON package build info <python>` for
+  more details on this.
+* It requires to have ``kim-property`` Python package installed, which can be
+  easily done using *pip* as ``pip install kim-property``, or from the
+  *conda-forge* channel as ``conda install kim-property`` if LAMMPS is built in
+  Conda. More detailed information is available at:
+  `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
+* It is also necessary to install
+  ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
+  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
+  ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
+  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+  to learn how to install a pre-built binary of the OpenKIM Repository of
+  Models or see
+  `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
+  to learn how to install the specific KIM models.
+
 ----------
 
 .. _kokkos:
@@ -482,11 +544,14 @@ They must be specified in uppercase.
    *  - VEGA906
       - GPU
       - AMD GPU MI50/MI60 GFX906
+   *  - VEGA908
+      - GPU
+      - AMD GPU GFX908
    *  - INTEL_GEN
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.2 of the Kokkos library.
+This list was last updated for version 3.3 of the Kokkos library.
 
 .. tabs::
 
@@ -732,6 +797,54 @@ be installed on your system.
 
 ----------
 
+.. _mliap:
+
+MLIAP package
+---------------------------
+
+Building the MLIAP package requires including the :ref:`SNAP <PKG-SNAP>`
+package.  There will be an error message if this requirement is not satisfied.
+Using the *mliappy* model also requires enabling Python support, which
+in turn requires the :ref:`PYTHON <PKG-PYTHON>`
+package **and** requires you have the `cython <https://cython.org>`_ software
+installed and with it a working ``cythonize`` command.  This feature requires
+compiling LAMMPS with Python version 3.6 or later.
+
+.. tabs::
+
+   .. tab:: CMake build
+
+      .. code-block:: bash
+
+         -D MLIAP_ENABLE_PYTHON=value   # enable mliappy model (default is autodetect)
+
+      Without this setting, CMake will check whether it can find a
+      suitable Python version and the ``cythonize`` command and choose
+      the default accordingly.  During the build procedure the provided
+      .pyx file(s) will be automatically translated to C++ code and compiled.
+      Please do **not** run ``cythonize`` manually in the ``src/MLIAP`` folder,
+      as that can lead to compilation errors if Python support is not enabled.
+      If you did by accident, please remove the generated .cpp and .h files.
+
+   .. tab:: Traditional make
+
+      The build uses the ``lib/python/Makefile.mliap_python`` file in the
+      compile/link process to add a rule to update the files generated by
+      the ``cythonize`` command in case the corresponding .pyx file(s) were
+      modified.  You may need to modify ``lib/python/Makefile.lammps``
+      if the LAMMPS build fails.
+      To manually enforce building MLIAP with Python support enabled,
+      you can add
+      ``-DMLIAP_PYTHON`` to the ``LMP_INC`` variable in your machine makefile.
+      You may have to manually run the ``cythonize`` command on .pyx file(s)
+      in the ``src`` folder, if this is not automatically done during
+      installing the MLIAP package.  Please do **not** run ``cythonize``
+      in the ``src/MLIAP`` folder, as that can lead to compilation errors
+      if Python support is not enabled.
+      If you did by accident, please remove the generated .cpp and .h files.
+
+----------
+
 .. _mscg:
 
 MSCG package

doc/src/Build_link.rst

@@ -20,16 +20,8 @@ the suffix ``.so.0`` (or some other number).
 .. note::
 
    Care should be taken to use the same MPI library for the calling code
-   and the LAMMPS library.  The ``library.h`` file includes ``mpi.h``
-   and uses definitions from it so those need to be available and
-   consistent.  When LAMMPS is compiled with the included STUBS MPI
-   library, then its ``mpi.h`` file needs to be included.  While it is
-   technically possible to use a full MPI library in the calling code
-   and link to a serial LAMMPS library compiled with MPI STUBS, it is
-   recommended to use the *same* MPI library for both, and then use
-   ``MPI_Comm_split()`` in the calling code to pass a suitable
-   communicator with a subset of MPI ranks to the function creating the
-   LAMMPS instance.
+   and the LAMMPS library unless LAMMPS is to be compiled without (real)
+   MPI support using the include STUBS MPI library.
 
 Link with LAMMPS as a static library
 ------------------------------------
@@ -110,7 +102,7 @@ executable, that are also required to link the LAMMPS executable.
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/lib/poems \
                       -L${HOME}/lammps/src/STUBS -L${HOME}/lammps/src \
                       -llammps_serial -lpoems -lmpi_stubs
@@ -174,7 +166,7 @@ the POEMS package installed becomes:
 
       .. code-block:: bash
 
-         gcc -c -O -I${HOME}/lammps/src/STUBS -I${HOME}/lammps/src -caller.c
+         gcc -c -O -I${HOME}/lammps/src -caller.c
          g++ -o caller caller.o -L${HOME}/lammps/src -llammps_serial
 
 Locating liblammps.so at runtime

doc/src/Build_manual.rst

@@ -73,8 +73,12 @@ after the documentation folder is returned to a pristine state with
 For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
 that virtual environment via the ``pip`` tool.  For rendering embedded
-LaTeX code also the `MathJax <https://www.mathjax.org/>`_ and the
-`Polyfill <https://polyfill.io/>`_ JavaScript engines need to be downloaded.
+LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
+engine needs to be downloaded.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
+at beginning of the makefile.
 
 The actual translation is then done via ``make`` commands in the doc
 folder.  The following ``make`` commands are available:
@@ -108,7 +112,10 @@ installation of the HTML manual pages into the "install" step when
 installing LAMMPS after the CMake build via ``cmake --build . --target
 install``.  The documentation build is included in the default build
 target, but can also be requested independently with
-``cmake --build . --target doc``.
+``cmake --build . --target doc``.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable.
 
 .. code-block:: bash
 

doc/src/Build_package.rst

@@ -160,6 +160,7 @@ one of them as a starting point and customize it to your needs.
     cmake -C ../cmake/presets/clang.cmake    [OPTIONS] ../cmake  # change settings to use the Clang compilers by default
     cmake -C ../cmake/presets/gcc.cmake      [OPTIONS] ../cmake  # change settings to use the GNU compilers by default
     cmake -C ../cmake/presets/intel.cmake    [OPTIONS] ../cmake  # change settings to use the Intel compilers by default
+    cmake -C ../cmake/presets/pgi.cmake      [OPTIONS] ../cmake  # change settings to use the PGI compilers by default
     cmake -C ../cmake/presets/all_on.cmake   [OPTIONS] ../cmake  # enable all packages
     cmake -C ../cmake/presets/all_off.cmake  [OPTIONS] ../cmake  # disable all packages
     mingw64-cmake -C ../cmake/presets/mingw-cross.cmake [OPTIONS] ../cmake  #  compile with MinGW cross compilers

doc/src/Commands_all.rst

@@ -60,11 +60,7 @@ An alphabetic list of all general LAMMPS commands.
    * :doc:`include <include>`
    * :doc:`info <info>`
    * :doc:`jump <jump>`
-   * :doc:`kim_init <kim_commands>`
-   * :doc:`kim_interactions <kim_commands>`
-   * :doc:`kim_param <kim_commands>`
-   * :doc:`kim_property <kim_commands>`
-   * :doc:`kim_query <kim_commands>`
+   * :doc:`kim <kim_commands>`
    * :doc:`kspace_modify <kspace_modify>`
    * :doc:`kspace_style <kspace_style>`
    * :doc:`label <label>`
@@ -90,6 +86,7 @@ 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

@@ -35,6 +35,7 @@ OPT.
    * :doc:`class2 (ko) <bond_class2>`
    * :doc:`fene (iko) <bond_fene>`
    * :doc:`fene/expand (o) <bond_fene_expand>`
+   * :doc:`gaussian <bond_gaussian>`
    * :doc:`gromos (o) <bond_gromos>`
    * :doc:`harmonic (iko) <bond_harmonic>`
    * :doc:`harmonic/shift (o) <bond_harmonic_shift>`
@@ -84,6 +85,7 @@ OPT.
    * :doc:`dipole (o) <angle_dipole>`
    * :doc:`fourier (o) <angle_fourier>`
    * :doc:`fourier/simple (o) <angle_fourier_simple>`
+   * :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
    * :doc:`harmonic (iko) <angle_harmonic>`
    * :doc:`mm3 <angle_mm3>`
    * :doc:`quartic (o) <angle_quartic>`
@@ -124,7 +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

@@ -62,6 +62,7 @@ OPT.
    * :doc:`efield <fix_efield>`
    * :doc:`ehex <fix_ehex>`
    * :doc:`electron/stopping <fix_electron_stopping>`
+   * :doc:`electron/stopping/fit <fix_electron_stopping>`
    * :doc:`enforce2d (k) <fix_enforce2d>`
    * :doc:`eos/cv <fix_eos_cv>`
    * :doc:`eos/table <fix_eos_table>`
@@ -113,7 +114,7 @@ OPT.
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
    * :doc:`nphug <fix_nphug>`
-   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt (giko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
    * :doc:`npt/cauchy <fix_npt_cauchy>`
@@ -121,8 +122,8 @@ OPT.
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
    * :doc:`numdiff <fix_numdiff>`
-   * :doc:`nve (iko) <fix_nve>`
-   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve (giko) <fix_nve>`
+   * :doc:`nve/asphere (gi) <fix_nve_asphere>`
    * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
    * :doc:`nve/awpmd <fix_nve_awpmd>`
    * :doc:`nve/body <fix_nve_body>`
@@ -137,7 +138,7 @@ OPT.
    * :doc:`nve/spin <fix_nve_spin>`
    * :doc:`nve/tri <fix_nve_tri>`
    * :doc:`nvk <fix_nvk>`
-   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt (giko) <fix_nh>`
    * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`
@@ -195,7 +196,7 @@ OPT.
    * :doc:`saed/vtk <fix_saed_vtk>`
    * :doc:`setforce (k) <fix_setforce>`
    * :doc:`setforce/spin <fix_setforce>`
-   * :doc:`shake <fix_shake>`
+   * :doc:`shake (k) <fix_shake>`
    * :doc:`shardlow (k) <fix_shardlow>`
    * :doc:`smd <fix_smd>`
    * :doc:`smd/adjust_dt <fix_smd_adjust_dt>`
@@ -220,6 +221,8 @@ OPT.
    * :doc:`temp/rescale <fix_temp_rescale>`
    * :doc:`temp/rescale/eff <fix_temp_rescale_eff>`
    * :doc:`tfmc <fix_tfmc>`
+   * :doc:`tgnpt/drude <fix_tgnh_drude>`
+   * :doc:`tgnvt/drude <fix_tgnh_drude>`
    * :doc:`thermal/conductivity <fix_thermal_conductivity>`
    * :doc:`ti/spring <fix_ti_spring>`
    * :doc:`tmd <fix_tmd>`

doc/src/Commands_pair.rst

@@ -96,6 +96,7 @@ OPT.
    * :doc:`eam/cd <pair_eam>`
    * :doc:`eam/cd/old <pair_eam>`
    * :doc:`eam/fs (gikot) <pair_eam>`
+   * :doc:`eam/he <pair_eam>`
    * :doc:`edip (o) <pair_edip>`
    * :doc:`edip/multi <pair_edip>`
    * :doc:`edpd <pair_mesodpd>`
@@ -121,7 +122,7 @@ OPT.
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`line/lj <pair_line_lj>`
-   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
    * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
@@ -162,6 +163,7 @@ OPT.
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/sdk (gko) <pair_sdk>`
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
@@ -185,7 +187,7 @@ 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>`
@@ -241,6 +243,7 @@ OPT.
    * :doc:`spin/dipole/long <pair_spin_dipole>`
    * :doc:`spin/dmi <pair_spin_dmi>`
    * :doc:`spin/exchange <pair_spin_exchange>`
+   * :doc:`spin/exchange/biquadratic <pair_spin_exchange>`
    * :doc:`spin/magelec <pair_spin_magelec>`
    * :doc:`spin/neel <pair_spin_neel>`
    * :doc:`srp <pair_srp>`
@@ -261,6 +264,7 @@ OPT.
    * :doc:`ufm (got) <pair_ufm>`
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
+   * :doc:`wf/cut <pair_wf_cut>`
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_parse.rst

@@ -162,3 +162,26 @@ LAMMPS:
    triple quotes can be nested in the usual manner.  See the doc pages
    for those commands for examples.  Only one of level of nesting is
    allowed, but that should be sufficient for most use cases.
+
+.. admonition:: ASCII versus UTF-8
+        :class: note
+
+   LAMMPS expects and processes 7-bit ASCII format text internally.
+   Many modern environments use UTF-8 encoding, which is a superset
+   of the 7-bit ASCII character table and thus mostly compatible.
+   However, there are several non-ASCII characters that can look
+   very similar to their ASCII equivalents or are invisible (so they
+   look like a blank), but are encoded differently.  Web browsers,
+   PDF viewers, document editors are known to sometimes replace one
+   with the other for a better looking output.  However, that can
+   lead to problems, for instance, when using cut-n-paste of input
+   file examples from web pages, or when using a document editor
+   (not a dedicated plain text editor) for writing LAMMPS inputs.
+   LAMMPS will try to detect this and substitute the non-ASCII
+   characters with their ASCII equivalents where known.  There also
+   is going to be a warning printed, if this occurs.  It is
+   recommended to avoid such characters altogether in LAMMPS input,
+   data and potential files.  The replacement tables are likely
+   incomplete and dependent on users reporting problems processing
+   correctly looking input containing UTF-8 encoded non-ASCII
+   characters.

doc/src/Developer.rst

@@ -13,5 +13,8 @@ of time and requests from the LAMMPS user community.
    Developer_org
    Developer_flow
    Developer_write
+   Developer_notes
+   Developer_plugins
+   Developer_unittest
    Classes
    Developer_utils

doc/src/Developer_notes.rst

@@ -0,0 +1,227 @@
+Notes for developers and code maintainers
+-----------------------------------------
+
+This section documents how some of the code functionality within
+LAMMPS works at a conceptual level.  Comments on code in source files
+typically document what a variable stores, what a small section of
+code does, or what a function does and its input/outputs.  The topics
+on this page are intended to document code functionality at a higher level.
+
+Fix contributions to instantaneous energy, virial, and cumulative energy
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes can calculate contributions to the instantaneous energy and/or
+virial of the system, both in a global and peratom sense.  Fixes that
+perform thermostatting or barostatting can calculate the cumulative
+energy they add to or subtract from the system, which is accessed by
+the *ecouple* and *econserve* thermodynamic keywords.  This subsection
+explains how both work and what flags to set in a new fix to enable
+this functionality.
+
+Let's start with thermostatting and barostatting fixes.  Examples are
+the :doc:`fix langevin <fix_langevin>` and :doc:`fix npt <fix_nh>`
+commands.  Here is what the fix needs to do:
+
+* Set the variable *ecouple_flag* = 1 in the constructor.  Also set
+  *scalar_flag* = 1, *extscalar* = 1, and *global_freq* to a timestep
+  increment which matches how often the fix is invoked.
+* Implement a compute_scalar() method that returns the cumulative
+  energy added or subtracted by the fix, e.g. by rescaling the
+  velocity of atoms.  The sign convention is that subtracted energy is
+  positive, added energy is negative.  This must be the total energy
+  added to the entire system, i.e. an "extensive" quantity, not a
+  per-atom energy.  Cumulative means the summed energy since the fix
+  was instantiated, even across multiple runs.  This is because the
+  energy is used by the *econserve* thermodynamic keyword to check
+  that the fix is conserving the total energy of the system,
+  i.e. potential energy + kinetic energy + coupling energy = a
+  constant.
+
+And here is how the code operates:
+
+* The Modify class makes a list of all fixes that set *ecouple_flag* = 1.
+* The :doc:`thermo_style custom <thermo_style>` command defines
+  *ecouple* and *econserve* keywords.
+* These keywords sum the energy contributions from all the
+  *ecouple_flag* = 1 fixes by invoking the energy_couple() method in
+  the Modify class, which calls the compute_scalar() method of each
+  fix in the list.
+
+------------------
+
+Next, here is how a fix contributes to the instantaneous energy and
+virial of the system.  First, it sets any or all of these flags to a
+value of 1 in their constructor:
+
+* *energy_global_flag* to contribute to global energy, example: :doc:`fix indent <fix_indent>`
+* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
+* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
+* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`
+
+The fix must also do the following:
+
+* For global energy, implement a compute_scalar() method that returns
+  the energy added or subtracted on this timestep.  Here the sign
+  convention is that added energy is positive, subtracted energy is
+  negative.
+* For peratom energy, invoke the ev_init(eflag,vflag) function each
+  time the fix is invoked, which initializes per-atom energy storage.
+  The value of eflag may need to be stored from an earlier call to the
+  fix during the same timestep.  See how the :doc:`fix cmap
+  <fix_cmap>` command does this in src/MOLECULE/fix_cmap.cpp.  When an
+  energy for one or more atoms is calculated, invoke the ev_tally()
+  function to tally the contribution to each atom.  Both the ev_init()
+  and ev_tally() methods are in the parent Fix class.
+* For global and/or peratom virial, invoke the v_init(vflag) function
+  each time the fix is invoked, which initializes virial storage.
+  When forces on one or more atoms are calculated, invoke the
+  v_tally() function to tally the contribution.  Both the v_init() and
+  v_tally() methods are in the parent Fix class.  Note that there are
+  several variants of v_tally(); choose the one appropriate to your
+  fix.
+
+.. note::
+
+   The ev_init() and ev_tally() methods also account for global and
+   peratom virial contributions.  Thus you do not need to invoke the
+   v_init() and v_tally() methods, if the fix also calculates peratom
+   energies.
+
+The fix must also specify whether (by default) to include or exclude
+these contributions to the global/peratom energy/virial of the system.
+For the fix to include the contributions, set either of both of these
+variables in the constructor:
+
+* *thermo_energy* = 1, for global and peratom energy
+* *thermo_virial* = 1, for global and peratom virial
+
+Note that these variables are zeroed in fix.cpp.  Thus if you don't
+set the variables, the contributions will be excluded (by default)
+
+However, the user has ultimate control over whether to include or
+exclude the contributions of the fix via the :doc:`fix modify
+<fix_modify>` command:
+
+* fix modify *energy yes* to include global and peratom energy contributions
+* fix modify *virial yes* to include global and peratom virial contributions
+
+If the fix contributes to any of the global/peratom energy/virial
+values for the system, it should be explained on the fix doc page,
+along with the default values for the *energy yes/no* and *virial
+yes/no* settings of the :doc:`fix modify <fix_modify>` command.
+
+Finally, these 4 contributions are included in the output of 4
+computes:
+
+* global energy in :doc:`compute pe <compute_pe>`
+* peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
+* global virial in :doc:`compute pressure <compute_pressure>`
+* peratom virial in :doc:`compute stress/atom <compute_stress_atom>`
+
+These computes invoke a method of the Modify class to include
+contributions from fixes that have the corresponding flags set,
+e.g. *energy_peratom_flag* and *thermo_energy* for :doc:`compute
+pe/atom <compute_pe_atom>`.
+
+Note that each compute has an optional keyword to either include or
+exclude all contributions from fixes.  Also note that :doc:`compute pe
+<compute_pe>` and :doc:`compute pressure <compute_pressure>` are what
+is used (by default) by :doc:`thermodynamic output <thermo_style>` to
+calculate values for its *pe* and *press* keywords.
+
+KSpace PPPM FFT grids
+^^^^^^^^^^^^^^^^^^^^^
+
+The various :doc:`KSpace PPPM <kspace_style>` styles in LAMMPS use
+FFTs to solve Poisson's equation.  This subsection describes:
+
+* how FFT grids are defined
+* how they are decomposed across processors
+* how they are indexed by each processor
+* how particle charge and electric field values are mapped to/from
+  the grid
+
+An FFT grid cell is a 3d volume; grid points are corners of a grid
+cell and the code stores values assigned to grid points in vectors or
+3d arrays.  A global 3d FFT grid has points indexed 0 to N-1 inclusive
+in each dimension.
+
+Each processor owns two subsets of the grid, each subset is
+brick-shaped.  Depending on how it is used, these subsets are
+allocated as a 1d vector or 3d array.  Either way, the ordering of
+values within contiguous memory x fastest, then y, z slowest.
+
+For the ``3d decomposition`` of the grid, the global grid is
+partitioned into bricks that correspond to the sub-domains of the
+simulation box that each processor owns.  Often, this is a regular 3d
+array (Px by Py by Pz) of bricks, where P = number of processors =
+Px * Py * Pz.  More generally it can be a tiled decomposition, where
+each processor owns a brick and the union of all the bricks is the
+global grid.  Tiled decompositions are produced by load balancing with
+the RCB algorithm; see the :doc:`balance rcb <balance>` command.
+
+For the ``FFT decompostion`` of the grid, each processor owns a brick
+that spans the entire x dimension of the grid while the y and z
+dimensions are partitioned as a regular 2d array (P1 by P2), where P =
+P1 * P2.
+
+The following indices store the inclusive bounds of the brick a
+processor owns, within the global grid:
+
+.. parsed-literal::
+
+   nxlo_in,nxhi_in,nylo_in,nyhi_in,nzlo_in,nzhi_in = 3d decomposition brick
+   nxlo_fft,nxhi_fft,nylo_fft,nyhi_fft,nzlo_fft,nzhi_fft = FFT decomposition brick
+   nxlo_out,nxhi_out,nylo_out,nyhi_out,nzlo_out,nzhi_out = 3d decomposition brick + ghost cells
+
+The ``in`` and ``fft`` indices are from 0 to N-1 inclusive in each
+dimension, where N is the grid size.
+
+The ``out`` indices index an array which stores the ``in`` subset of
+the grid plus ghost cells that surround it.  These indices can thus be
+< 0 or >= N.
+
+The number of ghost cells a processor owns in each of the 6 directions
+is a function of:
+
+.. parsed-literal::
+
+   neighbor skin distance (since atoms can move outside a proc subdomain)
+   qdist = offset or charge from atom due to TIP4P fictitious charge
+   order = mapping stencil size
+   shift = factor used when order is an even number (see below)
+
+Here is an explanation of how the PPPM variables ``order``,
+``nlower`` / ``nupper``, ``shift``, and ``OFFSET`` work. They are the
+relevant variables that determine how atom charge is mapped to grid
+points and how field values are mapped from grid points to atoms:
+
+.. parsed-literal::
+
+   order = # of nearby grid points in each dim that atom charge/field are mapped to/from
+   nlower,nupper = extent of stencil around the grid point an atom is assigned to
+   OFFSET = large integer added/subtracted when mapping to avoid int(-0.75) = 0 when -1 is the desired result
+
+The particle_map() method assigns each atom to a grid point.
+
+If order is even, say 4:
+
+.. parsed-literal::
+
+   atom is assigned to grid point to its left (in each dim)
+   shift = OFFSET
+   nlower = -1, nupper = 2, which are offsets from assigned grid point
+   window of mapping grid pts is thus 2 grid points to left of atom, 2 to right
+
+If order is odd, say 5:
+
+.. parsed-literal::
+
+   atom is assigned to left/right grid pt it is closest to (in each dim)
+   shift = OFFSET + 0.5
+   nlower = 2, nupper = 2
+   if point is in left half of cell, then window of affected grid pts is 3 grid points to left of atom, 2 to right
+   if point is in right half of cell, then window of affected grid pts is 2 grid points to left of atom, 3 to right
+
+These settings apply to each dimension, so that if order = 5, an
+atom's charge is mapped to 125 grid points that surround the atom.

doc/src/Developer_org.rst

@@ -1,68 +1,75 @@
 Source files
 ------------
 
-The source files of the LAMMPS code are found in two
-directories of the distribution: ``src`` and ``lib``.
-Most of the code is C++ but there are small numbers of files
-in several other languages.
+The source files of the LAMMPS code are found in two directories of the
+distribution: ``src`` and ``lib``.  Most of the code is written in C++
+but there are small a number of files in several other languages like C,
+Fortran, Shell script, or Python.
 
-The core of the code is located in the
-``src`` folder and its sub-directories.
-A sizable number of these files are in the ``src`` directory
-itself, but there are plenty of :doc:`packages <Packages>`, which can be
-included or excluded when LAMMPS is built.  See the :doc:`Include
-packages in build <Build_package>` section of the manual for more
-information about that part of the build process.  LAMMPS currently
-supports building with :doc:`conventional makefiles <Build_make>` and
-through :doc:`CMake <Build_cmake>` which differ in how packages are
-enabled or disabled for a LAMMPS binary.  The source files for each
+The core of the code is located in the ``src`` folder and its
+sub-directories.  A sizable number of these files are in the ``src``
+directory itself, but there are plenty of :doc:`packages <Packages>`,
+which can be included or excluded when LAMMPS is built.  See the
+:doc:`Include packages in build <Build_package>` section of the manual
+for more information about that part of the build process.  LAMMPS
+currently supports building with :doc:`conventional makefiles
+<Build_make>` and through :doc:`CMake <Build_cmake>`.  Those procedures
+differ in how packages are enabled or disabled for inclusion into a
+LAMMPS binary so they cannot be mixed.  The source files for each
 package are in all-uppercase sub-directories of the ``src`` folder, for
 example ``src/MOLECULE`` or ``src/USER-MISC``.  The ``src/STUBS``
 sub-directory is not a package but contains a dummy MPI library, that is
 used when building a serial version of the code. The ``src/MAKE``
-directory contains makefiles with settings and flags for a variety of
-configuration and machines for the build process with traditional
-makefiles.
+directory and its sub-directories contain makefiles with settings and
+flags for a variety of configuration and machines for the build process
+with traditional makefiles.
 
 The ``lib`` directory contains the source code for several supporting
 libraries or files with configuration settings to use globally installed
-libraries, that are required by some of the optional packages.
-Each sub-directory, like ``lib/poems`` or ``lib/gpu``, contains the
-source files, some of which are in different languages such as Fortran
-or CUDA. These libraries are linked to during a LAMMPS build, if the
-corresponding package is installed.
+libraries, that are required by some of the optional packages.  They may
+include python scripts that can transparently download additional source
+code on request.  Each sub-directory, like ``lib/poems`` or ``lib/gpu``,
+contains the source files, some of which are in different languages such
+as Fortran or CUDA. These libraries included in the LAMMPS build,
+if the corresponding package is installed.
 
 LAMMPS C++ source files almost always come in pairs, such as
 ``src/run.cpp`` (implementation file) and ``src/run.h`` (header file).
-Each pair of files defines a C++
-class, for example the :cpp:class:`LAMMPS_NS::Run` class which contains
-the code invoked by the :doc:`run <run>` command in a LAMMPS input script.
-As this example illustrates, source file and class names often have a
-one-to-one correspondence with a command used in a LAMMPS input script.
-Some source files and classes do not have a corresponding input script
+Each pair of files defines a C++ class, for example the
+:cpp:class:`LAMMPS_NS::Run` class which contains the code invoked by the
+:doc:`run <run>` command in a LAMMPS input script.  As this example
+illustrates, source file and class names often have a one-to-one
+correspondence with a command used in a LAMMPS input script.  Some
+source files and classes do not have a corresponding input script
 command, e.g. ``src/force.cpp`` and the :cpp:class:`LAMMPS_NS::Force`
 class.  They are discussed in the next section.
 
-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.
+The names of all source files are in lower case and may use the
+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.
 
 Class topology
 --------------
 
 Though LAMMPS has a lot of source files and classes, its class topology
-is relative flat, as outlined in the :ref:`class-topology` figure.  Each
-name refers to a class and has a pair of associated source files in the
-``src`` folder, for example the class :cpp:class:`LAMMPS_NS::Memory`
-corresponds to the files ``memory.cpp`` and ``memory.h``, or the class
-:cpp:class:`LAMMPS_NS::AtomVec` corresponds to the files
-``atom_vec.cpp`` and ``atom_vec.h``.  Full lines in the figure represent
-compositing: that is the class to the left holds a pointer to an
-instance of the class to the right.  Dashed lines instead represent
-inheritance: the class to the right is derived from the class on the
-left. Classes with a red boundary are not instantiated directly, but
-they represent the base classes for "styles".  Those "styles" make up
-the bulk of the LAMMPS code and only a few typical examples are included
-in the figure for demonstration purposes.
+is not very deep, which can be seen from the :ref:`class-topology`
+figure.  In that figure, each name refers to a class and has a pair of
+associated source files in the ``src`` folder, for example the class
+:cpp:class:`LAMMPS_NS::Memory` corresponds to the files ``memory.cpp``
+and ``memory.h``, or the class :cpp:class:`LAMMPS_NS::AtomVec`
+corresponds to the files ``atom_vec.cpp`` and ``atom_vec.h``.  Full
+lines in the figure represent compositing: that is the class at the base
+of the arrow holds a pointer to an instance of the class at the tip.
+Dashed lines instead represent inheritance: the class to the tip of the
+arrow is derived from the class at the base.  Classes with a red boundary
+are not instantiated directly, but they represent the base classes for
+"styles".  Those "styles" make up the bulk of the LAMMPS code and only
+a few representative examples are included in the figure so it remains
+readable.
 
 .. _class-topology:
 .. figure:: JPG/lammps-classes.png
@@ -82,69 +89,76 @@ in the figure for demonstration purposes.
    derived classes, which may also hold instances of other classes.
 
 The :cpp:class:`LAMMPS_NS::LAMMPS` class is the topmost class and
-represents what is referred to an "instance" of LAMMPS.  It is a
-composite holding references to instances of other core classes
+represents what is generally referred to an "instance" of LAMMPS.  It is
+a composite holding pointers to instances of other core classes
 providing the core functionality of the MD engine in LAMMPS and through
 them abstractions of the required operations.  The constructor of the
 LAMMPS class will instantiate those instances, process the command line
 flags, initialize MPI (if not already done) and set up file pointers for
-input and output. The destructor will shut everything down and free all
+input and output.  The destructor will shut everything down and free all
 associated memory.  Thus code for the standalone LAMMPS executable in
 ``main.cpp`` simply initializes MPI, instantiates a single instance of
-LAMMPS, and passes it the command line flags and input script. It
+LAMMPS while passing it the command line flags and input script. It
 deletes the LAMMPS instance after the method reading the input returns
 and shuts down the MPI environment before it exits the executable.
 
 The :cpp:class:`LAMMPS_NS::Pointers` is not shown in the
-:ref:`class-topology` figure, it holds references to members of the
-`LAMMPS_NS::LAMMPS`, so that all classes derived from
-:cpp:class:`LAMMPS_NS::Pointers` have direct access to those reference.
-From the class topology all classes with blue boundary are referenced in
-this class and all classes in the second and third columns, that are not
-listed as derived classes are instead derived from
-:cpp:class:`LAMMPS_NS::Pointers`.
+:ref:`class-topology` figure for clarity.  It holds references to many
+of the members of the `LAMMPS_NS::LAMMPS`, so that all classes derived
+from :cpp:class:`LAMMPS_NS::Pointers` have direct access to those
+reference.  From the class topology all classes with blue boundary are
+referenced in the Pointers class and all classes in the second and third
+columns, that are not listed as derived classes are instead derived from
+:cpp:class:`LAMMPS_NS::Pointers`.  To initialize the pointer references
+in Pointers, a pointer to the LAMMPS class instance needs to be passed
+to the constructor and thus all constructors for classes derived from it
+must do so and pass this pointer to the constructor for Pointers.
 
-Since all storage is encapsulated, the LAMMPS class can also be
-instantiated multiple times by a calling code, and that can be either
-simultaneously or consecutively.  When running in parallel with MPI,
-care has to be taken, that suitable communicators are used to not
-create conflicts between different instances.
+Since all storage is supposed to be encapsulated (there are a few
+exceptions), the LAMMPS class can also be instantiated multiple times by
+a calling code.  Outside of the aforementioned exceptions, those LAMMPS
+instances can be used alternately.  As of the time of this writing
+(early 2021) LAMMPS is not yet sufficiently thread-safe for concurrent
+execution.  When running in parallel with MPI, care has to be taken,
+that suitable copies of communicators are used to not create conflicts
+between different instances.
 
-The LAMMPS class currently holds instances of 19 classes representing
-different core functionalities There are a handful of virtual parent
-classes in LAMMPS that define what LAMMPS calls ``styles``.  They are
-shaded red in the :ref:`class-topology` figure.  Each of these are
+The LAMMPS class currently (early 2021) holds instances of 19 classes
+representing the core functionality.  There are a handful of virtual
+parent classes in LAMMPS that define what LAMMPS calls ``styles``.  They
+are shaded red in the :ref:`class-topology` figure.  Each of these are
 parents of a number of child classes that implement the interface
 defined by the parent class.  There are two main categories of these
 ``styles``: some may only have one instance active at a time (e.g. atom,
 pair, bond, angle, dihedral, improper, kspace, comm) and there is a
-dedicated pointer variable in the composite class that manages them.
+dedicated pointer variable for each of them in the composite class.
 Setups that require a mix of different such styles have to use a
-*hybrid* class that manages and forwards calls to the corresponding
-sub-styles for the designated subset of atoms or data. or the composite
-class may have lists of class instances, e.g. Modify handles lists of
-compute and fix styles, while Output handles dumps class instances.
+*hybrid* class that takes the place of the one allowed instance and then
+manages and forwards calls to the corresponding sub-styles for the
+designated subset of atoms or data.  The composite class may also have
+lists of class instances, e.g. Modify handles lists of compute and fix
+styles, while Output handles a list of dump class instances.
 
-The exception to this scheme are the ``command`` style classes. These
-implement specific commands that can be invoked before, after, or between
-runs or are commands which launch a simulation.  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.
+The exception to this scheme are the ``command`` style classes.  These
+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.
 
 For all those ``styles`` certain naming conventions are employed: for
-the fix nve command the class is called FixNVE and the files are
+the fix nve command the class is called FixNVE and the source files are
 ``fix_nve.h`` and ``fix_nve.cpp``. Similarly for fix ave/time we have
-FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``. Style names
+FixAveTime and ``fix_ave_time.h`` and ``fix_ave_time.cpp``.  Style names
 are lower case and without spaces or special characters. A suffix or
-multiple appended with a forward slash '/' denotes a variant of the
-corresponding class without the suffix. To connect the style name and
-the class name, LAMMPS uses macros like the following ATOM\_CLASS,
-PAIR\_CLASS, BOND\_CLASS, REGION\_CLASS, FIX\_CLASS, COMPUTE\_CLASS,
-or DUMP\_CLASS in the corresponding header file.  During compilation
-files with the pattern ``style_name.h`` are created that contain include
-statements including all headers of all styles of a given type that
-are currently active (or "installed).
+words are appended with a forward slash '/' which denotes a variant of
+the corresponding class without the suffix.  To connect the style name
+and the class name, LAMMPS uses macros like: ``AtomStyle()``,
+``PairStyle()``, ``BondStyle()``, ``RegionStyle()``, and so on in the
+corresponding header file.  During configuration or compilation files
+with the pattern ``style_<name>.h`` are created that consist of a list
+of include statements including all headers of all styles of a given
+type that are currently active (or "installed).
 
 
 More details on individual classes in the :ref:`class-topology` are as
@@ -152,11 +166,11 @@ follows:
 
 - The Memory class handles allocation of all large vectors and arrays.
 
-- The Error class prints all error and warning messages.
+- The Error class prints all (terminal) error and warning messages.
 
-- The Universe class sets up partitions of processors so that multiple
-  simulations can be run, each on a subset of the processors allocated
-  for a run, e.g. by the mpirun command.
+- The Universe class sets up one or more partitions of processors so
+  that one or multiple simulations can be run, on the processors
+  allocated for a run, e.g. by the mpirun command.
 
 - The Input class reads and processes input input strings and files,
   stores variables, and invokes :doc:`commands <Commands_all>`.
@@ -241,7 +255,8 @@ follows:
 .. TODO section on "Spatial decomposition and parallel operations"
 ..       diagram of 3d processor grid, brick vs. tiled. local vs. ghost
 ..       atoms, 6-way communication with pack/unpack functions,
-..       PBC as part of the communication
+..       PBC as part of the communication, forward and reverse communication
+..       rendezvous communication, ring communication.
 
 .. TODO section on "Fixes, Computes, and Variables"
 ..      how and when data is computed and provided and how it is

doc/src/Developer_plugins.rst

@@ -0,0 +1,258 @@
+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, or improper styles
+   * - creator.v2
+     - Pointer to factory function for compute, fix, or region styles
+   * - creator.v3
+     - Pointer to factory function for command 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.
+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.
+The "creator.v3" element takes the same arguments as "creator.v3" but is
+specific to creating command styles: the factory function has to instantiate
+the command style locally passing the LAMMPS pointer as argument and then
+call its "command" member function with the number and list of arguments.
+The factory function pointer needs to be cast to the
+``lammpsplugin_factory3`` 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`` 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``, 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
+^^^^^^^^^^^^^^^^^^^^^
+For command styles there is a third variant of factory function as
+demonstrated in the following example, which also shows that the
+implementation of the plugin class may also be within the same
+file as the plugin interface code:
+
+.. code-block:: C++
+
+   #include "lammpsplugin.h"
+
+   #include "comm.h"
+   #include "error.h"
+   #include "pointers.h"
+   #include "version.h"
+
+   #include <cstring>
+
+   namespace LAMMPS_NS {
+     class Hello : protected Pointers {
+      public:
+       Hello(class LAMMPS *lmp) : Pointers(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, int argc, char **argv)
+   {
+     Hello hello(lmp);
+     hello.command(argc,argv);
+   }
+
+   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 v1.0";
+     plugin.author  = "Axel Kohlmeyer (akohlmey@gmail.com)";
+     plugin.creator.v3 = (lammpsplugin_factory3 *) &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

@@ -0,0 +1,536 @@
+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 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
+set up, not all tests will be unit tests in the strict definition of
+the term.  They are rather executed on a more abstract level by issuing
+LAMMPS script commands and then inspecting the changes to the internal
+data.  For some classes of tests, generic test programs have been
+written that can be applied to parts of LAMMPS that use the same
+interface (via polymorphism) and those are driven by input files, so
+tests can be added by simply adding more of those input files.  Those
+tests should be seen more as a hybrid between unit and regression tests.
+
+When adding tests it is recommended to also :ref:`enable support for
+code coverage reporting <testing>`, and study the coverage reports
+so that it is possible to monitor which parts of the code of a given
+file are executed during the tests and which tests would need to be
+added to increase the coverage.
+
+The tests are grouped into categories and corresponding folders.
+The following sections describe how the tests are implemented and
+executed in those categories with increasing complexity of tests
+and implementation.
+
+
+Tests for utility functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These tests are driven by programs in the ``unittest/utils`` folder
+and most closely resemble conventional unit tests. There is one test
+program for each namespace or group of classes or file. The naming
+convention for the sources and executables is that they start with
+with ``test_``.  The following sources and groups of tests are currently
+available:
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+   :align: left
+
+   * - 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
+   * - ``test_math_eigen_impl.cpp``
+     - MathEigen
+     - Tests for ``MathEigen::`` classes and functions
+   * - ``test_mempool.cpp``
+     - MemPool
+     - Tests for :cpp:class:`MyPage <LAMMPS_NS::MyPage>` and :cpp:class:`MyPoolChunk <LAMMPS_NS::MyPoolChunk>`
+   * - ``test_tokenizer.cpp``
+     - Tokenizer
+     - Tests for :cpp:class:`Tokenizer <LAMMPS_NS::Tokenizer>` and :cpp:class:`ValueTokenizer <LAMMPS_NS::ValueTokenizer>`
+   * - ``test_utils.cpp``
+     - Utils
+     - Tests for ``utils::`` :doc:`functions <Developer_utils>`
+
+To add tests either an existing source file needs to be modified or a
+new source file needs to be added to the distribution and enabled for
+testing.  To add a new file suitable CMake script code needs to be added
+to the ``CMakeLists.txt`` file in the ``unittest/utils`` folder.  Example:
+
+.. code-block:: cmake
+
+   add_executable(test_tokenizer test_tokenizer.cpp)
+   target_link_libraries(test_tokenizer PRIVATE lammps GTest::GMockMain GTest::GMock GTest::GTest)
+   add_test(Tokenizer test_tokenizer)
+
+This adds instructions to build the ``test_tokenizer`` executable from
+``test_tokenizer.cpp`` and links it with the GoogleTest libraries and the
+LAMMPS library as well as it uses the ``main()`` function from the
+GoogleMock library of GoogleTest.  The third line registers the executable
+as a test program to be run from ``ctest`` under the name ``Tokenizer``.
+
+The test executable itself will execute multiple individual tests
+through the GoogleTest framework. In this case each test consists of
+creating a tokenizer class instance with a given string and explicit or
+default separator choice, and then executing member functions of the
+class and comparing their results with expected values. A few examples:
+
+.. code-block:: c++
+
+   TEST(Tokenizer, empty_string)
+   {
+       Tokenizer t("", " ");
+       ASSERT_EQ(t.count(), 0);
+   }
+
+   TEST(Tokenizer, two_words)
+   {
+       Tokenizer t("test word", " ");
+       ASSERT_EQ(t.count(), 2);
+   }
+
+   TEST(Tokenizer, default_separators)
+   {
+       Tokenizer t(" \r\n test \t word \f");
+       ASSERT_THAT(t.next(), Eq("test"));
+       ASSERT_THAT(t.next(), Eq("word"));
+       ASSERT_EQ(t.count(), 2);
+   }
+
+Each of these TEST functions will become an individual
+test run by the test program. When using the ``ctest``
+command as a front end to run the tests, their output
+will be suppressed and only a summary printed, but adding
+the '-V' option will then produce output from the tests
+above like the following:
+
+.. code-block::
+
+   [...]
+   1: [ RUN      ] Tokenizer.empty_string
+   1: [       OK ] Tokenizer.empty_string (0 ms)
+   1: [ RUN      ] Tokenizer.two_words
+   1: [       OK ] Tokenizer.two_words (0 ms)
+   1: [ RUN      ] Tokenizer.default_separators
+   1: [       OK ] Tokenizer.default_separators (0 ms)
+   [...]
+
+The MathEigen test collection has been adapted from a standalone test
+and does not use the GoogleTest framework and thus not representative.
+The other test sources, however, can serve as guiding examples for
+additional tests.
+
+Tests for individual LAMMPS commands
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The tests ``unittest/commands`` are a bit more complex as they require
+to first create a :cpp:class:`LAMMPS <LAMMPS_NS::LAMMPS>` class instance
+and then use the :doc:`C++ API <Cplusplus>` to pass individual commands
+to that LAMMPS instance.  For that reason these tests use a GoogleTest
+"test fixture", i.e. a class derived from ``testing::Test`` that will
+create (and delete) the required LAMMPS class instance for each set of
+tests in a ``TEST_F()`` function.  Please see the individual source files
+for different examples of setting up suitable test fixtures.  Here is an
+example for implementing a test using a fixture by first checking the
+default value and then issuing LAMMPS commands and checking whether they
+have the desired effect:
+
+.. code-block:: c++
+
+   TEST_F(SimpleCommandsTest, ResetTimestep)
+   {
+       ASSERT_EQ(lmp->update->ntimestep, 0);
+
+       BEGIN_HIDE_OUTPUT();
+       command("reset_timestep 10");
+       END_HIDE_OUTPUT();
+       ASSERT_EQ(lmp->update->ntimestep, 10);
+
+       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 ``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
+"death tests".  Here the LAMMPS code will operate differently depending
+on whether it was configured to throw C++ exceptions on errors or call
+either ``exit()`` or ``MPI_Abort()``.  In the latter case, the test code
+also needs to detect whether LAMMPS was compiled with the OpenMPI
+library, as OpenMPI is **only** compatible the death test options of the
+GoogleTest library when C++ exceptions are enabled; otherwise those
+"death tests" must be skipped to avoid reporting bogus failures.  The
+specifics of this step are implemented in the ``TEST_FAILURE()``
+macro. These tests operate by capturing the screen output when executing
+the failing command and then comparing that with a provided regular
+expression string pattern.  Example:
+
+.. code-block:: C++
+
+   TEST_F(SimpleCommandsTest, UnknownCommand)
+   {
+       TEST_FAILURE(".*ERROR: Unknown command.*", lmp->input->one("XXX one two"););
+   }
+
+The following test programs are currently available:
+
+.. list-table::
+   :header-rows: 1
+   :widths: auto
+   :align: left
+
+   * - File name:
+     - Test name:
+     - Description:
+   * - ``test_simple_commands.cpp``
+     - SimpleCommands
+     - Tests for LAMMPS commands that do not require a box
+   * - ``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>`
+   * - ``test_reset_ids.cpp``
+     - ResetIDs
+     - Tests to validate the :doc:`reset_atom_ids <reset_atom_ids>` and :doc:`reset_mol_ids <reset_mol_ids>` commands
+
+
+Tests for the C-style library interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Tests for validating the LAMMPS C-style library interface are in the
+``unittest/c-library`` folder.  They are implemented in either way used
+for utility functions and for LAMMPS commands, but use the functions
+implemented in the ``src/library.cpp`` file as much as possible.  There
+may be some overlap with other tests, but only in as much as is required
+to test the C-style library API.  The tests are distributed over
+multiple test programs which tries to match the grouping of the
+functions in the source code and :ref:`in the manual <lammps_c_api>`.
+
+This group of tests also includes tests invoking LAMMPS in parallel
+through the library interface, provided that LAMMPS was compiled with
+MPI support.  These include tests where LAMMPS is run in multi-partition
+mode or only on a subset of the MPI world communicator.  The CMake
+script code for adding this kind of test looks like this:
+
+.. code-block:: CMake
+
+   if (BUILD_MPI)
+     add_executable(test_library_mpi test_library_mpi.cpp)
+     target_link_libraries(test_library_mpi PRIVATE lammps GTest::GTest GTest::GMock)
+     target_compile_definitions(test_library_mpi PRIVATE ${TEST_CONFIG_DEFS})
+     add_mpi_test(NAME LibraryMPI NUM_PROCS 4 COMMAND $<TARGET_FILE:test_library_mpi>)
+   endif()
+
+Note the custom function ``add_mpi_test()`` which adapts how ``ctest``
+will execute the test so it is launched in parallel (with 4 MPI ranks).
+
+Tests for the Python module and package
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/python`` folder contains primarily tests for classes and
+functions in the LAMMPS python module but also for commands in the
+PYTHON package.  These tests are only enabled, if the necessary
+prerequisites are detected or enabled during configuration and
+compilation of LAMMPS (shared library build enabled, Python interpreter
+found, Python development files found).
+
+The Python tests are implemented using the ``unittest`` standard Python
+module and split into multiple files with similar categories as the
+tests for the C-style library interface.
+
+Tests for the Fortran interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Tests for using the Fortran module are in the ``unittest/fortran``
+folder.  Since they are also using the GoogleTest library, they require
+to also implement test wrappers in C++ that will call fortran functions
+which provide a C function interface through ISO_C_BINDINGS that will in
+turn call the functions in the LAMMPS Fortran module.  This part of the
+unit tests is incomplete since the Fortran module it is based on is
+incomplete as well.
+
+Tests for the C++-style library interface
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The tests in the ``unittest/cplusplus`` folder are somewhat similar to
+the tests for the C-style library interface, but do not need to test the
+several convenience and utility functions that are only available through
+the C-style interface.  Instead it can focus on the more generic features
+that are used internally.  This part of the unit tests is currently still
+mostly in the planning stage.
+
+Tests for reading and writing file formats
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/formats`` folder contains test programs for reading and
+writing files like data files, restart files, potential files or dump files.
+This covers simple things like the file i/o convenience functions in the
+``utils::`` namespace to complex tests of atom styles where creating and
+deleting of atoms with different properties is tested in different ways
+and through script commands or reading and writing of data or restart files.
+
+Tests for styles computing or modifying forces
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+These are tests common configurations for pair styles, bond styles,
+angle styles, kspace styles and certain fix styles.  Those are tests
+driven by some test executables build from sources in the
+``unittest/force-styles`` folder and use LAMMPS input template and data
+files as well as input files in YAML format from the
+``unittest/force-styles/tests`` folder. The YAML file names have to
+follow some naming conventions so they get associated with the test
+programs and categorized and listed with canonical names in the list
+of tests as displayed by ``ctest -N``.  If you add a new YAML file,
+you need to re-run CMake to update the corresponding list of tests.
+
+A minimal YAML file for a (molecular) pair style test will looks
+something like the following (see ``mol-pair-zero.yaml``):
+
+.. code-block:: yaml
+
+   ---
+   lammps_version: 24 Aug 2020
+   date_generated: Tue Sep 15 09:44:21 202
+   epsilon: 1e-14
+   prerequisites: ! |
+     atom full
+     pair zero
+   pre_commands: ! ""
+   post_commands: ! ""
+   input_file: in.fourmol
+   pair_style: zero 8.0
+   pair_coeff: ! |
+     * *
+   extract: ! ""
+   natoms: 29
+   init_vdwl: 0
+   init_coul: 0
+
+   [...]
+
+The following table describes the available keys and their purpose for
+testing pair styles:
+
+.. list-table::
+   :header-rows: 1
+
+   * - Key:
+     - Description:
+   * - lammps_version
+     - LAMMPS version used to last update the reference data
+   * - date_generated
+     - date when the file was last updated
+   * - epsilon
+     - base value for the relative precision required for tests to pass
+   * - prerequisites
+     - list of style kind / style name pairs required to run the test
+   * - pre_commands
+     - LAMMPS commands to be executed before the input template file is read
+   * - post_commands
+     - LAMMPS commands to be executed right before the actual tests
+   * - input_file
+     - LAMMPS input file template based on pair style zero
+   * - pair_style
+     - arguments to the pair_style command to be tested
+   * - pair_coeff
+     - list of pair_coeff arguments to set parameters for the input template
+   * - extract
+     - list of keywords supported by ``Pair::extract()`` and their dimension
+   * - natoms
+     - number of atoms in the input file template
+   * - init_vdwl
+     - non-Coulomb pair energy after "run 0"
+   * - init_coul
+     - Coulomb pair energy after "run 0"
+   * - init_stress
+     - stress tensor after "run 0"
+   * - init_forces
+     - forces on atoms after "run 0"
+   * - run_vdwl
+     - non-Coulomb pair energy after "run 4"
+   * - run_coul
+     - Coulomb pair energy after "run 4"
+   * - run_stress
+     - stress tensor after "run 4"
+   * - run_forces
+     - forces on atoms after "run 4"
+
+The test program will read all this data from the YAML file and then
+create a LAMMPS instance, apply the settings/commands from the YAML file
+as needed and then issue a "run 0" command, write out a restart file, a
+data file and a coeff file. The actual test will then compare computed
+energies, stresses, and forces with the reference data, issue a "run 4"
+command and compare to the second set of reference data.  This will be
+run with both the newton_pair setting enabled and disabled and is
+expected to generate the same results (allowing for some numerical
+noise). Then it will restart from the previously generated restart and
+compare with the reference and also start from the data file.  A final
+check will use multi-cutoff r-RESPA (if supported by the pair style) at
+a 1:1 split and compare to the Verlet results.  These sets of tests are
+run with multiple test fixtures for accelerated styles (OPT, USER-OMP,
+USER-INTEL) and for the latter two with 4 OpenMP threads enabled.  For
+these tests the relative error (epsilon) is lowered by a common factor
+due to the additional numerical noise, but the tests are still comparing
+to the same reference data.
+
+Additional tests will check whether all listed extract keywords are
+supported and have the correct dimensionality and the final set of tests
+will set up a few pairs of atoms explicitly and in such a fashion that
+the forces on the atoms computed from ``Pair::compute()`` will match
+individually with the results from ``Pair::single()``, if the pair style
+does support that functionality.
+
+With this scheme a large fraction of the code of any tested pair style
+will be executed and consistent results are required for different
+settings and between different accelerated pair style variants and the
+base class, as well as for computing individual pairs through the
+``Pair::single()`` where supported.
+
+The ``test_pair_style`` tester is used with 4 categories of test inputs:
+
+- pair styles compatible with molecular systems using bonded
+  interactions and exclusions.  For pair styles requiring a KSpace style
+  the KSpace computations are disabled.  The YAML files match the
+  pattern "mol-pair-\*.yaml" and the tests are correspondingly labeled
+  with "MolPairStyle:\*"
+- pair styles not compatible with the previous input template.
+  The YAML files match the pattern "atomic-pair-\*.yaml" and the tests are
+  correspondingly labeled with "AtomicPairStyle:\*"
+- manybody pair styles.
+  The YAML files match the pattern "atomic-pair-\*.yaml" and the tests are
+  correspondingly labeled with "AtomicPairStyle:\*"
+- kspace styles.
+  The YAML files match the pattern "kspace-\*.yaml" and the tests are
+  correspondingly labeled with "KSpaceStyle:\*". In these cases a compatible
+  pair style is defined, but the computation of the pair style contributions
+  is disabled.
+
+The ``test_bond_style`` and ``test_angle_style`` are set up in a similar
+fashion and share support functions with the pair style tester.  The final
+group of tests in this section is for fix styles that add/manipulate forces
+and velocities, e.g. for time integration, thermostats and more.
+
+Adding a new test is easiest done by copying and modifying an existing test
+for a style that is similar to one to be tested.  The file name should follow
+the naming conventions described above and after copying the file, the first
+step is to replace the style names where needed.  The coefficient values
+do not have to be meaningful, just in a reasonable range for the given system.
+It does not matter if some forces are large, for as long as they do not diverge.
+
+The template input files define a large number of index variables at the top
+that can be modified inside the YAML file to control the behavior.  For example,
+if a pair style requires a "newton on" setting, the following can be used in
+as the "pre_commands" section:
+
+.. code-block:: yaml
+
+   pre_commands: ! |
+     variable newton_pair delete
+     variable newton_pair index on
+
+And for a pair style requiring a kspace solver the following would be used as
+the "post_commands" section:
+
+.. code-block:: yaml
+
+   post_commands: ! |
+     pair_modify table 0
+     kspace_style pppm/tip4p 1.0e-6
+     kspace_modify gewald 0.3
+     kspace_modify compute no
+
+Note that this disables computing the kspace contribution, but still will run
+the setup.  The "gewald" parameter should be set explicitly to speed up the run.
+For styles with long-range electrostatics, typically two tests are added one using
+the (slower) analytic approximation of the erfc() function and the other using
+the tabulated coulomb, to test both code paths. The reference results in the YAML
+files then should be compared manually, if they agree well enough within the limits
+of those two approximations.
+
+The ``test_pair_style`` and equivalent programs have special command line options
+to update the YAML files. Running a command like
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml -g new.yaml
+
+will read the settings from the ``mol-pair-lennard_mdf.yaml`` file and then compute
+the reference data and write a new file with to ``new.yaml``.  If this step fails,
+there are likely some (LAMMPS or YAML) syntax issues in the YAML file that need to
+be resolved and then one can compare the two files to see if the output is as expected.
+
+It is also possible to do an update in place with:
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml -u
+
+And one can finally run the full set of tests with:
+
+.. code-block:: bash
+
+   $ test_pair_style mol-pair-lennard_mdf.yaml
+
+This will just print a summary of the groups of tests.  When using the "-v" flag
+the test will also keep any LAMMPS output and when using the "-s" flag, there
+will be some statistics reported on the relative errors for the individual checks
+which can help to figure out what would be a good choice of the epsilon parameter.
+It should be as small as possible to catch any unintended side effects from changes
+elsewhere, but large enough to accommodate the numerical noise due to the implementation
+of the potentials and differences in compilers.
+
+.. note::
+
+   These kinds of tests can be very sensitive to compiler optimization and
+   thus the expectation is that they pass with compiler optimization turned
+   off. When compiler optimization is enabled, there may be some failures, but
+   one has to carefully check whether those are acceptable due to the enhanced
+   numerical noise from reordering floating-point math operations or due to
+   the compiler mis-compiling the code. That is not always obvious.
+
+
+Tests for programs in the tools folder
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+The ``unittest/tools`` folder contains tests for programs in the
+``tools`` folder.  This currently only contains tests for the LAMMPS
+shell, which are implemented as a python scripts using the ``unittest``
+Python module and launching the tool commands through the ``subprocess``
+Python module.

doc/src/Developer_utils.rst

@@ -71,12 +71,21 @@ and parsing files or arguments.
 
 ----------
 
+.. doxygenfunction:: strdup
+   :project: progguide
+
 .. doxygenfunction:: trim
    :project: progguide
 
 .. doxygenfunction:: trim_comment
    :project: progguide
 
+.. doxygenfunction:: has_utf8
+   :project: progguide
+
+.. doxygenfunction:: utf8_subst
+   :project: progguide
+
 .. doxygenfunction:: count_words(const char *text)
    :project: progguide
 
@@ -92,9 +101,15 @@ and parsing files or arguments.
 .. doxygenfunction:: split_words
    :project: progguide
 
+.. doxygenfunction:: split_lines
+   :project: progguide
+
 .. doxygenfunction:: strmatch
    :project: progguide
 
+.. doxygenfunction:: strfind
+   :project: progguide
+
 .. doxygenfunction:: is_integer
    :project: progguide
 
@@ -286,6 +301,50 @@ This code example should produce the following output:
 
 ----------
 
+
+Argument parsing classes
+---------------------------
+
+The purpose of argument parsing classes it to simplify and unify how
+arguments of commands in LAMMPS are parsed and to make abstractions of
+repetitive tasks.
+
+The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
+for parsing references to compute or fix styles or variables. These
+would start with a "c\_", "f\_", "v\_" followed by the ID or name of
+than instance and may be postfixed with one or two array indices
+"[<number>]" with numbers > 0.
+
+A typical code segment would look like this:
+
+.. code-block:: C++
+   :caption: Usage example for ArgInfo class
+
+   int nvalues = 0;
+   for (iarg = 0; iarg < nargnew; iarg++) {
+     ArgInfo argi(arg[iarg]);
+
+     which[nvalues] = argi.get_type();
+     argindex[nvalues] = argi.get_index1();
+     ids[nvalues] = argi.copy_name();
+
+     if ((which[nvalues] == ArgInfo::UNKNOWN)
+          || (which[nvalues] == ArgInfo::NONE)
+          || (argi.get_dim() > 1))
+       error->all(FLERR,"Illegal compute XXX command");
+
+     nvalues++;
+   }
+
+----------
+
+.. doxygenclass:: LAMMPS_NS::ArgInfo
+   :project: progguide
+   :members:
+
+
+----------
+
 File reader classes
 -------------------
 

doc/src/Errors_warnings.rst

@@ -119,7 +119,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
    :doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.
 
 *Communication cutoff is shorter than a bond length based estimate. This may lead to errors.*
-
    Since LAMMPS stores topology data with individual atoms, all atoms
    comprising a bond, angle, dihedral or improper must be present on any
    sub-domain that "owns" the atom with the information, either as a

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

@@ -296,6 +296,8 @@ Some common CMake variables
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
      - root directory of install location for ``make install``  (default: ``$HOME/.local``)
+   * - ``LAMMPS_INSTALL_RPATH``
+     - set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
    * - ``CMAKE_BUILD_TYPE``
      - controls compilation options:
        one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``
@@ -409,10 +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_drude.rst

@@ -42,10 +42,11 @@ screening. It may be necessary to use the *extra/special/per/atom*
 keyword of the :doc:`read_data <read_data>` command. If using :doc:`fix shake <fix_shake>`, make sure no Drude particle is in this fix
 group.
 
-There are two ways to thermostat the Drude particles at a low
+There are three ways to thermostat the Drude particles at a low
 temperature: use either :doc:`fix langevin/drude <fix_langevin_drude>`
 for a Langevin thermostat, or :doc:`fix drude/transform/\* <fix_drude_transform>` for a Nose-Hoover
-thermostat. The former requires use of the command :doc:`comm_modify vel yes <comm_modify>`. The latter requires two separate integration
+thermostat, or :doc:`fix tgnvt/drude <fix_tgnh_drude>` for a temperature-grouped Nose-Hoover thermostat.
+The first and third require use of the command :doc:`comm_modify vel yes <comm_modify>`. The second requires two separate integration
 fixes like *nvt* or *npt*\ . The correct temperatures of the reduced
 degrees of freedom can be calculated using the :doc:`compute temp/drude <compute_temp_drude>`. This requires also to use the
 command *comm_modify vel yes*.

doc/src/Howto_drude2.rst

@@ -36,7 +36,7 @@ polarizability :math:`\alpha` by
 
 Ideally, the mass of the Drude particle should be small, and the
 stiffness of the harmonic bond should be large, so that the Drude
-particle remains close ot the core. The values of Drude mass, Drude
+particle remains close to the core. The values of Drude mass, Drude
 charge, and force constant can be chosen following different
 strategies, as in the following examples of polarizable force
 fields:
@@ -221,6 +221,14 @@ modification of forces but no position/velocity updates), the fix
 
    fix NVE all nve
 
+To avoid the flying ice cube artifact, where the atoms progressively freeze and the
+center of mass of the whole system drifts faster and faster, the *fix momentum*
+can be used. For instance:
+
+.. code-block:: LAMMPS
+
+   fix MOMENTUM all momentum 100 linear 1 1 1
+
 Finally, do not forget to update the atom type elements if you use
 them in a *dump_modify ... element ...* command, by adding the element
 type of the DPs. Here for instance
@@ -376,14 +384,7 @@ For our phenol example, the groups would be defined as
 
 Note that with the fixes *drude/transform*\ , it is not required to
 specify *comm_modify vel yes* because the fixes do it anyway (several
-times and for the forces also).  To avoid the flying ice cube artifact
-:ref:`(Lamoureux and Roux) <Lamoureux2>`, where the atoms progressively freeze and the
-center of mass of the whole system drifts faster and faster, the *fix
-momentum* can be used. For instance:
-
-.. code-block:: LAMMPS
-
-   fix MOMENTUM all momentum 100 linear 1 1 1
+times and for the forces also).
 
 It is a bit more tricky to run a NPT simulation with Nose-Hoover
 barostat and thermostat.  First, the volume should be integrated only
@@ -404,6 +405,31 @@ instructions for thermostatting and barostatting will look like
    fix NVT DRUDES nvt temp 1. 1. 20
    fix INVERSE all drude/transform/inverse
 
+Another option for thermalizing the Drude model is to use the
+temperature-grouped Nose-Hoover (TGNH) thermostat proposed by :ref:`(Son) <TGNH-SON>`.
+This is implemented as :doc:`fix tgnvt/drude <fix_tgnh_drude>` and :doc:`fix tgnpt/drude <fix_tgnh_drude>`.
+It separates the kinetic energy into three contributions:
+the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs,
+and the relative motion of atom-Drude pairs.
+An independent Nose-Hoover chain is applied to each type of motion.
+When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with :doc:`thermo_style` command.
+
+NVT simulation with TGNH thermostat
+
+.. code-block:: LAMMPS
+
+   comm_modify vel yes
+   fix TGNVT all tgnvt/drude temp 300. 300. 100 1. 20
+   thermo_style custom f_TGNVT[1] f_TGNVT[2] f_TGNVT[3]
+
+NPT simulation with TGNH thermostat
+
+.. code-block:: LAMMPS
+
+   comm_modify vel yes
+   fix TGNPT all tgnpt/drude temp 300. 300. 100 1. 20 iso 1. 1. 500
+   thermo_style custom f_TGNPT[1] f_TGNPT[2] f_TGNPT[3]
+
 ----------
 
 **Rigid bodies**
@@ -480,3 +506,7 @@ NPT ensemble using Nose-Hoover thermostat:
 
 **(SWM4-NDP)** Lamoureux, Harder, Vorobyov, Roux, MacKerell, Chem Phys
 Let, 418, 245-249 (2006)
+
+.. _TGNH-Son:
+
+**(Son)** Son, McDaniel, Cui and Yethiraj, J Phys Chem Lett, 10, 7523 (2019).

doc/src/Howto_github.rst

@@ -72,7 +72,7 @@ explained in more detail here: `feature branch workflow <https://www.atlassian.c
 
 **Feature branches**
 
-First of all, create a clone of your version on github on your local
+First of all, create a clone of your version on GitHub on your local
 machine via HTTPS:
 
 .. code-block:: bash
@@ -155,7 +155,7 @@ useful message that explains the change.
 
 .. code-block:: bash
 
-     $ git commit -m 'Finally updated the github tutorial'
+     $ git commit -m 'Finally updated the GitHub tutorial'
 
 After the commit, the changes can be pushed to the same branch on GitHub:
 

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_pylammps.rst

@@ -9,8 +9,8 @@ Overview
 ``PyLammps`` is a Python wrapper class for LAMMPS which can be created
 on its own or use an existing lammps Python object.  It creates a simpler,
 more "pythonic" interface to common LAMMPS functionality, in contrast to
-the ``lammps.py`` wrapper for the C-style LAMMPS library interface which
-is written using `Python ctypes <ctypes_>`_.  The ``lammps.py`` wrapper
+the ``lammps`` wrapper for the C-style LAMMPS library interface which
+is written using `Python ctypes <ctypes_>`_.  The ``lammps`` wrapper
 is discussed on the :doc:`Python_head` doc page.
 
 Unlike the flat ``ctypes`` interface, PyLammps exposes a discoverable

doc/src/Howto_walls.rst

@@ -67,5 +67,5 @@ rotate.
 
 The only frictional idealized walls currently in LAMMPS are flat or
 curved surfaces specified by the :doc:`fix wall/gran <fix_wall_gran>`
-command.  At some point we plan to allow regoin surfaces to be used as
+command.  At some point we plan to allow region surfaces to be used as
 frictional walls, as well as triangulated surfaces.

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/Install_tarball.rst

@@ -33,22 +33,19 @@ in its name, e.g. lammps-23Jun18.
 
 ----------
 
-You can also download a zip file via the "Clone or download" button on
-the `LAMMPS GitHub site <git_>`_.  The file name will be lammps-master.zip
-which can be unzipped with the following command, to create
-a lammps-master dir:
+You can also download a compressed tar or zip archives from the
+"Assets" sections of the `LAMMPS GitHub releases site <git_>`_.
+The file name will be lammps-<version>.zip which can be unzipped
+with the following command, to create a lammps-<version> dir:
 
 .. code-block:: bash
 
    $ unzip lammps*.zip
 
-This version is the most up-to-date LAMMPS development version.  It
-will have the date of the most recent patch release (see the file
-src/version.h).  But it will also include any new bug-fixes or
-features added since the last patch release.  They will be included in
-the next patch release tarball.
+This version corresponds to the selected LAMMPS patch or stable
+release.
 
-.. _git: https://github.com/lammps/lammps
+.. _git: https://github.com/lammps/lammps/releases
 
 ----------
 

doc/src/Intro_citing.rst

@@ -24,29 +24,32 @@ DOI for the LAMMPS code
 LAMMPS developers use the `Zenodo service at CERN
 <https://zenodo.org/>`_ to create digital object identifies (DOI) for
 stable releases of the LAMMPS code. There are two types of DOIs for the
-LAMMPS source code: 1) the canonical DOI for **all** versions of LAMMPS,
-which will always point to the latest stable release version is:
+LAMMPS source code: the canonical DOI for **all** versions of LAMMPS,
+which will always point to the **latest** stable release version is:
 
-  `DOI: 10.5281/zenodo.3726416 <https://dx.doi/org/10.5281/zenodo.3726416>`_
+- DOI: `10.5281/zenodo.3726416 <https://dx.doi.org/10.5281/zenodo.3726416>`_
 
-In addition there are DOIs for individual stable releases starting with
-the `3 March 2020 version, DOI:10.5281/zenodo.3726417 <https://dx.doi/org/10.5281/zenodo.3726416>`_
+In addition there are DOIs for individual stable releases. Currently there are:
+
+- 3 March 2020 version: `DOI:10.5281/zenodo.3726417 <https://dx.doi.org/10.5281/zenodo.3726417>`_
+- 29 October 2020 version: `DOI:10.5281/zenodo.4157471 <https://dx.doi.org/10.5281/zenodo.4157471>`_
 
 
 Home page
 ^^^^^^^^^
 
-The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
-location for information about LAMMPS and more detailed lists of publications
-using LAMMPS and contributing features.
+The LAMMPS website at `https://lammps.sandia.gov/
+<https://lammps.sandia.gov>`_ is the canonical location for information
+about LAMMPS and its features.
 
 Citing contributions
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS has many features and uses previously published methods and
-algorithms or novel features. It also includes potential parameter
-filed for specific models.  You can look up relevant publications either
-in the LAMMPS output to the screen, the ``log.cite`` file (which is
-populated with references to relevant papers through embedding them into
-the source code) and in the documentation of the :doc:`corresponding commands
+LAMMPS has many features and that use either previously published
+methods and algorithms or novel features.  It also includes potential
+parameter filed for specific models.  Where available, a reminder about
+references for optional features used in a specific run is printed to
+the screen and log file.  Style and output location can be selected with
+the :ref:`-cite command-line switch <cite>`.  Additional references are
+given in the documentation of the :doc:`corresponding commands
 <Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

doc/src/Intro_features.rst

@@ -85,7 +85,7 @@ commands)
 * water potentials: TIP3P, TIP4P, SPC
 * implicit solvent potentials: hydrodynamic lubrication, Debye
 * force-field compatibility with common CHARMM, AMBER, DREIDING,     OPLS, GROMACS, COMPASS options
-* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim_init, kim_interactions, and kim_query <kim_commands>` commands
+* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via     :doc:`kim command <kim_commands>`
 * hybrid potentials: multiple pair, bond, angle, dihedral, improper     potentials can be used in one simulation
 * overlaid potentials: superposition of multiple pair potentials
 

doc/src/Library_config.rst

@@ -14,6 +14,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_config_has_package`
 - :cpp:func:`lammps_config_package_count`
 - :cpp:func:`lammps_config_package_name`
+- :cpp:func:`lammps_config_accelerator`
 - :cpp:func:`lammps_has_style`
 - :cpp:func:`lammps_style_count`
 - :cpp:func:`lammps_style_name`
@@ -126,6 +127,11 @@ approach.
 
 -----------------------
 
+.. doxygenfunction:: lammps_config_accelerator
+   :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

@@ -21,10 +21,16 @@ where all LAMMPS development is coordinated.
 
 ----------
 
-The content for this manual is part of the LAMMPS distribution.  You can
-build a local copy of the Manual as HTML pages or a PDF file, by
-following the steps on the :doc:`Build_manual` page.  The manual is
-organized in two parts:
+The content for this manual is part of the LAMMPS distribution.  The
+online version always corresponds to the latest development version.
+If needed, you can download or build a local copy of the manual as
+HTML pages or a PDF file by following the steps on the
+:doc:`Build_manual` page. If you have difficulties viewing the pages
+please :ref:`see this note <webbrowser>`.
+
+-----------
+
+The manual is organized in two parts:
 1) the :ref:`User Guide <user_documentation>` for how to install
 and use LAMMPS and 2) the :ref:`Programmer Guide <programmer_documentation>`
 for how to write programs using the LAMMPS library from different
@@ -107,3 +113,15 @@ Indices and tables
 
    * :ref:`genindex`
    * :ref:`search`
+
+.. _webbrowser:
+.. 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
+   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
+   broken or mathematical expressions not typeset).  In that case we
+   recommend to install/use a different/newer web browser or use
+   the `PDF version of the manual <https://lammps.sandia.gov/doc/Manual.pdf>`_.

doc/src/Modify_contribute.rst

@@ -206,16 +206,22 @@ packages in the src directory for examples. If you are uncertain, please ask.
   algorithm/science behind the feature itself, or its initial usage, or
   its implementation in LAMMPS), you can add the citation to the \*.cpp
   source file.  See src/USER-EFF/atom_vec_electron.cpp for an example.
-  A LaTeX citation is stored in a variable at the top of the file and a
-  single line of code that references the variable is added to the
-  constructor of the class.  Whenever a user invokes your feature from
-  their input script, this will cause LAMMPS to output the citation to a
-  log.cite file and prompt the user to examine the file.  Note that you
-  should only use this for a paper you or your group authored.
-  E.g. adding a cite in the code for a paper by Nose and Hoover if you
-  write a fix that implements their integrator is not the intended
-  usage.  That kind of citation should just be in the doc page you
-  provide.
+  A LaTeX citation is stored in a variable at the top of the file and
+  a single line of code registering this variable is added to the
+  constructor of the class.  If there is additional functionality (which
+  may have been added later) described in a different publication,
+  additional citation descriptions may be added for as long as they
+  are only registered when the corresponding keyword activating this
+  functionality is used.  With these options it is possible to have
+  LAMMPS output a specific citation reminder whenever a user invokes
+  your feature from their input script.  Note that you should only use
+  this for the most relevant paper for a feature and a publication that
+  you or your group authored.  E.g. adding a citation in the code for
+  a paper by Nose and Hoover if you write a fix that implements their
+  integrator is not the intended usage.  That kind of citation should
+  just be included in the documentation page you provide describing
+  your contribution.  If you are not sure what the best option would
+  be, please contact the LAMMPS developers for advice.
 
 Finally, as a general rule-of-thumb, the more clear and
 self-explanatory you make your documentation and README files, and the

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>`
@@ -367,17 +368,19 @@ KIM package
 
 **Contents:**
 
-This package contains a set of commands that serve as a wrapper on the
+This package contains a command with a set of sub-commands that serve as a
+wrapper on the
 `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
 repository of interatomic models (IMs) enabling compatible ones to be used in
 LAMMPS simulations.
 
-This includes :doc:`kim_init <kim_commands>`, and
-:doc:`kim_interactions <kim_commands>` commands to select, initialize and
-instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
+
+This includes :doc:`kim init <kim_commands>`, and
+:doc:`kim interactions <kim_commands>` commands to select, initialize and
+instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
 queries for material property predictions of OpenKIM IMs, a
-:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
-LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
+:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
+LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
 properties computed in LAMMPS to standard KIM property instance format.
 
 Support for KIM IMs that conform to the
@@ -386,8 +389,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
 
 .. note::
 
-   The command *pair_style kim* is called by *kim_interactions* and
-   is not recommended to be directly used in input scripts.
+   The command *pair_style kim* is called by *kim interactions* and is not
+   recommended to be directly used in input scripts.
 
 To use this package you must have the KIM API library available on your
 system. The KIM API is available for download on the
@@ -404,7 +407,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
 API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
 Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
 Daniel Karls (U Minnesota) contributed to the
-:doc:`kim_commands <kim_commands>` interface in close collaboration with
+:doc:`kim command <kim_commands>` interface in close collaboration with
 Ryan Elliott.
 
 **Install:**
@@ -414,7 +417,7 @@ This package has :ref:`specific installation instructions <kim>` on the
 
 **Supporting info:**
 
-* :doc:`kim_commands <kim_commands>`
+* :doc:`kim command <kim_commands>`
 * :doc:`pair_style kim <pair_kim>`
 * src/KIM: filenames -> commands
 * src/KIM/README
@@ -662,19 +665,31 @@ MLIAP package
 
 **Contents:**
 
-A general interface for machine-learning interatomic potentials.
+A general interface for machine-learning interatomic potentials, including PyTorch.
 
 **Install:**
 
-To use this package, also the :ref:`SNAP package <PKG-SNAP>` needs to be installed.
+To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
+to be installed.  To make the *mliappy* model available, also the
+:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
+of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
+must be installed.
 
-**Author:** Aidan Thompson (Sandia).
+**Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
 **Supporting info:**
 
 * src/MLIAP: filenames -> commands
+* src/MLIAP/README
 * :doc:`pair_style mliap <pair_mliap>`
-* examples/mliap
+* :doc:`compute_style mliap <compute_mliap>`
+* examples/mliap (see README)
+
+When built with the *mliappy* model this package includes an extension for
+coupling with Python models, including PyTorch. In this case, the Python
+interpreter linked to LAMMPS will need the ``cython`` and ``numpy`` modules
+installed.  The provided examples build models with PyTorch, which would
+therefore also needs to be installed to run those examples.
 
 ----------
 
@@ -829,6 +844,28 @@ 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
@@ -1036,9 +1073,11 @@ the usual manner via MD.  Various pair, fix, and compute styles.
 * :doc:`pair_style spin/dipole/long <pair_spin_dipole>`
 * :doc:`pair_style spin/dmi <pair_spin_dmi>`
 * :doc:`pair_style spin/exchange <pair_spin_exchange>`
+* :doc:`pair_style spin/exchange/biquadratic <pair_spin_exchange>`
 * :doc:`pair_style spin/magelec <pair_spin_magelec>`
 * :doc:`pair_style spin/neel <pair_spin_neel>`
 * :doc:`fix nve/spin <fix_nve_spin>`
+* :doc:`fix langevin/spin <fix_langevin_spin>`
 * :doc:`fix precession/spin <fix_precession_spin>`
 * :doc:`compute spin <compute_spin>`
 * :doc:`neb/spin <neb_spin>`
@@ -1416,8 +1455,8 @@ oscillators as a model of polarization.  See the :doc:`Howto drude <Howto_drude>
 for an overview of how to use the package.  There are auxiliary tools
 for using this package in tools/drude.
 
-**Authors:** Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
-Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
+**Authors:** Alain Dequidt (U Clermont Auvergne), Julien
+Devemy (CNRS), and Agilio Padua (ENS de Lyon).
 
 **Supporting info:**
 
@@ -1484,7 +1523,7 @@ methods for performing FEP simulations by using a :doc:`fix adapt/fep <fix_adapt
 which have a "soft" in their style name.  There are auxiliary tools
 for using this package in tools/fep; see its README file.
 
-**Author:** Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
+**Author:** Agilio Padua (ENS de Lyon)
 
 **Supporting info:**
 
@@ -2440,6 +2479,6 @@ 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/Python_atoms.rst

@@ -50,7 +50,7 @@ against invalid accesses.
 
       **Numpy Methods**:
 
-      * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
+      * :py:meth:`numpy.extract_atom() <lammps.numpy_wrapper.numpy_wrapper.extract_atom()>`: extract a per-atom quantity as numpy array
 
    .. tab:: PyLammps/IPyLammps API
 

doc/src/Python_config.rst

@@ -39,7 +39,9 @@ about compile time settings and included packages and styles.
 * :py:attr:`lammps.has_jpeg_support <lammps.lammps.has_jpeg_support>`
 * :py:attr:`lammps.has_ffmpeg_support <lammps.lammps.has_ffmpeg_support>`
 
-* :py:attr:`lammps.installed_packages <lammps.lammps.installed_pages>`
+* :py:attr:`lammps.installed_packages <lammps.lammps.installed_packages>`
+
+* :py:meth:`lammps.get_accelerator_config <lammps.lammps.accelerator_config>`
 
 * :py:meth:`lammps.has_style() <lammps.lammps.has_style()>`
 * :py:meth:`lammps.available_styles() <lammps.lammps.available_styles()>`

doc/src/Python_ext.rst

@@ -9,7 +9,7 @@ This means you can extend the Python wrapper by following these steps:
 * Add a new interface function to ``src/library.cpp`` and
   ``src/library.h``.
 * Rebuild LAMMPS as a shared library.
-* Add a wrapper method to ``python/lammps.py`` for this interface
+* Add a wrapper method to ``python/lammps/core.py`` for this interface
   function.
 * Define the corresponding ``argtypes`` list and ``restype``
   in the ``lammps.__init__()`` function.

doc/src/Python_formats.rst

@@ -0,0 +1,11 @@
+Output Readers
+==============
+
+.. py:module:: lammps.formats
+
+The Python package contains the :py:mod:`lammps.formats` module, which
+provides classes to post-process some of the output files generated by LAMMPS.
+
+.. automodule:: lammps.formats
+   :members:
+   :noindex:

doc/src/Python_head.rst

@@ -13,6 +13,7 @@ together.
    Python_module
    Python_ext
    Python_call
+   Python_formats
    Python_examples
    Python_error
    Python_trouble

doc/src/Python_install.rst

@@ -8,9 +8,9 @@ module.  Because of the dynamic loading, it is required that LAMMPS is
 compiled in :ref:`"shared" mode <exe>`.  It is also recommended to
 compile LAMMPS with :ref:`C++ exceptions <exceptions>` enabled.
 
-Two files are necessary for Python to be able to invoke LAMMPS code:
+Two components are necessary for Python to be able to invoke LAMMPS code:
 
-* The LAMMPS Python Module (``lammps.py``) from the ``python`` folder
+* The LAMMPS Python Package (``lammps``) from the ``python`` folder
 * The LAMMPS Shared Library (``liblammps.so``, ``liblammps.dylib`` or
   ``liblammps.dll``) from the folder where you compiled LAMMPS.
 
@@ -25,10 +25,10 @@ Installing the LAMMPS Python Module and Shared Library
 ======================================================
 
 Making LAMMPS usable within Python and vice versa requires putting the
-LAMMPS Python module file (``lammps.py``) into a location where the
+LAMMPS Python package (``lammps``) into a location where the
 Python interpreter can find it and installing the LAMMPS shared library
-into a folder that the dynamic loader searches or into the same folder
-where the ``lammps.py`` file is.  There are multiple ways to achieve
+into a folder that the dynamic loader searches or inside of the installed
+``lammps`` package folder.  There are multiple ways to achieve
 this.
 
 #. Do a full LAMMPS installation of libraries, executables, selected
@@ -36,13 +36,13 @@ this.
    available via CMake), which can also be either system-wide or into
    user specific folders.
 
-#. Install both files into a Python ``site-packages`` folder, either
+#. Install both components into a Python ``site-packages`` folder, either
    system-wide or in the corresponding user-specific folder. This way no
    additional environment variables need to be set, but the shared
    library is otherwise not accessible.
 
-#. Do an installation into a virtual environment. This can either be
-   an installation of the python module only or a full installation.
+#. Do an installation into a virtual environment. This can either be an
+   installation of the Python package only or a full installation of LAMMPS.
 
 #. Leave the files where they are in the source/development tree and
    adjust some environment variables.
@@ -69,7 +69,7 @@ this.
          cd build
 
          # configure LAMMPS compilation
-         cmake -C cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
+         cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
                -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
 
          # compile LAMMPS
@@ -81,40 +81,42 @@ this.
 
       This leads to an installation to the following locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$HOME/.local/lib/`` (32bit)                           |                                                             |
-      |                        | * ``$HOME/.local/lib64/`` (64bit)                         |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$HOME/.local/bin/``                                   |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/``               | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python package  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$HOME/.local/lib/`` (32bit)                                 | Set shared loader environment variable to this path         |
+      |                        | * ``$HOME/.local/lib64/`` (64bit)                               | (see below for more info on this)                           |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``$HOME/.local/bin/``                                         |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``$HOME/.local/share/lammps/potentials/``                     | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       For a system-wide installation you need to set
       ``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
-      ``/usr/local``).  The installation step (**not** the
+      ``/usr/local``); the default is ``${HOME}/.local``.  The
+      installation step for a system folder installation (**not** the
       configuration/compilation) needs to be done with superuser
       privilege, e.g. by using ``sudo cmake --install .``.  The
-      installation folders will then by changed to:
+      installation folders will then be changed to (assuming ``/usr`` as
+      prefix):
 
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                          | Notes                                                       |
-      +========================+===================================================+=============================================================+
-      | LAMMPS Python Module   | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``/usr/lib/`` (32bit)                           |                                                             |
-      |                        | * ``/usr/lib64/`` (64bit)                         |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``/usr/bin/``                                   |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``/usr/share/lammps/potentials/``               |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                | Notes                                                       |
+      +========================+=========================================================+=============================================================+
+      | LAMMPS Python package  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``/usr/lib/`` (32bit)                                 |                                                             |
+      |                        | * ``/usr/lib64/`` (64bit)                               |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``/usr/bin/``                                         |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``/usr/share/lammps/potentials/``                     |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
 
       To be able to use the "user" installation you have to ensure that
       the folder containing the LAMMPS shared library is either included
@@ -146,7 +148,7 @@ this.
       necessary due to files installed in system folders that are loaded
       automatically when a login shell is started.
 
-   .. tab:: Python module only
+   .. tab:: Python package only
 
       Compile LAMMPS with either :doc:`CMake <Build_cmake>` or the
       :doc:`traditional make <Build_make>` procedure in :ref:`shared
@@ -157,37 +159,37 @@ this.
 
          make install-python
 
-      This will try to install (only) the shared library and the python
-      module into a system folder and if that fails (due to missing
+      This will try to install (only) the shared library and the Python
+      package into a system folder and if that fails (due to missing
       write permissions) will instead do the installation to a user
       folder under ``$HOME/.local``.  For a system-wide installation you
       would have to gain superuser privilege, e.g. though ``sudo``
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$HOME/.local/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python package  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$HOME/.local/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$HOME/.local/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       For a system-wide installation those folders would then become.
 
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                          | Notes                                                       |
-      +========================+===================================================+=============================================================+
-      | LAMMPS Python Module   | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``/usr/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``/usr/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+---------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                | Notes                                                       |
+      +========================+=========================================================+=============================================================+
+      | LAMMPS Python package  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``/usr/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``/usr/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
 
       No environment variables need to be set for those, as those
       folders are searched by default by Python or the LAMMPS Python
-      module.
+      package.
 
       For the traditional make process you can override the python
       version to version x.y when calling ``make`` with
@@ -199,9 +201,9 @@ this.
 
       .. code-block:: bash
 
-         $ python install.py -m <python module> -l <shared library> -v <version.h file> [-d <pydir>]
+         $ python install.py -p <python package> -l <shared library> -v <version.h file> [-d <pydir>]
 
-      * The ``-m`` flag points to the ``lammps.py`` python module file to be installed,
+      * The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
       * the ``-l`` flag points to the LAMMPS shared library file to be installed,
       * the ``-v`` flag points to the ``version.h`` file in the LAMMPS source
       * and the optional ``-d`` flag to a custom (legacy) installation folder
@@ -249,38 +251,38 @@ this.
       When using CMake to build LAMMPS, you need to set
       ``CMAKE_INSTALL_PREFIX`` to the value of the ``$VIRTUAL_ENV``
       environment variable during the configuration step. For the
-      traditional make procedure, not additional steps are needed.
-      After compiling LAMMPS you can do a "Python module only"
+      traditional make procedure, no additional steps are needed.
+      After compiling LAMMPS you can do a "Python package only"
       installation with ``make install-python`` and the LAMMPS Python
-      module and the shared library file are installed into the
+      package and the shared library file are installed into the
       following locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       If you do a full installation (CMake only) with "install", this
       leads to the following installation locations:
 
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | File                   | Location                                                  | Notes                                                       |
-      +========================+===========================================================+=============================================================+
-      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/`` (32bit)   | ``X.Y`` depends on the installed Python version             |
-      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/`` (64bit) |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/`` (32bit)                           |                                                             |
-      |                        | * ``$VIRTUAL_ENV/lib64/`` (64bit)                         |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS executable      | * ``$VIRTUAL_ENV/bin/``                                   |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
-      | LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/``               |                                                             |
-      +------------------------+-----------------------------------------------------------+-------------------------------------------------------------+
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | File                   | Location                                                        | Notes                                                       |
+      +========================+=================================================================+=============================================================+
+      | LAMMPS Python Module   | * ``$VIRTUAL_ENV/lib/pythonX.Y/site-packages/lammps`` (32bit)   | ``X.Y`` depends on the installed Python version             |
+      |                        | * ``$VIRTUAL_ENV/lib64/pythonX.Y/site-packages/lammps`` (64bit) |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS shared library  | * ``$VIRTUAL_ENV/lib/`` (32bit)                                 | Set shared loader environment variable to this path         |
+      |                        | * ``$VIRTUAL_ENV/lib64/`` (64bit)                               | (see below for more info on this)                           |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS executable      | * ``$VIRTUAL_ENV/bin/``                                         |                                                             |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
+      | LAMMPS potential files | * ``$VIRTUAL_ENV/share/lammps/potentials/``                     | Set ``LAMMPS_POTENTIALS`` environment variable to this path |
+      +------------------------+-----------------------------------------------------------------+-------------------------------------------------------------+
 
       In that case you need to modify the ``$HOME/myenv/bin/activate``
       script in a similar fashion you need to update your
@@ -296,15 +298,15 @@ this.
          echo 'export LD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
 
          # MacOS
-         echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$LD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
+         echo 'export DYLD_LIBRARY_PATH=$VIRTUAL_ENV/lib:$DYLD_LIBRARY_PATH' >> $HOME/myenv/bin/activate
 
    .. tab:: In place usage
 
       You can also :doc:`compile LAMMPS <Build>` as usual in
       :ref:`"shared" mode <exe>` leave the shared library and Python
-      module files inside the source/compilation folders. Instead of
+      package inside the source/compilation folders. Instead of
       copying the files where they can be found, you need to set the environment
-      variables ``PYTHONPATH`` (for the Python module) and
+      variables ``PYTHONPATH`` (for the Python package) and
       ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH`` on MacOS
 
       For Bourne shells (bash, ksh and similar) the commands are:
@@ -325,6 +327,10 @@ this.
       You can make those changes permanent by editing your ``$HOME/.bashrc``
       or ``$HOME/.login`` files, respectively.
 
+      .. note::
+
+         The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
+
 
 To verify if LAMMPS can be successfully started from Python, start the
 Python interpreter, load the ``lammps`` Python module and create a
@@ -346,7 +352,7 @@ output similar to the following:
 .. note::
 
    Unless you opted for "In place use", you will have to rerun the installation
-   any time you recompile LAMMPS to ensure the latest Python module and shared
+   any time you recompile LAMMPS to ensure the latest Python package and shared
    library are installed and used.
 
 .. note::

doc/src/Python_module.rst

@@ -3,12 +3,12 @@ The ``lammps`` Python module
 
 .. py:module:: lammps
 
-The LAMMPS Python interface is implemented as a module called
-:py:mod:`lammps` in the ``lammps.py`` file in the ``python`` folder of
-the LAMMPS source code distribution.  After compilation of LAMMPS, the
-module can be installed into a Python system folder or a user folder
-with ``make install-python``.  Components of the module can then loaded
-into a Python session with the ``import`` command.
+The LAMMPS Python interface is implemented as a module called :py:mod:`lammps`
+which is defined in the ``lammps`` package in the ``python`` folder of the
+LAMMPS source code distribution.  After compilation of LAMMPS, the module can
+be installed into a Python system folder or a user folder with ``make
+install-python``.  Components of the module can then loaded into a Python
+session with the ``import`` command.
 
 There are multiple Python interface classes in the :py:mod:`lammps` module:
 
@@ -26,6 +26,23 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
 
 .. _mpi4py_url: https://mpi4py.readthedocs.io
 
+.. admonition:: Version check
+   :class: note
+
+   The :py:mod:`lammps` module stores the version number of the LAMMPS
+   version it is installed from.  When initializing the
+   :py:class:`lammps <lammps.lammps>` class, this version is checked to
+   be the same as the result from :py:func:`lammps.version`, the version
+   of the LAMMPS shared library that the module interfaces to.  If the
+   they are not the same an AttributeError exception is raised since a
+   mismatch of versions (e.g.  due to incorrect use of the
+   ``LD_LIBRARY_PATH`` or ``PYTHONPATH`` environment variables can lead
+   to crashes or data corruption and otherwise incorrect behavior.
+
+.. automodule:: lammps
+   :members:
+   :noindex:
+
 ----------
 
 The ``lammps`` class API
@@ -44,7 +61,7 @@ functions. Below is a detailed documentation of the API.
 .. autoclass:: lammps.lammps
    :members:
 
-.. autoclass:: lammps.numpy_wrapper
+.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
    :members:
 
 ----------
@@ -117,23 +134,23 @@ Style Constants
    to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_type_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
    to request  from computes  or fixes.  See :cpp:enum:`_LMP_TYPE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_vartype_constants:
 
@@ -153,6 +170,6 @@ Classes representing internal objects
    :members:
    :no-undoc-members:
 
-.. autoclass:: lammps.NumPyNeighList
+.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
    :members:
    :no-undoc-members:

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
@@ -14,5 +51,5 @@ Neighbor list access
 
 **NumPy Methods:**
 
-* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
-* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)
+* :py:meth:`lammps.numpy.get_neighlist() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist()>`: Get neighbor list for given index, which uses NumPy arrays for its element neighbor arrays
+* :py:meth:`lammps.numpy.get_neighlist_element_neighbors() <lammps.numpy_wrapper.numpy_wrapper.get_neighlist_element_neighbors()>`: Get element in neighbor list and its neighbors (as numpy array)

doc/src/Python_objects.rst

@@ -36,9 +36,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
       Python subscripting. The values will be zero for atoms not in the
       specified group.
 
-      :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`,
-      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`, and
-      :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>` are
+      :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`,
+      :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`, and
+      :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>` are
       equivalent NumPy implementations that return NumPy arrays instead of ``ctypes`` pointers.
 
       The :py:meth:`lammps.set_variable() <lammps.lammps.set_variable()>` method sets an
@@ -54,9 +54,9 @@ computes, fixes, or variables in LAMMPS using the :py:mod:`lammps` module.
 
       **NumPy Methods**:
 
-      * :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
-      * :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
-      * :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute()>`: extract value(s) from a compute, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix()>`: extract value(s) from a fix, return arrays as numpy arrays
+      * :py:meth:`lammps.numpy.extract_variable() <lammps.numpy_wrapper.numpy_wrapper.extract_variable()>`: extract value(s) from a variable, return arrays as numpy arrays
 
 
    .. tab:: PyLammps/IPyLammps API

doc/src/Python_overview.rst

@@ -2,9 +2,9 @@ Overview
 ========
 
 The LAMMPS distribution includes a ``python`` directory with the Python
-code needed to run LAMMPS from Python.  The ``python/lammps.py``
-contains :doc:`the "lammps" Python <Python_module>` that wraps the
-LAMMPS C-library interface.  This file makes it is possible to do the
+code needed to run LAMMPS from Python.  The ``python/lammps`` package
+contains :doc:`the "lammps" Python module <Python_module>` that wraps the
+LAMMPS C-library interface.  This module makes it is possible to do the
 following either from a Python script, or interactively from a Python
 prompt:
 
@@ -20,8 +20,8 @@ have a version of Python that extends Python to enable multiple
 instances of Python to read what you type.
 
 To do all of this, you must build LAMMPS in :ref:`"shared" mode <exe>`
-and make certain that your Python interpreter can find the ``lammps.py``
-file and the LAMMPS shared library file.
+and make certain that your Python interpreter can find the ``lammps``
+Python package and the LAMMPS shared library file.
 
 .. _ctypes: https://docs.python.org/3/library/ctypes.html
 

doc/src/Python_trouble.rst

@@ -33,7 +33,7 @@ the constructor call as follows (see :ref:`python_create_lammps` for more detail
    >>> lmp = lammps(name='mpi')
 
 You can also test the load directly in Python as follows, without
-first importing from the lammps.py file:
+first importing from the ``lammps`` module:
 
 .. code-block:: python
 

doc/src/Run_options.rst

@@ -11,6 +11,7 @@ letter abbreviation can be used:
 * :ref:`-k or -kokkos <run-kokkos>`
 * :ref:`-l or -log <log>`
 * :ref:`-m or -mpicolor <mpicolor>`
+* :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
@@ -62,15 +63,18 @@ used.
 
 **-in file**
 
-Specify a file to use as an input script.  This is an optional switch
-when running LAMMPS in one-partition mode.  If it is not specified,
-LAMMPS reads its script from standard input, typically from a script
-via I/O redirection; e.g. lmp_linux < in.run.  I/O redirection should
-also work in parallel, but if it does not (in the unlikely case that
-an MPI implementation does not support it), then use the -in flag.
+Specify a file to use as an input script.  This is an optional but
+recommended switch when running LAMMPS in one-partition mode.  If it
+is not specified, LAMMPS reads its script from standard input, typically
+from a script via I/O redirection; e.g. lmp_linux < in.run.
+With many MPI implementations I/O redirection also works in parallel,
+but using the -in flag will always work.
+
 Note that this is a required switch when running LAMMPS in
 multi-partition mode, since multiple processors cannot all read from
-stdin.
+stdin concurrently.  The file name may be "none" for starting
+multi-partition calculations without reading an initial input file
+from the library interface.
 
 ----------
 
@@ -217,14 +221,31 @@ links with from the lib/message directory.  See the
 
 ----------
 
+.. _cite:
+
+**-cite style or file name**
+
+Select how and where to output a reminder about citing contributions
+to the LAMMPS code that were used during the run. Available styles are
+"both", "none", "screen", or "log".  Any flag will be considered a file
+name to write the detailed citation info to.  Default is the "log" style
+where there is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See the :doc:`citation page <Intro_citing>` for more details on
+how to correctly reference and cite LAMMPS.
+
+----------
+
 .. _nocite:
 
 **-nocite**
 
-Disable writing the log.cite file which is normally written to list
-references for specific cite-able features used during a LAMMPS run.
-See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
-details.
+Disable generating a citation reminder (see above) at all.
 
 ----------
 
@@ -296,7 +317,7 @@ command-line option.
 **-pscreen file**
 
 Specify the base name for the partition screen file, so partition N
-writes screen information to file.N. If file is none, then no
+writes screen information to file.N. If file is "none", then no
 partition screen files are created.  This overrides the filename
 specified in the -screen command-line option.  This option is useful
 when working with large numbers of partitions, allowing the partition

doc/src/Speed_gpu.rst

@@ -1,11 +1,14 @@
 GPU package
 ===========
 
-The GPU package was developed by Mike Brown while at SNL and ORNL
-and his collaborators, particularly Trung Nguyen (now at Northwestern).
-It provides GPU versions of many pair styles and for parts of the
-:doc:`kspace_style pppm <kspace_style>` for long-range Coulombics.
-It has the following general features:
+The GPU package was developed by Mike Brown while at SNL and ORNL (now
+at Intel Corp.) and his collaborators, particularly Trung Nguyen (now at
+Northwestern).  Support for AMD GPUs via HIP was added by Vsevolod Nikolskiy
+and coworkers at HSE University.
+
+The GPU package provides GPU versions of many pair styles and for
+parts of the :doc:`kspace_style pppm <kspace_style>` for long-range
+Coulombics.  It has the following general features:
 
 * It is designed to exploit common GPU hardware configurations where one
   or more GPUs are coupled to many cores of one or more multi-core CPUs,
@@ -24,8 +27,9 @@ It has the following general features:
   force vectors.
 * LAMMPS-specific code is in the GPU package.  It makes calls to a
   generic GPU library in the lib/gpu directory.  This library provides
-  NVIDIA support as well as more general OpenCL support, so that the
-  same functionality is supported on a variety of hardware.
+  either Nvidia support, AMD support, or more general OpenCL support
+  (for Nvidia GPUs, AMD GPUs, Intel GPUs, and multi-core CPUs).
+  so that the same functionality is supported on a variety of hardware.
 
 **Required hardware/software:**
 
@@ -45,12 +49,23 @@ to have the OpenCL headers and the (vendor neutral) OpenCL library installed.
 In OpenCL mode, the acceleration depends on having an `OpenCL Installable Client Driver (ICD) <https://www.khronos.org/news/permalink/opencl-installable-client-driver-icd-loader>`_
 installed. There can be multiple of them for the same or different hardware
 (GPUs, CPUs, Accelerators) installed at the same time. OpenCL refers to those
-as 'platforms'.  The GPU library will select the **first** suitable platform,
-but this can be overridden using the device option of the :doc:`package <package>`
+as 'platforms'.  The GPU library will try to auto-select the best suitable platform,
+but this can be overridden using the platform option of the :doc:`package <package>`
 command. run lammps/lib/gpu/ocl_get_devices to get a list of available
 platforms and devices with a suitable ICD available.
 
-To compute and use this package in HIP mode, you have to have the AMD ROCm
+To compile and use this package for Intel GPUs, OpenCL or the Intel oneAPI
+HPC Toolkit can be installed using linux package managers. The latter also
+provides optimized C++, MPI, and many other libraries and tools. See:
+
+* https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit/download.html
+
+If you do not have a discrete GPU card installed, this package can still provide
+significant speedups on some CPUs that include integrated GPUs. Additionally, for
+many macs, OpenCL is already included with the OS and Makefiles are available
+in the lib/gpu directory.
+
+To compile and use this package in HIP mode, you have to have the AMD ROCm
 software installed. Versions of ROCm older than 3.5 are currently deprecated
 by AMD.
 
@@ -75,10 +90,20 @@ automatically if you create more MPI tasks/node than there are
 GPUs/mode.  E.g. with 8 MPI tasks/node and 2 GPUs, each GPU will be
 shared by 4 MPI tasks.
 
+The GPU package also has limited support for OpenMP for both
+multi-threading and vectorization of routines that are run on the CPUs.
+This requires that the GPU library and LAMMPS are built with flags to
+enable OpenMP support (e.g. -fopenmp). Some styles for time integration
+are also available in the GPU package. These run completely on the CPUs
+in full double precision, but exploit multi-threading and vectorization
+for faster performance.
+
 Use the "-sf gpu" :doc:`command-line switch <Run_options>`, which will
 automatically append "gpu" to styles that support it.  Use the "-pk
 gpu Ng" :doc:`command-line switch <Run_options>` to set Ng = # of
-GPUs/node to use.
+GPUs/node to use. If Ng is 0, the number is selected automatically as
+the number of matching GPUs that have the highest number of compute
+cores.
 
 .. code-block:: bash
 
@@ -87,8 +112,8 @@ GPUs/node to use.
    mpirun -np 48 -ppn 12 lmp_machine -sf gpu -pk gpu 2 -in in.script   # ditto on 4 16-core nodes
 
 Note that if the "-sf gpu" switch is used, it also issues a default
-:doc:`package gpu 1 <package>` command, which sets the number of
-GPUs/node to 1.
+:doc:`package gpu 0 <package>` command, which will result in
+automatic selection of the number of GPUs to use.
 
 Using the "-pk" switch explicitly allows for setting of the number of
 GPUs/node to use and additional options.  Its syntax is the same as
@@ -138,6 +163,13 @@ Likewise, you should experiment with the precision setting for the GPU
 library to see if single or mixed precision will give accurate
 results, since they will typically be faster.
 
+MPI parallelism typically outperforms OpenMP parallelism, but in some
+cases using fewer MPI tasks and multiple OpenMP threads with the GPU
+package can give better performance. 3-body potentials can often perform
+better with multiple OMP threads because the inter-process communication
+is higher for these styles with the GPU package in order to allow
+deterministic results.
+
 **Guidelines for best performance:**
 
 * Using multiple MPI tasks per GPU will often give the best performance,
@@ -161,6 +193,12 @@ results, since they will typically be faster.
   :doc:`angle <angle_style>`, :doc:`dihedral <dihedral_style>`,
   :doc:`improper <improper_style>`, and :doc:`long-range <kspace_style>`
   calculations will not be included in the "Pair" time.
+* Since only part of the pppm kspace style is GPU accelerated, it
+  may be faster to only use GPU acceleration for Pair styles with
+  long-range electrostatics.  See the "pair/only" keyword of the
+  package command for a shortcut to do that.  The work between kspace
+  on the CPU and non-bonded interactions on the GPU can be balanced
+  through adjusting the coulomb cutoff without loss of accuracy.
 * When the *mode* setting for the package gpu command is force/neigh,
   the time for neighbor list calculations on the GPU will be added into
   the "Pair" time, not the "Neigh" time.  An additional breakdown of the

doc/src/Speed_kokkos.rst

@@ -26,6 +26,15 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
 GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
 produce an executable compatible with a specific hardware.
 
+.. admonition:: C++14 support
+      :class: note
+
+   Kokkos requires using a compiler that supports the c++14 standard. For
+   some compilers, it may be necessary to add a flag to enable c++14 support.
+   For example, the GNU compiler uses the -std=c++14 flag. For a list of
+   compilers that have been tested with the Kokkos library, see the Kokkos
+   `README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
+
 .. admonition:: NVIDIA CUDA support
    :class: note
 
@@ -38,14 +47,14 @@ produce an executable compatible with a specific hardware.
    :class: note
 
    Kokkos with CUDA currently implicitly assumes that the MPI library is
-   CUDA-aware. This is not always the case, especially when using
+   GPU-aware. This is not always the case, especially when using
    pre-compiled MPI libraries provided by a Linux distribution. This is
    not a problem when using only a single GPU with a single MPI
    rank. When running with multiple MPI ranks, you may see segmentation
-   faults without CUDA-aware MPI support. These can be avoided by adding
-   the flags :doc:`-pk kokkos cuda/aware off <Run_options>` to the
+   faults without GPU-aware MPI support. These can be avoided by adding
+   the flags :doc:`-pk kokkos gpu/aware off <Run_options>` to the
    LAMMPS command line or by using the command :doc:`package kokkos
-   cuda/aware off <package>` in the input file.
+   gpu/aware off <package>` in the input file.
 
 .. admonition:: AMD GPU support
    :class: note
@@ -242,8 +251,8 @@ case, also packing/unpacking communication buffers on the host may give
 speedup (see the KOKKOS :doc:`package <package>` command). Using CUDA MPS
 is recommended in this scenario.
 
-Using a CUDA-aware MPI library is highly recommended. CUDA-aware MPI use can be
-avoided by using :doc:`-pk kokkos cuda/aware no <package>`. As above for
+Using a GPU-aware MPI library is highly recommended. GPU-aware MPI use can be
+avoided by using :doc:`-pk kokkos gpu/aware off <package>`. As above for
 multi-core CPUs (and no GPU), if N is the number of physical cores/node,
 then the number of MPI tasks/node should not exceed N.
 

doc/src/Speed_packages.rst

@@ -16,7 +16,7 @@ These are the accelerator packages currently in LAMMPS, either as
 standard or user packages:
 
 +-----------------------------------------+-------------------------------------------------------+
-| :doc:`GPU Package <Speed_gpu>`          | for NVIDIA GPUs as well as OpenCL support             |
+| :doc:`GPU Package <Speed_gpu>`          | for GPUs via CUDA, OpenCL, or ROCm HIP                |
 +-----------------------------------------+-------------------------------------------------------+
 | :doc:`USER-INTEL Package <Speed_intel>` | for Intel CPUs and Intel Xeon Phi                     |
 +-----------------------------------------+-------------------------------------------------------+
@@ -43,7 +43,7 @@ three kinds of hardware, via the listed packages:
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
 | Many-core CPUs  | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>`, :doc:`USER-OMP <Speed_omp>`, :doc:`OPT <Speed_opt>` packages |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
-| NVIDIA/AMD GPUs | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                               |
+| GPUs            | :doc:`GPU <Speed_gpu>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                               |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
 | Intel Phi/AVX   | :doc:`USER-INTEL <Speed_intel>`, :doc:`KOKKOS <Speed_kokkos>` packages                                                      |
 +-----------------+-----------------------------------------------------------------------------------------------------------------------------+
@@ -154,8 +154,8 @@ Here is a brief summary of what the various packages provide.  Details
 are in the individual accelerator sections.
 
 * Styles with a "gpu" suffix are part of the GPU package and can be run
-  on NVIDIA or AMD GPUs.  The speed-up on a GPU depends on a variety of
-  factors, discussed in the accelerator sections.
+  on Intel, NVIDIA, or AMD GPUs.  The speed-up on a GPU depends on a
+  variety of factors, discussed in the accelerator sections.
 * Styles with an "intel" suffix are part of the USER-INTEL
   package. These styles support vectorized single and mixed precision
   calculations, in addition to full double precision.  In extreme cases,

doc/src/Tools.rst

@@ -93,6 +93,7 @@ Miscellaneous tools
    * :ref:`i-pi <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
+   * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -267,7 +268,7 @@ data file in the required format.
 See the header of the polarizer.py file for details.
 
 The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
-at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
+at ens-lyon.fr, alain.dequidt at uca.fr
 
 ----------
 
@@ -341,8 +342,7 @@ The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
 simulations using the USER-FEP package.
 
-The scripts were contributed by Agilio Padua (Universite Blaise
-Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
+The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr.
 
 See README file in the tools/fep directory.
 
@@ -642,6 +642,39 @@ 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

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/angle_gaussian.rst

@@ -0,0 +1,69 @@
+.. index:: angle_style gaussian
+
+angle_style gaussian command
+================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   angle_style gaussian
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   angle_style gaussian
+   angle_coeff 1 300.0 2 0.0128 0.375 80.0 0.0730 0.148 123.0
+
+Description
+"""""""""""
+
+The *gaussian* angle style uses the potential:
+
+.. math::
+
+   E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(\theta-\theta_{i})^2}{w_i^2})\right) \right)
+
+This analytical form is a suitable potential for obtaining
+mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano1>`
+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>`
+or :doc:`read_restart <read_restart>` commands:
+
+* T temperature at which the potential was derived
+* :math:`n` (integer >=1)
+* :math:`A_1` (-)
+* :math:`w_1` (-)
+* :math:`\theta_1` (degrees)
+* ...
+* :math:`A_n` (-)
+* :math:`w_n` (-)
+* :math:`\theta_n` (degrees)
+
+
+Restrictions
+""""""""""""
+
+This angle 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:`angle_coeff <angle_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Milano1:
+
+**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

doc/src/angle_style.rst

@@ -87,6 +87,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
 * :doc:`dipole <angle_dipole>` - angle that controls orientation of a point dipole
 * :doc:`fourier <angle_fourier>` - angle with multiple cosine terms
 * :doc:`fourier/simple <angle_fourier_simple>` - angle with a single cosine term
+* :doc:`gaussian <angle_gaussian>` - multicentered Gaussian-based angle potential
 * :doc:`harmonic <angle_harmonic>` - harmonic angle
 * :doc:`mm3 <angle_mm3>` - anharmonic angle
 * :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms

doc/src/atc_output.rst

@@ -14,7 +14,7 @@ Syntax
 * AtC fixID = ID of :doc:`fix atc <fix_atc>` instance
 * *output* or *output index* = name of the AtC sub-command
 * filename_prefix = prefix for data files (for *output*)
-* frequency = frequency of output in time-steps (for *output*)
+* frequency = frequency of output in timesteps (for *output*)
 * optional keywords for *output*:
 
   - text = creates text output of index, step and nodal variable values for unique nodes

doc/src/atom_style.rst

@@ -42,6 +42,7 @@ Examples
    atom_style hybrid charge body nparticle 2 5
    atom_style spin
    atom_style template myMols
+   atom_style hybrid template twomols charge
    atom_style tdpd 2
 
 Description
@@ -239,6 +240,8 @@ can save memory for systems comprised of a large number of small
 molecules, all of a single type (or small number of types).  See the
 paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
 can be advantageous for large-scale coarse-grained systems.
+The ``examples/template`` directory has a few demo inputs and examples
+showing the use of the *template* atom style versus *molecular*.
 
 .. note::
 

doc/src/balance.rst

@@ -78,14 +78,16 @@ or particles and thus indirectly the computational cost (load) more
 evenly across processors.  The load balancing is "static" in the sense
 that this command performs the balancing once, before or between
 simulations.  The processor sub-domains will then remain static during
-the subsequent run.  To perform "dynamic" balancing, see the :doc:`fix balance <fix_balance>` command, which can adjust processor
-sub-domain sizes and shapes on-the-fly during a :doc:`run <run>`.
+the subsequent run.  To perform "dynamic" balancing, see the :doc:`fix
+balance <fix_balance>` command, which can adjust processor sub-domain
+sizes and shapes on-the-fly during a :doc:`run <run>`.
 
 Load-balancing is typically most useful if the particles in the
 simulation box have a spatially-varying density distribution or when
 the computational cost varies significantly between different
 particles.  E.g. a model of a vapor/liquid interface, or a solid with
-an irregular-shaped geometry containing void regions, or :doc:`hybrid pair style simulations <pair_hybrid>` which combine pair styles with
+an irregular-shaped geometry containing void regions, or :doc:`hybrid
+pair style simulations <pair_hybrid>` which combine pair styles with
 different computational cost.  In these cases, the LAMMPS default of
 dividing the simulation box volume into a regular-spaced grid of 3d
 bricks, with one equal-volume sub-domain per processor, may assign
@@ -101,13 +103,14 @@ which typically induces a different number of atoms assigned to each
 processor.  Details on the various weighting options and examples for
 how they can be used are :ref:`given below <weighted_balance>`.
 
-Note that the :doc:`processors <processors>` command allows some control
-over how the box volume is split across processors.  Specifically, for
-a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
-Pz, subject to the constraint that Px \* Py \* Pz = P, the total number
-of processors.  This is sufficient to achieve good load-balance for
-some problems on some processor counts.  However, all the processor
-sub-domains will still have the same shape and same volume.
+Note that the :doc:`processors <processors>` command allows some
+control over how the box volume is split across processors.
+Specifically, for a Px by Py by Pz grid of processors, it allows
+choice of Px, Py, and Pz, subject to the constraint that Px \* Py \*
+Pz = P, the total number of processors.  This is sufficient to achieve
+good load-balance for some problems on some processor counts.
+However, all the processor sub-domains will still have the same shape
+and same volume.
 
 The requested load-balancing operation is only performed if the
 current "imbalance factor" in particles owned by each processor
@@ -170,12 +173,12 @@ The method used to perform a load balance is specified by one of the
 listed styles (or more in the case of *x*\ ,\ *y*\ ,\ *z*\ ), which are
 described in detail below.  There are 2 kinds of styles.
 
-The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which produce
-a logical 3d grid of processors.  They operate by changing the cutting
-planes (or lines) between processors in 3d (or 2d), to adjust the
-volume (area in 2d) assigned to each processor, as in the following 2d
-diagram where processor sub-domains are shown and particles are
-colored by the processor that owns them.
+The *x*\ , *y*\ , *z*\ , and *shift* styles are "grid" methods which
+produce a logical 3d grid of processors.  They operate by changing the
+cutting planes (or lines) between processors in 3d (or 2d), to adjust
+the volume (area in 2d) assigned to each processor, as in the
+following 2d diagram where processor sub-domains are shown and
+particles are colored by the processor that owns them.
 
 .. |balance1| image:: img/balance_uniform.jpg
    :width: 32%
@@ -190,20 +193,20 @@ colored by the processor that owns them.
 
 The leftmost diagram is the default partitioning of the simulation box
 across processors (one sub-box for each of 16 processors); the middle
-diagram is after a "grid" method has been applied.  The *rcb* style is a
-"tiling" method which does not produce a logical 3d grid of processors.
-Rather it tiles the simulation domain with rectangular sub-boxes of
-varying size and shape in an irregular fashion so as to have equal
-numbers of particles (or weight) in each sub-box, as in the rightmost
-diagram above.
+diagram is after a "grid" method has been applied.  The *rcb* style is
+a "tiling" method which does not produce a logical 3d grid of
+processors.  Rather it tiles the simulation domain with rectangular
+sub-boxes of varying size and shape in an irregular fashion so as to
+have equal numbers of particles (or weight) in each sub-box, as in the
+rightmost diagram above.
 
-The "grid" methods can be used with either of the
-:doc:`comm_style <comm_style>` command options, *brick* or *tiled*\ .  The
-"tiling" methods can only be used with :doc:`comm_style tiled <comm_style>`.  Note that it can be useful to use a "grid"
-method with :doc:`comm_style tiled <comm_style>` to return the domain
-partitioning to a logical 3d grid of processors so that "comm_style
-brick" can afterwords be specified for subsequent :doc:`run <run>`
-commands.
+The "grid" methods can be used with either of the :doc:`comm_style
+<comm_style>` command options, *brick* or *tiled*\ .  The "tiling"
+methods can only be used with :doc:`comm_style tiled <comm_style>`.
+Note that it can be useful to use a "grid" method with
+:doc:`comm_style tiled <comm_style>` to return the domain partitioning
+to a logical 3d grid of processors so that "comm_style brick" can
+afterwords be specified for subsequent :doc:`run <run>` commands.
 
 When a "grid" method is specified, the current domain partitioning can
 be either a logical 3d grid or a tiled partitioning.  In the former
@@ -280,6 +283,14 @@ information, so that they become closer together over time.  Thus as
 the recursion progresses, the count of particles on either side of the
 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
+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
+dimensions.
+
 Once the re-balancing is complete and final processor sub-domains
 assigned, particles are migrated to their new owning processor, and
 the balance procedure ends.
@@ -293,7 +304,7 @@ the balance procedure ends.
    *Niter* is specified as 10, the cutting plane will typically be
    positioned to 1 part in 1000 accuracy (relative to the perfect target
    position).  For *Niter* = 20, it will be accurate to 1 part in a
-   million.  Thus there is no need ot set *Niter* to a large value.
+   million.  Thus there is no need to set *Niter* to a large value.
    LAMMPS will check if the threshold accuracy is reached (in a
    dimension) is less iterations than *Niter* and exit early.  However,
    *Niter* should also not be set too small, since it will take roughly
@@ -416,7 +427,8 @@ The *time* weight style uses :doc:`timer data <timer>` to estimate
 weights.  It assigns the same weight to each particle owned by a
 processor based on the total computational time spent by that
 processor.  See details below on what time window is used.  It uses
-the same timing information as is used for the :doc:`MPI task timing breakdown <Run_output>`, namely, for sections *Pair*\ , *Bond*\ ,
+the same timing information as is used for the :doc:`MPI task timing
+breakdown <Run_output>`, namely, for sections *Pair*\ , *Bond*\ ,
 *Kspace*\ , and *Neigh*\ .  The time spent in those portions of the
 timestep are measured for each MPI rank, summed, then divided by the
 number of particles owned by that processor.  I.e. the weight is an

doc/src/bond_gaussian.rst

@@ -0,0 +1,70 @@
+.. index:: bond_style gaussian
+
+bond_style gaussian command
+================================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   bond_style gaussian
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   bond_style gaussian
+   bond_coeff 1 300.0 2 0.0128 0.375 3.37 0.0730 0.148 3.63
+
+Description
+"""""""""""
+
+The *gaussian* bond style uses the potential:
+
+.. math::
+
+   E = -k_B T ln\left(\sum_{i=1}^{n} \frac{A_i}{w_i \sqrt{\pi/2}} exp\left( \frac{-(r-r_{i})^2}{w_i^2})\right) \right)
+
+This analytical form is a suitable potential for obtaining
+mesoscale effective force fields which can reproduce target atomistic distributions :ref:`(Milano) <Milano0>`
+
+The following coefficients must be defined for each bond type via the
+:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
+the data file or restart files read by the :doc:`read_data <read_data>`
+or :doc:`read_restart <read_restart>` commands:
+
+* T temperature at which the potential was derived
+* :math:`n` (integer >=1)
+* :math:`A_1` (-)
+* :math:`w_1` (-)
+* :math:`r_1` (length)
+* ...
+* :math:`A_n` (-)
+* :math:`w_n` (-)
+* :math:`r_n` (length)
+
+
+Restrictions
+""""""""""""
+
+This bond 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:`bond_coeff <bond_coeff>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Milano0:
+
+**(Milano)** G. Milano, S. Goudeau, F. Mueller-Plathe, J. Polym. Sci. B Polym. Phys. 43, 871 (2005).

doc/src/bond_style.rst

@@ -87,6 +87,7 @@ accelerated styles exist.
 * :doc:`class2 <bond_class2>` - COMPASS (class 2) bond
 * :doc:`fene <bond_fene>` - FENE (finite-extensible non-linear elastic) bond
 * :doc:`fene/expand <bond_fene_expand>` - FENE bonds with variable size particles
+* :doc:`gaussian <bond_gaussian>` - multicentered Gaussian-based bond potential
 * :doc:`gromos <bond_gromos>` - GROMOS force field bond
 * :doc:`harmonic <bond_harmonic>` - harmonic bond
 * :doc:`harmonic/shift <bond_harmonic_shift>` - shifted harmonic bond

doc/src/change_box.rst

@@ -301,9 +301,13 @@ command.
 
 .. note::
 
-   Changing a periodic boundary to a non-periodic one will also
-   cause the image flag for that dimension to be reset to 0 for
-   all atoms.  LAMMPS will print a warning message, if that happens.
+   Changing a periodic boundary to a non-periodic one will also cause
+   the image flag for that dimension of all atoms to be reset to 0.
+   LAMMPS will print a warning message, if that happens.
+   Please note that this reset can lead to undesired changes when
+   atoms are involved in bonded interactions that straddle periodic
+   boundaries and thus the values of the image flag differs for those
+   atoms.
 
 ----------