Fix merge conflicts

.github/ISSUE_TEMPLATE/help_request.md

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

README

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

SECURITY.md

@@ -14,14 +14,14 @@ and tested by the LAMMPS developers, so it is easy to import bad
 behavior from calling functions in one of those libraries.
 
 Thus is is quite easy to crash LAMMPS through malicious input and do all
-kinds of filesystem manipulations.  And because of that LAMMPS should
+kinds of file system manipulations.  And because of that LAMMPS should
 **NEVER** be compiled or **run** as superuser, either from a "root" or
 "administrator" account directly or indirectly via "sudo" or "su".
 
 Therefore what could be seen as a security vulnerability is usually
-either a user mistake or a bug in the code.  Bugs can be reported in
+either a user mistake or a bug in the code.  Bugs can be reported in the
-the LAMMPS project
+LAMMPS project [issue tracker on
-[issue tracker on GitHub](https://github.com/lammps/lammps/issues).
+GitHub](https://github.com/lammps/lammps/issues).
 
 To mitigate issues with using homoglyphs or bidirectional reordering in
 unicode, which have been demonstrated as a vector to obfuscate and hide
@@ -30,10 +30,18 @@ for unicode characters and only all-ASCII source code is accepted.
 
 # Version Updates
 
-LAMMPS follows continuous release development model.  We aim to keep all
+LAMMPS follows continuous release development model.  We aim to keep to
-release versions (stable or patch) fully functional and employ a variety
+keep the development version (develop branch) always fully functional
-of automatic testing procedures to detect failures of existing
+and employ a variety of automatic testing procedures to detect failures
-functionality from adding new features before releases are made.  Thus
+of existing functionality from adding or modifying features.  Most of
-bugfixes and updates are only integrated into the current development
+those tests are run on pull requests *before* merging to the development
-branch and thus the next (patch) release and users are recommended to
+branch.  The develop branch is protected, so all changes *must* be
-update regularly.
+submitted as a pull request and thus cannot avoid the automated tests.
+
+Additional tests are run *after* merging.  Before releases are made
+*all* tests must have cleared.  Then a release tag is applied and the
+release branch fast-forwarded to that tag.  Bug fixes and updates are
+applied to the current development branch and thus will be available in
+the next (patch) release.  For stable releases, selected bug fixes are
+back-ported and occasionally published as update releases.  There are
+only updates to the latest stable release.

cmake/CMakeLists.txt

@@ -7,11 +7,20 @@ cmake_minimum_required(VERSION 3.10)
 if(POLICY CMP0074)
   cmake_policy(SET CMP0074 NEW)
 endif()
+# set policy to silence warnings about ignoring  ${CMAKE_REQUIRED_LIBRARIES} but use it
+if(POLICY CMP0075)
+  cmake_policy(SET CMP0075 NEW)
+endif()
 # set policy to silence warnings about missing executable permissions in
 # pythonx.y-config when cross-compiling. review occasionally if it may be set to NEW
 if(POLICY CMP0109)
   cmake_policy(SET CMP0109 OLD)
 endif()
+# set policy to silence warnings about timestamps of downloaded files. review occasionally if it may be set to NEW
+if(POLICY CMP0135)
+  cmake_policy(SET CMP0135 OLD)
+endif()
+
 ########################################
 
 project(lammps CXX)
@@ -100,7 +109,7 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
     if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
       set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
     else()
-      set(CMAKE_TUNE_DEFAULT "-xHost")
+      set(CMAKE_TUNE_DEFAULT "-xHost -fp-model fast=2 -no-prec-div -qoverride-limits -diag-disable=10441 -diag-disable=2196")
     endif()
   endif()
 endif()
@@ -381,9 +390,9 @@ pkg_depends(EXTRA-MOLECULE MOLECULE)
 
 # detect if we may enable OpenMP support by default
 set(BUILD_OMP_DEFAULT OFF)
-find_package(OpenMP QUIET)
+find_package(OpenMP COMPONENTS CXX QUIET)
-if(OpenMP_FOUND)
+if(OpenMP_CXX_FOUND)
-  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  check_omp_h_include()
   if(HAVE_OMP_H_INCLUDE)
     set(BUILD_OMP_DEFAULT ON)
   endif()
@@ -392,8 +401,8 @@ endif()
 option(BUILD_OMP "Build with OpenMP support" ${BUILD_OMP_DEFAULT})
 
 if(BUILD_OMP)
-  find_package(OpenMP REQUIRED)
+  find_package(OpenMP COMPONENTS CXX REQUIRED)
-  check_include_file_cxx(omp.h HAVE_OMP_H_INCLUDE)
+  check_omp_h_include()
   if(NOT HAVE_OMP_H_INCLUDE)
     message(FATAL_ERROR "Cannot find the 'omp.h' header file required for full OpenMP support")
   endif()
@@ -727,18 +736,17 @@ list(FIND LANGUAGES "Fortran" _index)
 if(_index GREATER -1)
   target_link_libraries(lammps PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
 endif()
-set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h compute.h dihedral.h domain.h error.h fix.h force.h group.h improper.h
+set(LAMMPS_CXX_HEADERS angle.h atom.h bond.h citeme.h comm.h command.h compute.h dihedral.h domain.h
-  input.h info.h kspace.h lammps.h lattice.h library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h
+  error.h exceptions.h fix.h force.h group.h improper.h input.h info.h kspace.h lammps.h lattice.h
-  pair.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
+  library.h lmppython.h lmptype.h memory.h modify.h neighbor.h neigh_list.h output.h pair.h
-if(LAMMPS_EXCEPTIONS)
+  platform.h pointers.h region.h timer.h universe.h update.h utils.h variable.h)
-  list(APPEND LAMMPS_CXX_HEADERS exceptions.h)
+set(LAMMPS_FMT_HEADERS core.h format.h)
-endif()
 
 set_target_properties(lammps PROPERTIES OUTPUT_NAME lammps${LAMMPS_MACHINE})
 set_target_properties(lammps PROPERTIES SOVERSION ${SOVERSION})
 set_target_properties(lammps PROPERTIES PREFIX "lib")
 target_include_directories(lammps PUBLIC $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/lammps>)
-file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps)
+file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt)
 foreach(_HEADER ${LAMMPS_CXX_HEADERS})
   add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/${_HEADER})
   add_custom_target(${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/${_HEADER})
@@ -747,6 +755,14 @@ foreach(_HEADER ${LAMMPS_CXX_HEADERS})
     install(FILES ${LAMMPS_SOURCE_DIR}/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps)
   endif()
 endforeach()
+foreach(_HEADER ${LAMMPS_FMT_HEADERS})
+  add_custom_command(OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} COMMAND ${CMAKE_COMMAND} -E copy_if_different ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER} DEPENDS ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER})
+  add_custom_target(fmt_${_HEADER} DEPENDS ${CMAKE_CURRENT_BINARY_DIR}/includes/lammps/fmt/${_HEADER})
+  add_dependencies(lammps fmt_${_HEADER})
+  if(BUILD_SHARED_LIBS)
+    install(FILES ${LAMMPS_SOURCE_DIR}/fmt/${_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/lammps/fmt)
+  endif()
+endforeach()
 target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/includes>)
 add_library(LAMMPS::lammps ALIAS lammps)
 get_target_property(LAMMPS_DEFINES lammps INTERFACE_COMPILE_DEFINITIONS)
@@ -854,8 +870,11 @@ if(BUILD_SHARED_LIBS OR PKG_PYTHON)
     find_package(Python COMPONENTS Interpreter)
   endif()
   if(Python_EXECUTABLE)
-    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python)
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/lib)
-    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})")
+    file(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/python/src)
+    file(COPY ${LAMMPS_SOURCE_DIR}/version.h  DESTINATION ${CMAKE_BINARY_DIR}/python/src)
+    file(COPY ${LAMMPS_PYTHON_DIR}/README ${LAMMPS_PYTHON_DIR}/pyproject.toml ${LAMMPS_PYTHON_DIR}/setup.py ${LAMMPS_PYTHON_DIR}/lammps  DESTINATION ${CMAKE_BINARY_DIR}/python/lib)
+    install(CODE "if(\"\$ENV{DESTDIR}\" STREQUAL \"\")\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX})\n else()\n execute_process(COMMAND ${Python_EXECUTABLE} -m pip install -v ${CMAKE_BINARY_DIR}/python/lib --prefix=${CMAKE_INSTALL_PREFIX} --root=\$ENV{DESTDIR})\n endif()")
   endif()
 endif()
 
@@ -966,9 +985,6 @@ if(PKG_GPU)
   endif()
   message(STATUS "GPU precision:            ${GPU_PREC}")
 endif()
-if(PKG_KOKKOS)
-  message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
-endif()
 if(PKG_KSPACE)
   message(STATUS "<<< FFT settings >>>
 -- Primary FFT lib:  ${FFT}")

cmake/Modules/FindClangFormat.cmake

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

cmake/Modules/FindCythonize.cmake

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

cmake/Modules/LAMMPSUtils.cmake

@@ -24,6 +24,21 @@ function(validate_option name values)
     endif()
 endfunction(validate_option)
 
+# helper function to check for usable omp.h header
+function(check_omp_h_include)
+  find_package(OpenMP COMPONENTS CXX QUIET)
+  if(OpenMP_CXX_FOUND)
+    set(CMAKE_REQUIRED_FLAGS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_INCLUDES ${OpenMP_CXX_INCLUDE_DIRS})
+    set(CMAKE_REQUIRED_LINK_OPTIONS ${OpenMP_CXX_FLAGS})
+    set(CMAKE_REQUIRED_LIBRARIES ${OpenMP_CXX_LIBRARIES})
+    check_include_file_cxx(omp.h _have_omp_h)
+  else()
+    set(_have_omp_h FALSE)
+  endif()
+  set(HAVE_OMP_H_INCLUDE ${_have_omp_h} PARENT_SCOPE)
+endfunction()
+
 # helper function for getting the most recently modified file or folder from a glob pattern
 function(get_newest_file path variable)
   file(GLOB _dirs ${path})

cmake/Modules/Packages/KOKKOS.cmake

@@ -15,8 +15,9 @@ if(Kokkos_ENABLE_OPENMP)
   if(NOT BUILD_OMP)
     message(FATAL_ERROR "Must enable BUILD_OMP with Kokkos_ENABLE_OPENMP")
   else()
-    if(LAMMPS_OMP_COMPAT_LEVEL LESS 4)
+    # NVHPC does not seem to provide a detectable OpenMP version, but is far beyond version 3.1
-      message(FATAL_ERROR "Compiler must support OpenMP 4.0 or later with Kokkos_ENABLE_OPENMP")
+    if((OpenMP_CXX_VERSION VERSION_LESS 3.1) AND NOT (CMAKE_CXX_COMPILER_ID STREQUAL "NVHPC"))
+      message(FATAL_ERROR "Compiler must support OpenMP 3.1 or later with Kokkos_ENABLE_OPENMP")
     endif()
   endif()
 endif()
@@ -47,8 +48,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_CXX_EXTENSIONS=${CMAKE_CXX_EXTENSIONS}")
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
-  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.6.01.tar.gz" CACHE STRING "URL for KOKKOS tarball")
+  set(KOKKOS_URL "https://github.com/kokkos/kokkos/archive/3.7.00.tar.gz" CACHE STRING "URL for KOKKOS tarball")
-  set(KOKKOS_MD5 "0ec97fc0c356dd65bd2487defe81a7bf" CACHE STRING "MD5 checksum of KOKKOS tarball")
+  set(KOKKOS_MD5 "84991eca9f066383abe119a5bc7a11c4" CACHE STRING "MD5 checksum of KOKKOS tarball")
   mark_as_advanced(KOKKOS_URL)
   mark_as_advanced(KOKKOS_MD5)
   ExternalProject_Add(kokkos_build
@@ -72,7 +73,7 @@ if(DOWNLOAD_KOKKOS)
   add_dependencies(LAMMPS::KOKKOSCORE kokkos_build)
   add_dependencies(LAMMPS::KOKKOSCONTAINERS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.6.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.7.00 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
   target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
@@ -138,6 +139,12 @@ if(PKG_KSPACE)
   endif()
 endif()
 
+if(PKG_ML-IAP)
+  list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/mliap_data_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_descriptor_so3_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_model_linear_kokkos.cpp
+                                 ${KOKKOS_PKG_SOURCES_DIR}/mliap_so3_kokkos.cpp)
+endif()
 
 if(PKG_PHONON)
   list(APPEND KOKKOS_PKG_SOURCES ${KOKKOS_PKG_SOURCES_DIR}/dynamical_matrix_kokkos.cpp)

cmake/Modules/Packages/MDI.cmake

@@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
 
 if(DOWNLOAD_MDI)
   message(STATUS "MDI download requested - we will build our own")
-  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.11.tar.gz" CACHE STRING "URL for MDI tarball")
+  set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.12.tar.gz" CACHE STRING "URL for MDI tarball")
-  set(MDI_MD5 "3791fe5081405c14aac07d4687f1cc58" CACHE STRING "MD5 checksum for MDI tarball")
+  set(MDI_MD5 "7a222353ae8e03961d5365e6cd48baee" CACHE STRING "MD5 checksum for MDI tarball")
   mark_as_advanced(MDI_URL)
   mark_as_advanced(MDI_MD5)
   enable_language(C)
@@ -49,6 +49,14 @@ if(DOWNLOAD_MDI)
       set(MDI_USE_PYTHON_PLUGINS ON)
     endif()
   endif()
+  # python plugins are not supported and thus must be always off on Windows
+  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
+    unset(Python_Development_FOUND)
+    set(MDI_USE_PYTHON_PLUGINS OFF)
+    if(CMAKE_CROSSCOMPILING)
+      set(CMAKE_INSTALL_LIBDIR lib)
+    endif()
+  endif()
 
   # download/ build MDI library
   # always build static library with -fpic
@@ -57,8 +65,9 @@ if(DOWNLOAD_MDI)
   ExternalProject_Add(mdi_build
     URL     ${MDI_URL}
     URL_MD5 ${MDI_MD5}
+    PREFIX ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     CMAKE_ARGS
-    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+    -DCMAKE_INSTALL_PREFIX=${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext
     -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
     -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
     -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
@@ -70,23 +79,23 @@ if(DOWNLOAD_MDI)
     -Dplugins=ON
     -Dpython_plugins=${MDI_USE_PYTHON_PLUGINS}
     UPDATE_COMMAND ""
-    INSTALL_COMMAND ""
+    INSTALL_COMMAND ${CMAKE_COMMAND} --build ${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/src/mdi_build-build --target install
-    BUILD_BYPRODUCTS "<BINARY_DIR>/MDI_Library/libmdi.a"
+    BUILD_BYPRODUCTS "${CMAKE_CURRENT_BINARY_DIR}/mdi_build_ext/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
     )
 
   # where is the compiled library?
-  ExternalProject_get_property(mdi_build BINARY_DIR)
+  ExternalProject_get_property(mdi_build PREFIX)
-  set(MDI_BINARY_DIR "${BINARY_DIR}/MDI_Library")
   # workaround for older CMake versions
-  file(MAKE_DIRECTORY ${MDI_BINARY_DIR})
+  file(MAKE_DIRECTORY ${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi)
+  file(MAKE_DIRECTORY ${PREFIX}/include/mdi)
 
   # create imported target for the MDI library
   add_library(LAMMPS::MDI UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::MDI mdi_build)
   set_target_properties(LAMMPS::MDI PROPERTIES
-    IMPORTED_LOCATION "${MDI_BINARY_DIR}/libmdi.a"
+    IMPORTED_LOCATION "${PREFIX}/${CMAKE_INSTALL_LIBDIR}/mdi/${CMAKE_STATIC_LIBRARY_PREFIX}mdi${CMAKE_STATIC_LIBRARY_SUFFIX}"
-    INTERFACE_INCLUDE_DIRECTORIES ${MDI_BINARY_DIR}
+    INTERFACE_INCLUDE_DIRECTORIES ${PREFIX}/include/mdi
-    )
+  )
 
   set(MDI_DEP_LIBS "")
   # if compiling with python plugins we need

cmake/Modules/Packages/ML-IAP.cmake

@@ -2,7 +2,13 @@
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
   find_package(Cythonize QUIET)
-  if(Cythonize_FOUND)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy QUIET)
+  else()
+    # assume we have NumPy
+    set(Python_NumPy_FOUND ON)
+  endif()
+  if(Cythonize_FOUND AND Python_NumPy_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
 endif()
@@ -11,6 +17,9 @@ option(MLIAP_ENABLE_PYTHON "Build ML-IAP package with Python support" ${MLIAP_EN
 
 if(MLIAP_ENABLE_PYTHON)
   find_package(Cythonize REQUIRED)
+  if (CMAKE_VERSION VERSION_GREATER_EQUAL 3.14)
+    find_package(Python COMPONENTS NumPy REQUIRED)
+  endif()
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in ML-IAP")
   endif()
@@ -25,16 +34,18 @@ if(MLIAP_ENABLE_PYTHON)
   endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
-  set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/mliap_model_python_couple.pyx)
+  file(GLOB MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/ML-IAP/*.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
+  foreach(MLIAP_CYTHON_FILE ${MLIAP_CYTHON_SRC})
-          COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_SRC} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    get_filename_component(MLIAP_CYTHON_BASE ${MLIAP_CYTHON_FILE} NAME_WE)
-          COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
+    add_custom_command(OUTPUT  ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.h
-          WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            COMMAND            ${CMAKE_COMMAND} -E copy_if_different ${MLIAP_CYTHON_FILE} ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          MAIN_DEPENDENCY    ${MLIAP_CYTHON_SRC}
+            COMMAND            ${Cythonize_EXECUTABLE} -3 ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.pyx
-          COMMENT "Generating C++ sources with cythonize...")
+            WORKING_DIRECTORY  ${MLIAP_BINARY_DIR}
+            MAIN_DEPENDENCY    ${MLIAP_CYTHON_FILE}
+            COMMENT "Generating C++ sources with cythonize...")
+    target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
+  endforeach()
   target_compile_definitions(lammps PRIVATE -DMLIAP_PYTHON)
-  target_sources(lammps PRIVATE ${MLIAP_BINARY_DIR}/${MLIAP_CYTHON_BASE}.cpp)
   target_include_directories(lammps PRIVATE ${MLIAP_BINARY_DIR})
 endif()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.fix2.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.10.15.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "32394d799bc282bb57696c78c456e64f" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_MD5 "848ad6a6cc79fa82745927001fb1c9b5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
@@ -15,23 +15,9 @@ execute_process(
 )
 get_newest_file(${CMAKE_BINARY_DIR}/lammps-user-pace-* lib-pace)
 
-# enforce building libyaml-cpp as static library and turn off optional features
+add_subdirectory(${lib-pace} build-pace)
-set(YAML_BUILD_SHARED_LIBS OFF)
-set(YAML_CPP_BUILD_CONTRIB OFF)
-set(YAML_CPP_BUILD_TOOLS OFF)
-add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
-set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
-
-file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
-file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
-list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
-
-add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
 
-
-target_link_libraries(pace PRIVATE yaml-cpp-pace)
 if(CMAKE_PROJECT_NAME STREQUAL "lammps")
   target_link_libraries(lammps PRIVATE pace)
 endif()

cmake/Modules/Packages/ML-QUIP.cmake

@@ -58,12 +58,12 @@ if(DOWNLOAD_QUIP)
     BUILD_COMMAND env QUIP_ARCH=lammps make libquip
     INSTALL_COMMAND ""
     BUILD_IN_SOURCE YES
-    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/libquip.a
+    BUILD_BYPRODUCTS <SOURCE_DIR>/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}
   )
   ExternalProject_get_property(quip_build SOURCE_DIR)
   add_library(LAMMPS::QUIP UNKNOWN IMPORTED)
   set_target_properties(LAMMPS::QUIP PROPERTIES
-    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/libquip.a"
+    IMPORTED_LOCATION "${SOURCE_DIR}/build/lammps/${CMAKE_STATIC_LIBRARY_PREFIX}quip${CMAKE_STATIC_LIBRARY_SUFFIX}"
     INTERFACE_LINK_LIBRARIES "${LAPACK_LIBRARIES}")
   target_link_libraries(lammps PRIVATE LAMMPS::QUIP)
   add_dependencies(LAMMPS::QUIP quip_build)

cmake/Modules/Packages/PLUMED.cmake

@@ -47,15 +47,15 @@ if(DOWNLOAD_PLUMED)
   endif()
   message(STATUS "PLUMED download requested - we will build our own")
   if(PLUMED_MODE STREQUAL "STATIC")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX};<INSTALL_DIR>/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
+    set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_PREFIX}")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.8.1/plumed-src-2.8.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_MD5 "6bfe72ebdae63dc38a9ca27d9b0e08f8" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
@@ -78,12 +78,12 @@ if(DOWNLOAD_PLUMED)
   add_library(LAMMPS::PLUMED UNKNOWN IMPORTED)
   add_dependencies(LAMMPS::PLUMED plumed_build)
   if(PLUMED_MODE STREQUAL "STATIC")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed.a INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumed${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${PLUMED_LINK_LIBS};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "SHARED")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumed${CMAKE_SHARED_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX};${CMAKE_DL_LIBS}")
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${INSTALL_DIR}/lib/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/libplumedWrapper.a INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES IMPORTED_LOCATION ${INSTALL_DIR}/lib/${CMAKE_STATIC_LIBRARY_PREFIX}plumedWrapper${CMAKE_STATIC_LIBRARY_SUFFIX} INTERFACE_LINK_LIBRARIES "${CMAKE_DL_LIBS}")
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_INCLUDE_DIRECTORIES ${INSTALL_DIR}/include)
   file(MAKE_DIRECTORY ${INSTALL_DIR}/include)
@@ -96,7 +96,7 @@ else()
   elseif(PLUMED_MODE STREQUAL "SHARED")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.shared)
   elseif(PLUMED_MODE STREQUAL "RUNTIME")
-    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/libplumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
+    set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_COMPILE_DEFINITIONS "__PLUMED_DEFAULT_KERNEL=${PLUMED_LIBDIR}/${CMAKE_SHARED_LIBRARY_PREFIX}plumedKernel${CMAKE_SHARED_LIBRARY_SUFFIX}")
     include(${PLUMED_LIBDIR}/plumed/src/lib/Plumed.cmake.runtime)
   endif()
   set_target_properties(LAMMPS::PLUMED PROPERTIES INTERFACE_LINK_LIBRARIES "${PLUMED_LOAD}")

cmake/Modules/Packages/VTK.cmake

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

cmake/presets/clang.cmake

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

cmake/presets/gcc.cmake

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

cmake/presets/intel.cmake

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

cmake/presets/nvhpc.cmake

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

cmake/presets/oneapi.cmake

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

cmake/presets/pedantic.cmake

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

cmake/presets/pgi.cmake

@@ -7,10 +7,3 @@ 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

@@ -38,16 +38,14 @@ endif
 # override settings for PIP commands
 # PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
-#SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
-
 # temporarily disable caching so that the hack for the sphinx-tabs extensions to get proper non-html output works
-SPHINXEXTRA = -E -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
+SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())')
 
 # grab list of sources from doxygen config file.
 # we only want to use explicitly listed files.
 DOXYFILES      = $(shell sed -n -e 's/\#.*$$//' -e '/^ *INPUT \+=/,/^[A-Z_]\+ \+=/p' doxygen/Doxyfile.in | sed -e 's/@LAMMPS_SOURCE_DIR@/..\/src/g' -e 's/\\//g' -e 's/ \+/ /' -e 's/[A-Z_]\+ \+= *\(YES\|NO\|\)//') 
 
-.PHONY: help clean-all clean clean-spelling epub mobi rst html pdf spelling anchor_check style_check char_check xmlgen fasthtml
+.PHONY: help clean-all clean clean-spelling epub mobi html pdf spelling anchor_check style_check char_check xmlgen fasthtml
 
 # ------------------------------------------
 
@@ -89,6 +87,8 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build -E $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) html ;\
 		ln -sf Manual.html html/index.html;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
@@ -114,7 +114,9 @@ fasthtml: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@mkdir -p fasthtml
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build -j 4 -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
+		touch $(RSTDIR)/Fortran.rst ;\
+		sphinx-build $(SPHINXEXTRA) -b html -c $(SPHINXCONFIG) -d $(BUILDDIR)/fasthtml/doctrees $(RSTDIR) fasthtml ;\
 		deactivate ;\
 	)
 	@rm -rf fasthtml/_sources
@@ -144,6 +146,8 @@ epub: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@cp src/JPG/*.* epub/JPG
 	@(\
 		. $(VENV)/bin/activate ;\
+		sphinx-build -E $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build $(SPHINXEXTRA) -b epub -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) epub ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		deactivate ;\
@@ -163,7 +167,9 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
-		sphinx-build $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		touch $(RSTDIR)/Fortran.rst ;\
+		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\
 		rst_anchor_check src/*.rst ;\

doc/lammps.1

@@ -1,7 +1,7 @@
-.TH LAMMPS "1" "15 September 2022" "2022-9-15"
+.TH LAMMPS "1" "3 November 2022" "2022-11-3"
 .SH NAME
 .B LAMMPS
-\- Molecular Dynamics Simulator.  Version 15 September 2022
+\- Molecular Dynamics Simulator.  Version 3 November 2022
 
 .SH SYNOPSIS
 .B lmp

doc/src/Bibliography.rst

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

doc/src/Build_development.rst

@@ -140,13 +140,23 @@ of the LAMMPS project on GitHub.
 The unit testing facility is integrated into the CMake build process
 of the LAMMPS source code distribution itself.  It can be enabled by
 setting ``-D ENABLE_TESTING=on`` during the CMake configuration step.
-It requires the `YAML <http://pyyaml.org/>`_ library and development
+It requires the `YAML <https://pyyaml.org/>`_ library and development
 headers (if those are not found locally a recent version will be
 downloaded and compiled along with LAMMPS and the test program) to
 compile and will download and compile a specific recent version of the
 `Googletest <https://github.com/google/googletest/>`_ C++ test framework
 for implementing the tests.
 
+.. admonition:: Software version requirements for testing
+   :class: note
+
+   The compiler and library version requirements for the testing
+   framework are more strict than for the main part of LAMMPS.  For
+   example the default GNU C++ and Fortran compilers of RHEL/CentOS 7.x
+   (version 4.8.x) are not sufficient.  The CMake configuration will try
+   to detect compatible versions and either skip incompatible tests or
+   stop with an error.
+
 After compilation is complete, the unit testing is started in the build
 folder using the ``ctest`` command, which is part of the CMake software.
 The output of this command will be looking something like this::

doc/src/Build_extras.rst

@@ -234,7 +234,7 @@ LAMMPS code.  This also applies to the ``-DLAMMPS_BIGBIG``\ ,
 Makefile you use.
 
 You can also build the library in one step from the ``lammps/src`` dir,
-using a command like these, which simply invoke the ``lib/gpu/Install.py``
+using a command like these, which simply invokes the ``lib/gpu/Install.py``
 script with the specified args:
 
 .. code-block:: bash
@@ -314,7 +314,7 @@ detailed information is available at:
 
 In addition to installing the KIM API, it is also necessary to install the
 library of KIM models (interatomic potentials).
-See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_ to
+See `Obtaining KIM Models <https://openkim.org/doc/usage/obtaining-models>`_ to
 learn how to install a pre-build binary of the OpenKIM Repository of Models.
 See the list of all KIM models here: https://openkim.org/browse/models
 
@@ -350,7 +350,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
       You can download and build the KIM library manually if you prefer;
       follow the instructions in ``lib/kim/README``.  You can also do
       this in one step from the lammps/src directory, using a command like
-      these, which simply invoke the ``lib/kim/Install.py`` script with
+      these, which simply invokes the ``lib/kim/Install.py`` script with
       the specified args.
 
       .. code-block:: bash
@@ -432,7 +432,7 @@ Enabling the extra unit tests have some requirements,
   ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
   ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
   ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
-  See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
+  See `Obtaining KIM Models <https://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>`_
@@ -483,6 +483,9 @@ They must be specified in uppercase.
    *  - **Arch-ID**
       - **HOST or GPU**
       - **Description**
+   *  - NATIVE
+      - HOST
+      - Local machine
    *  - AMDAVX
       - HOST
       - AMD 64-bit x86 CPU (AVX 1)
@@ -522,9 +525,21 @@ They must be specified in uppercase.
    *  - BDW
       - HOST
       - Intel Broadwell Xeon E-class CPU (AVX 2 + transactional mem)
+   *  - SKL
+      - HOST
+      - Intel Skylake Client CPU
    *  - SKX
       - HOST
-      - Intel Sky Lake Xeon E-class HPC CPU (AVX512 + transactional mem)
+      - Intel Skylake Xeon Server CPU (AVX512)
+   *  - ICL
+      - HOST
+      - Intel Ice Lake Client CPU (AVX512)
+   *  - ICX
+      - HOST
+      - Intel Ice Lake Xeon Server CPU (AVX512)
+   *  - SPR
+      - HOST
+      - Intel Sapphire Rapids Xeon Server CPU (AVX512)
    *  - KNC
       - HOST
       - Intel Knights Corner Xeon Phi
@@ -596,7 +611,10 @@ They must be specified in uppercase.
       - AMD GPU MI100 GFX908
    *  - VEGA90A
       - GPU
-      - AMD GPU
+      - AMD GPU MI200 GFX90A
+   *  - INTEL_GEN
+      - GPU
+      - SPIR64-based devices, e.g. Intel GPUs, using JIT
    *  - INTEL_DG1
       - GPU
       - Intel Iris XeMAX GPU
@@ -611,9 +629,12 @@ They must be specified in uppercase.
       - Intel GPU Gen12LP
    *  - INTEL_XEHP
       - GPU
-      - Intel GPUs Xe-HP
+      - Intel GPU Xe-HP
+   *  - INTEL_PVC
+      - GPU
+      - Intel GPU Ponte Vecchio
 
-This list was last updated for version 3.5.0 of the Kokkos library.
+This list was last updated for version 3.7.0 of the Kokkos library.
 
 .. tabs::
 
@@ -933,7 +954,7 @@ more details.
       You can download and build the MS-CG library manually if you
       prefer; follow the instructions in ``lib/mscg/README``\ .  You can
       also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/mscg/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -990,7 +1011,7 @@ POEMS package
       ``lib/poems``\ .  You can do this manually if you prefer; follow
       the instructions in ``lib/poems/README``\ .  You can also do it in
       one step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/poems/Install.py`` script with the
+      which simply invokes the ``lib/poems/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1053,7 +1074,7 @@ VORONOI package
 -----------------------------
 
 To build with this package, you must download and build the
-`Voro++ library <http://math.lbl.gov/voro++>`_ or install a
+`Voro++ library <https://math.lbl.gov/voro++>`_ or install a
 binary package provided by your operating system.
 
 .. tabs::
@@ -1079,7 +1100,7 @@ binary package provided by your operating system.
       You can download and build the Voro++ library manually if you
       prefer; follow the instructions in ``lib/voronoi/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/voronoi/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -1158,7 +1179,7 @@ The ATC package requires the MANYBODY package also be installed.
       ``lib/atc``.  You can do this manually if you prefer; follow the
       instructions in ``lib/atc/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/atc/Install.py`` script with the
+      which simply invokes the ``lib/atc/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1209,7 +1230,7 @@ AWPMD package
       ``lib/awpmd``.  You can do this manually if you prefer; follow the
       instructions in ``lib/awpmd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/awpmd/Install.py`` script with the
+      which simply invokes the ``lib/awpmd/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1272,7 +1293,7 @@ be built for the most part with all major versions of the C++ language.
 
       In general, it is safer to use build setting consistent with the
       rest of LAMMPS.  This is best carried out from the LAMMPS src
-      directory using a command like these, which simply invoke the
+      directory using a command like these, which simply invokes the
       ``lib/colvars/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -1313,20 +1334,30 @@ This package depends on the KSPACE package.
 
    .. tab:: CMake build
 
-      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and ``-D
+      No additional settings are needed besides ``-D PKG_KSPACE=yes`` and
-      PKG_ELECTRODE=yes``.
+      ``-D PKG_ELECTRODE=yes``.
 
    .. tab:: Traditional make
 
-      The package is activated with ``make yes-KSPACE`` and ``make
+      Before building LAMMPS, you must configure the ELECTRODE support
-      yes-ELECTRODE``
+      libraries and settings in ``lib/electrode``.  You can do this
+      manually, if you prefer, or do it in one step from the
+      ``lammps/src`` dir, using a command like these, which simply
+      invokes the ``lib/electrode/Install.py`` script with the specified
+      args:
+
+      .. code-block:: bash
+
+         $ make lib-electrode                   # print help message
+         $ make lib-electrode args="-m serial"  # build with GNU g++ compiler and MPI STUBS (settings as with "make serial")
+         $ make lib-electrode args="-m mpi"     # build with default MPI compiler (settings as with "make mpi")
 
 
-      Note that the ``Makefile.lammps`` file has settings for the BLAS and
+      Note that the ``Makefile.lammps`` file has settings for the BLAS
-      LAPACK linear algebra libraries.  As explained in ``lib/awpmd/README``
+      and LAPACK linear algebra libraries.  These can either exist on
-      these can either exist on your system, or you can use the files provided
+      your system, or you can use the files provided in ``lib/linalg``.
-      in ``lib/linalg``.  In the latter case you also need to build the library
+      In the latter case you also need to build the library in
-      in ``lib/linalg`` with a command like these:
+      ``lib/linalg`` with a command like these:
 
       .. code-block:: bash
 
@@ -1335,6 +1366,9 @@ This package depends on the KSPACE package.
          $ make lib-linalg args="-m mpi"       # build with default MPI Fortran compiler (settings as with "make mpi")
          $ make lib-linalg args="-m gfortran"  # build with GNU Fortran compiler
 
+      The package itself is activated with ``make yes-KSPACE`` and
+      ``make yes-ELECTRODE``
+
 ----------
 
 .. _ml-pace:
@@ -1534,7 +1568,7 @@ the HDF5 library.
       ``lib/h5md``.  You can do this manually if you prefer; follow the
       instructions in ``lib/h5md/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/h5md/Install.py`` script with the
+      which simply invokes the ``lib/h5md/Install.py`` script with the
       specified args:
 
       .. code-block:: bash
@@ -1590,7 +1624,7 @@ details please see ``lib/hdnnp/README`` and the `n2p2 build documentation
       You can download and build the *n2p2* library manually if you prefer;
       follow the instructions in ``lib/hdnnp/README``\ . You can also do it in
       one step from the ``lammps/src`` dir, using a command like these, which
-      simply invoke the ``lib/hdnnp/Install.py`` script with the specified args:
+      simply invokes the ``lib/hdnnp/Install.py`` script with the specified args:
 
       .. code-block:: bash
 
@@ -1727,7 +1761,7 @@ they will be downloaded the first time this package is installed.
       Before building LAMMPS, you must build the *mesont* library in
       ``lib/mesont``\ .  You can also do it in one step from the
       ``lammps/src`` dir, using a command like these, which simply
-      invoke the ``lib/mesont/Install.py`` script with the specified
+      invokes the ``lib/mesont/Install.py`` script with the specified
       args:
 
       .. code-block:: bash
@@ -1896,7 +1930,7 @@ verified to work in February 2020 with Quantum Espresso versions 6.3 to
       ``lib/qmmm``.  You can do this manually if you prefer; follow the
       first two steps explained in ``lib/qmmm/README``.  You can also do
       it in one step from the ``lammps/src`` dir, using a command like
-      these, which simply invoke the ``lib/qmmm/Install.py`` script with
+      these, which simply invokes the ``lib/qmmm/Install.py`` script with
       the specified args:
 
       .. code-block:: bash
@@ -2004,7 +2038,7 @@ To build with this package, you must download and build the
       You can download and build the ScaFaCoS library manually if you
       prefer; follow the instructions in ``lib/scafacos/README``.  You
       can also do it in one step from the ``lammps/src`` dir, using a
-      command like these, which simply invoke the
+      command like these, which simply invokes the
       ``lib/scafacos/Install.py`` script with the specified args:
 
       .. code-block:: bash
@@ -2048,7 +2082,7 @@ Eigen3 is a template library, so you do not need to build it.
       You can download the Eigen3 library manually if you prefer; follow
       the instructions in ``lib/smd/README``.  You can also do it in one
       step from the ``lammps/src`` dir, using a command like these,
-      which simply invoke the ``lib/smd/Install.py`` script with the
+      which simply invokes the ``lib/smd/Install.py`` script with the
       specified args:
 
       .. code-block:: bash

doc/src/Build_manual.rst

@@ -176,7 +176,7 @@ math expressions transparently into embedded images.
 For converting the generated ePUB file to a MOBI format file (for e-book
 readers, like Kindle, that cannot read ePUB), you also need to have the
 ``ebook-convert`` tool from the "calibre" software
-installed. `http://calibre-ebook.com/ <http://calibre-ebook.com/>`_
+installed. `https://calibre-ebook.com/ <https://calibre-ebook.com/>`_
 Typing ``make mobi`` will first create the ePUB file and then convert
 it.  On the Kindle readers in particular, you also have support for PDF
 files, so you could download and view the PDF version as an alternative.
@@ -216,9 +216,20 @@ be multiple tests run automatically:
 - A test that only standard, printable ASCII text characters are used.
   This runs the command ``env LC_ALL=C grep -n '[^ -~]' src/*.rst`` and
   thus prints all offending lines with filename and line number
-  prepended to the screen.  Special characters like the Angstrom
+  prepended to the screen.  Special characters like Greek letters
-  :math:`\mathrm{\mathring{A}}` should be typeset with embedded math
+  (:math:`\alpha~~\sigma~~\epsilon`), super- or subscripts
-  (like this ``:math:`\mathrm{\mathring{A}}```\ ).
+  (:math:`x^2~~\mathrm{U}_{LJ}`), mathematical expressions
+  (:math:`\frac{1}{2}\mathrm{N}~~x\to\infty`), or the Angstrom symbol
+  (:math:`\AA`) should be typeset with embedded LaTeX (like this
+  ``:math:`\alpha \sigma \epsilon```, ``:math:`x^2 \mathrm{E}_{LJ}```,
+  ``:math:`\frac{1}{2}\mathrm{N} x\to\infty```, or ``:math:`\AA```\ ).
+
+- Embedded LaTeX is rendered in HTML output with `MathJax
+  <https://www.mathjax.org/>`_ and in PDF output by passing the embedded
+  text to LaTeX.  Some care has to be taken, though, since there are
+  limitations which macros and features can be used in either mode, so
+  it is recommended to always check whether any new or changed
+  documentation does translate and render correctly with either output.
 
 - A test whether all styles are documented and listed in their
   respective overview pages.  A typical output with warnings looks like this:

doc/src/Build_settings.rst

@@ -111,26 +111,25 @@ LAMMPS can use them if they are available on your system.
       files in its default search path.  You must specify ``FFT_LIB``
       with the appropriate FFT libraries to include in the link.
 
-The `KISS FFT library <http://kissfft.sf.net>`_ is included in the LAMMPS
+The `KISS FFT library <https://github.com/mborgerding/kissfft>`_ is
-distribution.  It is portable across all platforms.  Depending on the size
+included in the LAMMPS distribution.  It is portable across all
-of the FFTs and the number of processors used, the other libraries listed
+platforms.  Depending on the size of the FFTs and the number of
-here can be faster.
+processors used, the other libraries listed here can be faster.
 
 However, note that long-range Coulombics are only a portion of the
-per-timestep CPU cost, FFTs are only a portion of long-range
+per-timestep CPU cost, FFTs are only a portion of long-range Coulombics,
-Coulombics, and 1d FFTs are only a portion of the FFT cost (parallel
+and 1d FFTs are only a portion of the FFT cost (parallel communication
-communication can be costly).  A breakdown of these timings is printed
+can be costly).  A breakdown of these timings is printed to the screen
-to the screen at the end of a run when using the
+at the end of a run when using the :doc:`kspace_style pppm
-:doc:`kspace_style pppm <kspace_style>` command. The
+<kspace_style>` command. The :doc:`Screen and logfile output
-:doc:`Screen and logfile output <Run_output>`
+<Run_output>` page gives more details.  A more detailed (and time
-page gives more details.  A more detailed (and time consuming)
+consuming) report of the FFT performance is generated with the
-report of the FFT performance is generated with the
 :doc:`kspace_modify fftbench yes <kspace_modify>` command.
 
 FFTW is a fast, portable FFT library that should also work on any
-platform and can be faster than the KISS FFT library.  You can
+platform and can be faster than the KISS FFT library.  You can download
-download it from `www.fftw.org <http://www.fftw.org>`_.  LAMMPS requires
+it from `www.fftw.org <https://www.fftw.org>`_.  LAMMPS requires version
-version 3.X; the legacy version 2.1.X is no longer supported.
+3.X; the legacy version 2.1.X is no longer supported.
 
 Building FFTW for your box should be as simple as ``./configure; make;
 make install``.  The install command typically requires root privileges

doc/src/Commands_pair.rst

@@ -205,7 +205,7 @@ OPT.
    * :doc:`mesont/tpm <pair_mesont_tpm>`
    * :doc:`mgpt <pair_mgpt>`
    * :doc:`mie/cut (g) <pair_mie>`
-   * :doc:`mliap <pair_mliap>`
+   * :doc:`mliap (k) <pair_mliap>`
    * :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>`
    * :doc:`momb <pair_momb>`
    * :doc:`morse (gkot) <pair_morse>`
@@ -236,6 +236,7 @@ OPT.
    * :doc:`oxrna2/xstk <pair_oxrna2>`
    * :doc:`oxrna2/coaxstk <pair_oxrna2>`
    * :doc:`pace (k) <pair_pace>`
+   * :doc:`pace/extrapolation <pair_pace>`
    * :doc:`pod <pair_pod>`
    * :doc:`peri/eps <pair_peri>`
    * :doc:`peri/lps (o) <pair_peri>`
@@ -295,6 +296,7 @@ OPT.
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
    * :doc:`wf/cut <pair_wf_cut>`
+   * :doc:`ylz <pair_ylz>`
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Developer_updating.rst

@@ -7,7 +7,7 @@ source files provided as a supplement to a publication) that are written
 for an older version of LAMMPS and thus need to be updated to be
 compatible with the current version of LAMMPS.  Due to the active
 development of LAMMPS it is likely to always be incomplete.  Please
-contact developer@lammps.org in case you run across an issue that is not
+contact developers@lammps.org in case you run across an issue that is not
 (yet) listed here.  Please also review the latest information about the
 LAMMPS :doc:`programming style conventions <Modify_style>`, especially
 if you are considering to submit the updated version for inclusion into

doc/src/Errors_debug.rst

@@ -75,7 +75,7 @@ Using the GDB debugger to get a stack trace
 There are two options to use the GDB debugger for identifying the origin
 of the segmentation fault or similar crash. The GDB debugger has many
 more features and options, as can be seen for example its `online
-documentation <http://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
+documentation <https://sourceware.org/gdb/current/onlinedocs/gdb/>`_.
 
 Run LAMMPS from within the debugger
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

doc/src/Howto.rst

@@ -85,6 +85,7 @@ Packages howto
    Howto_coreshell
    Howto_drude
    Howto_drude2
+   Howto_peri
    Howto_manifold
    Howto_spins
 

doc/src/Howto_amoeba.rst

@@ -281,7 +281,7 @@ Here is more information about the extended XYZ format defined and
 used by Tinker, and links to programs that convert standard PDB files
 to the extended XYZ format:
 
-* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
+* `https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <https://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
 * `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
 * `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
 

doc/src/Howto_bioFF.rst

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

doc/src/Howto_bpm.rst

@@ -33,46 +33,6 @@ reference state of a bond. Bonds that are created midway into a run,
 such as those created by pouring grains using :doc:`fix pour
 <fix_pour>`, are initialized on that timestep.
 
-As bonds can be broken between neighbor list builds, the
-:doc:`special_bonds <special_bonds>` command works differently for BPM
-bond styles. There are two possible settings which determine how pair
-interactions work between bonded particles.  First, one can turn off
-all pair interactions between bonded particles.  Unlike :doc:`bond
-quartic <bond_quartic>`, this is not done by subtracting pair forces
-during the bond computation but rather by dynamically updating the
-special bond list. This is the default behavior of BPM bond styles and
-is done by updating the 1-2 special bond list as bonds break.  To do
-this, LAMMPS requires :doc:`newton <newton>` bond off such that all
-processors containing an atom know when a bond breaks. Additionally,
-one must do either (A) or (B).
-
-A) Use the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj 0 1 1 coul 1 1 1
-
-   These settings accomplish two goals. First, they turn off 1-3 and 1-4
-   special bond lists, which are not currently supported for BPMs. As
-   BPMs often have dense bond networks, generating 1-3 and 1-4 special
-   bond lists is expensive.  By setting the lj weight for 1-2 bonds to
-   zero, this turns off pairwise interactions.  Even though there are no
-   charges in BPM models, setting a nonzero coul weight for 1-2 bonds
-   ensures all bonded neighbors are still included in the neighbor list
-   in case bonds break between neighbor list builds.
-
-B) Alternatively, one can simply overlay pair interactions such that all
-   bonded particles also feel pair interactions. This can be
-   accomplished by using the *overlay/pair* keyword present in all bpm
-   bond styles and by using the following special bond settings
-
-   .. code-block:: LAMMPS
-
-      special_bonds lj/coul 1 1 1
-
-See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
-more information.
-
 ----------
 
 Currently there are two types of bonds included in the BPM
@@ -91,12 +51,6 @@ This also requires a unique integrator :doc:`fix nve/bpm/sphere
 <fix_nve_bpm_sphere>` which numerically integrates orientation similar
 to :doc:`fix nve/asphere <fix_nve_asphere>`.
 
-To monitor the fracture of bonds in the system, all BPM bond styles
-have the ability to record instances of bond breakage to output using
-the :doc:`dump local <dump>` command. Additionally, one can use
-:doc:`compute nbond/atom <compute_nbond_atom>` to tally the current
-number of bonds per atom.
-
 In addition to bond styles, a new pair style :doc:`pair bpm/spring
 <pair_bpm_spring>` was added to accompany the bpm/spring bond
 style. This pair style is simply a hookean repulsion with similar
@@ -104,6 +58,73 @@ velocity damping as its sister bond style.
 
 ----------
 
+Bond data can be output using a combination of standard LAMMPS commands.
+A list of IDs for bonded atoms can be generated using the
+:doc:`compute property/local <compute_property_local>` command.
+Various properties of bonds can be computed using the
+:doc:`compute bond/local <compute_bond_local>` command. This
+command allows one to access data saved to the bond's history
+such as the reference length of the bond. More information on
+bond history data can be found on the documentation pages for the specific
+BPM bond styles. Finally, this data can be output using a :doc:`dump local <dump>`
+command. As one may output many columns from the same compute, the
+:doc:`dump modify <dump_modify>` *colname* option may be used to provide
+more helpful column names. An example of this procedure is found in
+/examples/bpm/pour/. External software, such as OVITO, can read these dump
+files to render bond data.
+
+----------
+
+As bonds can be broken between neighbor list builds, the
+:doc:`special_bonds <special_bonds>` command works differently for BPM
+bond styles. There are two possible settings which determine how pair
+interactions work between bonded particles.  First, one can overlay
+pair forces with bond forces such that all bonded particles also
+feel pair interactions. This can be accomplished by using the *overlay/pair*
+keyword present in all bpm bond styles and by using the following special
+bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj/coul 1 1 1
+
+Alternatively, one can turn off all pair interactions between bonded
+particles. Unlike :doc:`bond quartic <bond_quartic>`, this is not done
+by subtracting pair forces during the bond computation but rather by
+dynamically updating the special bond list. This is the default behavior
+of BPM bond styles and is done by updating the 1-2 special bond list as
+bonds break.  To do this, LAMMPS requires :doc:`newton <newton>` bond off
+such that all processors containing an atom know when a bond breaks.
+Additionally, one must use the following special bond settings
+
+   .. code-block:: LAMMPS
+
+      special_bonds lj 0 1 1 coul 1 1 1
+
+These settings accomplish two goals. First, they turn off 1-3 and 1-4
+special bond lists, which are not currently supported for BPMs. As
+BPMs often have dense bond networks, generating 1-3 and 1-4 special
+bond lists is expensive.  By setting the lj weight for 1-2 bonds to
+zero, this turns off pairwise interactions.  Even though there are no
+charges in BPM models, setting a nonzero coul weight for 1-2 bonds
+ensures all bonded neighbors are still included in the neighbor list
+in case bonds break between neighbor list builds.
+
+To monitor the fracture of bonds in the system, all BPM bond styles
+have the ability to record instances of bond breakage to output using
+the :doc:`dump local <dump>` command. Since one may frequently output
+a list of broken bonds and the time they broke, the
+:doc:`dump modify <dump_modify>` option *header no* may be useful to
+avoid repeatedly printing the header of the dump file. An example of
+this procedure is found in /examples/bpm/impact/. Additionally,
+one can use :doc:`compute nbond/atom <compute_nbond_atom>` to tally the
+current number of bonds per atom.
+
+See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for
+more information.
+
+----------
+
 While LAMMPS has many utilities to create and delete bonds, *only*
 the following are currently compatible with BPM bond styles:
 

doc/src/Howto_github.rst

@@ -10,7 +10,7 @@ changes or additions you have made to LAMMPS into the official LAMMPS
 distribution.  It uses the process of updating this very tutorial as an
 example to describe the individual steps and options.  You need to be
 familiar with git and you may want to have a look at the `git book
-<http://git-scm.com/book/>`_ to familiarize yourself with some of the
+<https://git-scm.com/book/>`_ to familiarize yourself with some of the
 more advanced git features used below.
 
 As of fall 2016, submitting contributions to LAMMPS via pull requests

doc/src/Howto_manifold.rst

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

doc/src/Howto_spc.rst

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

doc/src/Howto_spins.rst

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

doc/src/Howto_tip3p.rst

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

doc/src/Howto_tip4p.rst

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

doc/src/Howto_viz.rst

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

doc/src/Install_conda.rst

@@ -5,7 +5,7 @@ Binaries are available for MacOS or Linux via `Conda <conda_>`_.
 
 First, one must setup the Conda package manager on your system.  Follow the
 instructions to install `Miniconda <mini_conda_install_>`_, then create a conda
-environment (named `my-lammps-env` or whatever you prefer) for your lammps
+environment (named `my-lammps-env` or whatever you prefer) for your LAMMPS
 install:
 
 .. code-block:: bash
@@ -13,7 +13,7 @@ install:
    % conda config --add channels conda-forge
    % conda create -n my-lammps-env
 
-Then, you can install lammps on your system with the following command:
+Then, you can install LAMMPS on your system with the following command:
 
 .. code-block:: bash
 

doc/src/Install_windows.rst

@@ -6,7 +6,7 @@ Windows system can be downloaded from this site:
 
 .. parsed-literal::
 
-  `http://packages.lammps.org/windows.html <http://packages.lammps.org/windows.html>`_
+  `https://packages.lammps.org/windows.html <https://packages.lammps.org/windows.html>`_
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for

doc/src/Intro_authors.rst

@@ -4,13 +4,13 @@ Authors of LAMMPS
 The primary LAMMPS developers are at Sandia National Labs and Temple
 University:
 
-* `Steve Plimpton <sjp_>`_, sjplimp at sandia.gov
+* `Steve Plimpton <sjp_>`_, sjplimp at gmail.com
 * Aidan Thompson, athomps at sandia.gov
 * Stan Moore, stamoor at sandia.gov
 * Axel Kohlmeyer, akohlmey at gmail.com
 * Richard Berger, richard.berger at outlook.com
 
-.. _sjp: http://www.cs.sandia.gov/~sjplimp
+.. _sjp: https://sjplimp.github.io
 .. _lws: https://www.lammps.org
 
 Past developers include Paul Crozier and Mark Stevens, both at Sandia,

doc/src/Intro_citing.rst

@@ -27,7 +27,7 @@ namely https://www.lammps.org.
 The original publication describing the parallel algorithms used in the
 initial versions of LAMMPS is:
 
-  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <http://www.sandia.gov/~sjplimp/papers/jcompphys95.pdf>`_
+  `S. Plimpton, Fast Parallel Algorithms for Short-Range Molecular Dynamics, J Comp Phys, 117, 1-19 (1995). <https://doi.org/10.1006/jcph.1995.1039>`_
 
 
 DOI for the LAMMPS source code

doc/src/Intro_features.rst

@@ -95,7 +95,7 @@ commands)
 * metal-organic framework potentials (QuickFF, MO-FF)
 * 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 command <kim_commands>`
+* access to the `OpenKIM Repository <https://openkim.org>`_ of potentials via the :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 (including many-body) with optional scale factor
 
@@ -205,7 +205,7 @@ Pre- and post-processing
 
 .. _pizza: https://lammps.github.io/pizza
 
-.. _python: http://www.python.org
+.. _python: https://www.python.org
 
 .. _special:
 

doc/src/Intro_nonfeatures.rst

@@ -33,7 +33,7 @@ Here are suggestions on how to perform these tasks:
   linear bead-spring polymer chains.  The moltemplate program is a true
   molecular builder that will generate complex molecular models.  See
   the :doc:`Tools <Tools>` page for details on tools packaged with
-  LAMMPS.  The `Pre/post processing page <http:/www.lammps.org/prepost.html>`_ of the LAMMPS website
+  LAMMPS.  The `Pre/post processing page <https:/www.lammps.org/prepost.html>`_ of the LAMMPS website
   describes a variety of third party tools for this task.  Furthermore,
   some LAMMPS internal commands allow to reconstruct, or selectively add
   topology information, as well as provide the option to insert molecule
@@ -80,5 +80,5 @@ Here are suggestions on how to perform these tasks:
   `Pizza.py <https://lammps.github.io/pizza>`_ which can do certain kinds of
   setup, analysis, plotting, and visualization (via OpenGL) for LAMMPS
   simulations.  It thus provides some functionality for several of the
-  above bullets.  Pizza.py is written in `Python <http://www.python.org>`_
+  above bullets.  Pizza.py is written in `Python <https://www.python.org>`_
-  and is available for download from `this page <http://www.cs.sandia.gov/~sjplimp/download.html>`_.
+  and is available for download from `this page <https://sjplimp.github.io/download.html>`_.

doc/src/Intro_opensource.rst

@@ -23,9 +23,9 @@ applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
 
 .. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
 
-.. _gnuorg: http://www.gnu.org
+.. _gnuorg: https://www.gnu.org
 
-.. _opensource: http://www.opensource.org
+.. _opensource: https://www.opensource.org
 
 Here is a more specific summary of what the GPL means for LAMMPS users:
 

doc/src/Library.rst

@@ -2,12 +2,13 @@ LAMMPS Library Interfaces
 *************************
 
 As described on the :doc:`library interface to LAMMPS <Howto_library>`
-page, LAMMPS can be built as a library (static or shared), so that
+page, LAMMPS can be built as a library (static or shared), so that it
-it can be called by another code, used in a :doc:`coupled manner
+can be called by another code, used in a :doc:`coupled manner
 <Howto_couple>` with other codes, or driven through a :doc:`Python
-script <Python_head>`.  Even the LAMMPS standalone executable is
+script <Python_head>`.  The LAMMPS standalone executable itself is
-essentially a thin wrapper on top of the LAMMPS library, creating a
+essentially a thin wrapper on top of the LAMMPS library, which creates a
-LAMMPS instance, processing input and then existing.
+LAMMPS instance, passes the input for processing to that instance, and
+then exits.
 
 Most of the APIs described below are based on C language wrapper
 functions in the files ``src/library.h`` and ``src/library.cpp``, but
@@ -87,6 +88,18 @@ run LAMMPS in serial mode.
    message retrieved <lammps_get_last_error_message>`.  We thus
    recommend enabling C++ exceptions when using the library interface,
 
+.. admonition:: Using the C library interface as a plugin
+   :class: note
+
+   Rather than including the C library directly and link to the LAMMPS
+   library at compile time, you can use the ``liblammpsplugin.h`` header
+   file and the ``liblammpsplugin.c`` C code in the
+   ``examples/COUPLE/plugin`` folder for an interface to LAMMPS that is
+   largely identical to the regular library interface, only that it will
+   load a LAMMPS shared library file at runtime.  This can be useful for
+   applications where the interface to LAMMPS would be an optional
+   feature.
+
 .. warning::
 
    No checks are made on the arguments of the function calls of the C
@@ -163,5 +176,3 @@ The following links provide some examples and references to the C++ API.
    :maxdepth: 1
 
    Cplusplus
-
-

doc/src/Library_create.rst

@@ -11,6 +11,7 @@ This section documents the following functions:
 - :cpp:func:`lammps_mpi_finalize`
 - :cpp:func:`lammps_kokkos_finalize`
 - :cpp:func:`lammps_python_finalize`
+- :cpp:func:`lammps_error`
 
 --------------------
 
@@ -115,3 +116,8 @@ calling program.
 
 .. doxygenfunction:: lammps_python_finalize
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_error
+   :project: progguide

doc/src/Library_objects.rst

@@ -6,6 +6,7 @@ fixes, or variables in LAMMPS using the following functions:
 
 - :cpp:func:`lammps_extract_compute`
 - :cpp:func:`lammps_extract_fix`
+- :cpp:func:`lammps_extract_variable_datatype`
 - :cpp:func:`lammps_extract_variable`
 - :cpp:func:`lammps_set_variable`
 
@@ -21,6 +22,11 @@ fixes, or variables in LAMMPS using the following functions:
 
 -----------------------
 
+.. doxygenfunction:: lammps_extract_variable_datatype
+   :project: progguide
+
+-----------------------
+
 .. doxygenfunction:: lammps_extract_variable
    :project: progguide
 
@@ -36,3 +42,5 @@ fixes, or variables in LAMMPS using the following functions:
 .. doxygenenum:: _LMP_STYLE_CONST
 
 .. doxygenenum:: _LMP_TYPE_CONST
+
+.. doxygenenum:: _LMP_VAR_CONST

doc/src/Library_properties.rst

@@ -15,21 +15,21 @@ This section documents the following functions:
 
 --------------------
 
-The library interface allows extraction of different kinds of
+The library interface allows the extraction of different kinds of
-information about the active simulation instance and also
+information about the active simulation instance and also---in some
-modifications to it.  This enables combining of a LAMMPS simulation
+cases---to apply modifications to it.  This enables combining of a
-with other processing and simulation methods computed by the calling
+LAMMPS simulation with other processing and simulation methods computed
-code, or by another code that is coupled to LAMMPS via the library
+by the calling code, or by another code that is coupled to LAMMPS via
-interface.  In some cases the data returned is direct reference to the
+the library interface.  In some cases the data returned is direct
-original data inside LAMMPS, cast to a void pointer.  In that case the
+reference to the original data inside LAMMPS, cast to a void pointer.
-data needs to be cast to a suitable pointer for the calling program to
+In that case the data needs to be cast to a suitable pointer for the
-access it, and you may need to know the correct dimensions and
+calling program to access it, and you may need to know the correct
-lengths.  This also means you can directly change those value(s) from
+dimensions and lengths.  This also means you can directly change those
-the calling program, e.g. to modify atom positions.  Of course, this
+value(s) from the calling program (e.g., to modify atom positions).  Of
-should be done with care.  When accessing per-atom data, please note
+course, changing values should be done with care.  When accessing per-atom
-that this data is the per-processor **local** data and is indexed
+data, please note that these data are the per-processor **local** data and are
-accordingly. Per-atom data can change sizes and ordering at every
+indexed accordingly. Per-atom data can change sizes and ordering at
-neighbor list rebuild or atom sort event as atoms migrate between
+every neighbor list rebuild or atom sort event as atoms migrate between
 sub-domains and processors.
 
 .. code-block:: C

doc/src/Library_utility.rst

@@ -19,6 +19,7 @@ functions.  They do not directly call the LAMMPS library.
 - :cpp:func:`lammps_force_timeout`
 - :cpp:func:`lammps_has_error`
 - :cpp:func:`lammps_get_last_error_message`
+- :cpp:func:`lammps_python_api_version`
 
 The :cpp:func:`lammps_free` function is a clean-up function to free
 memory that the library had allocated previously via other function
@@ -100,3 +101,9 @@ where such memory buffers were allocated that require the use of
 
 .. doxygenfunction:: lammps_get_last_error_message
    :project: progguide
+
+-----------------------
+
+.. doxygenfunction:: lammps_python_api_version
+   :project: progguide
+

doc/src/Manual.rst

@@ -42,7 +42,7 @@ descriptions of all commands included in the LAMMPS code.
 .. only:: html
 
    Once you are familiar with LAMMPS, you may want to bookmark
-   :doc:`this page <Commands_all>` since it gives quick access
+   :doc:`this page <Commands_all>` since it gives quick access to
    the documentation for all LAMMPS commands.
 
 .. _lws: https://www.lammps.org

doc/src/Modify_style.rst

@@ -359,6 +359,12 @@ you are uncertain, please ask.
 
 - I/O is done via the C-style stdio library and **not** iostreams.
 
+- Do not use so-called "alternative tokens" like ``and``, ``or``,
+  ``not`` and similar, but rather use the corresponding operators
+  ``&&``, ``||``, and ``!``.  The alternative tokens are not available
+  by default on all compilers, and also we want to maintain a consistent
+  programming style.
+
 - Output to the screen and the logfile should be using the corresponding
   FILE pointers and only be done on MPI rank 0.  Use the :cpp:func:`utils::logmesg`
   convenience function where possible.

doc/src/Packages_details.rst

@@ -135,6 +135,8 @@ commands to write and read data using the ADIOS library.
 
 **Authors:** Norbert Podhorszki (ORNL) from the ADIOS developer team.
 
+.. versionadded:: 28Feb2019
+
 **Install:**
 
 This package has :ref:`specific installation instructions <adios>` on the :doc:`Build extras <Build_extras>` page.
@@ -199,6 +201,7 @@ particle models including ellipsoids, 2d lines, and 3d triangles.
 * :doc:`Howto spherical <Howto_spherical>`
 * :doc:`pair_style gayberne <pair_gayberne>`
 * :doc:`pair_style resquared <pair_resquared>`
+* :doc:`pair_style ylz <pair_ylz>`
 * `doc/PDF/pair_gayberne_extra.pdf <PDF/pair_gayberne_extra.pdf>`_
 * `doc/PDF/pair_resquared_extra.pdf <PDF/pair_resquared_extra.pdf>`_
 * examples/ASPHERE
@@ -365,6 +368,8 @@ and also support self-propelled particles.
 **Authors:** Sam Cameron (University of Bristol),
 Stefan Paquay (while at Brandeis University) (initial version of fix propel/self)
 
+.. versionadded:: 14May2021
+
 Example inputs are in the examples/PACKAGES/brownian folder.
 
 ----------
@@ -593,6 +598,8 @@ To use this package, also the :ref:`KSPACE <PKG-KSPACE>` and
 
 **Author:** Trung Nguyen and Monica Olvera de la Cruz (Northwestern U)
 
+.. versionadded:: 2Jul2021
+
 **Supporting info:**
 
 * src/DIELECTRIC: filenames -> commands
@@ -1072,7 +1079,7 @@ H5MD is a format for molecular simulations, built on top of HDF5.
 This package implements a :doc:`dump h5md <dump_h5md>` command to output
 LAMMPS snapshots in this format.
 
-.. _HDF5: http://www.hdfgroup.org/HDF5
+.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
 
 To use this package you must have the HDF5 library available on your
 system.
@@ -1513,6 +1520,8 @@ workflows via the `MolSSI Driver Interface
 
 **Author:** Taylor Barnes - MolSSI, taylor.a.barnes at gmail.com
 
+.. versionadded:: 14May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <mdi>` on
@@ -1597,6 +1606,8 @@ of Alabama), Leonid V. Zhigilei (University of Virginia)
 **Author of the *mesocnt* styles:**
 Philipp Kloza (U Cambridge)
 
+.. versionadded:: 15Jun2020
+
 **Supporting info:**
 
 * src/MESONT: filenames -> commands
@@ -1689,6 +1700,8 @@ compiled on your system.
 
 **Author:** Andreas Singraber
 
+.. versionadded:: 27May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-hdnnp>` on the
@@ -1723,6 +1736,8 @@ must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
 
+.. versionadded:: 30Jun2020
+
 **Supporting info:**
 
 * src/ML-IAP: filenames -> commands
@@ -1767,6 +1782,8 @@ Aidan Thompson^3, Gabor Csanyi^2, Christoph Ortner^4, Ralf Drautz^1.
 
  ^4: University of British Columbia, Vancouver, BC, Canada
 
+.. versionadded:: 14May2021
+
 **Install:**
 
 This package has :ref:`specific installation instructions <ml-pace>` on the
@@ -1868,6 +1885,8 @@ of a neural network.
 This package was written by Christopher Barrett
 with contributions by Doyl Dickel, Mississippi State University.
 
+.. versionadded:: 27May2021
+
 **Supporting info:**
 
 * src/ML-RANN: filenames -> commands
@@ -1993,7 +2012,7 @@ support for new file formats can be added to LAMMPS (or VMD or other
 programs that use them) without having to re-compile the application
 itself.  More information about the VMD molfile plugins can be found
 at
-`http://www.ks.uiuc.edu/Research/vmd/plugins/molfile <http://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
+`https://www.ks.uiuc.edu/Research/vmd/plugins/molfile <https://www.ks.uiuc.edu/Research/vmd/plugins/molfile>`_.
 
 **Author:** Axel Kohlmeyer (Temple U).
 
@@ -2084,7 +2103,7 @@ NETCDF package
 Dump styles for writing NetCDF formatted dump files.  NetCDF is a
 portable, binary, self-describing file format developed on top of
 HDF5. The file contents follow the AMBER NetCDF trajectory conventions
-(http://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
+(https://ambermd.org/netcdf/nctraj.xhtml), but include extensions.
 
 To use this package you must have the NetCDF library available on your
 system.
@@ -2095,7 +2114,7 @@ tools:
 * `Ovito <ovito_>`_ (Ovito supports the AMBER convention and the extensions mentioned above)
 * `VMD <vmd-home_>`_
 
-.. _ovito: http://www.ovito.org
+.. _ovito: https://www.ovito.org
 
 .. _vmd-home: https://www.ks.uiuc.edu/Research/vmd/
 
@@ -2239,6 +2258,7 @@ Foster (UTSA).
 **Supporting info:**
 
 * src/PERI: filenames -> commands
+* :doc:`Peridynamics Howto <Howto_peri>`
 * `doc/PDF/PDLammps_overview.pdf <PDF/PDLammps_overview.pdf>`_
 * `doc/PDF/PDLammps_EPS.pdf <PDF/PDLammps_EPS.pdf>`_
 * `doc/PDF/PDLammps_VES.pdf <PDF/PDLammps_VES.pdf>`_
@@ -2303,6 +2323,8 @@ try to load the contained plugins automatically at start-up.
 
 **Authors:** Axel Kohlmeyer (Temple U)
 
+.. versionadded:: 8Apr2021
+
 **Supporting info:**
 
 * src/PLUGIN: filenames -> commands
@@ -2456,7 +2478,7 @@ A :doc:`fix qmmm <fix_qmmm>` command which allows LAMMPS to be used as
 the MM code in a QM/MM simulation.  This is currently only available
 in combination with the `Quantum ESPRESSO <espresso_>`_ package.
 
-.. _espresso: http://www.quantum-espresso.org
+.. _espresso: https://www.quantum-espresso.org
 
 To use this package you must have Quantum ESPRESSO (QE) available on
 your system and include its coupling library in the compilation and
@@ -2868,7 +2890,7 @@ collection of atoms by wrapping the `Voro++ library <voro-home_>`_.  This
 can be used to calculate the local volume or each atoms or its near
 neighbors.
 
-.. _voro-home: http://math.lbl.gov/voro++
+.. _voro-home: https://math.lbl.gov/voro++
 
 To use this package you must have the Voro++ library available on your
 system.
@@ -2902,9 +2924,9 @@ A :doc:`dump vtk <dump_vtk>` command which outputs snapshot info in the
 `VTK format <vtk_>`_, enabling visualization by `Paraview <paraview_>`_ or
 other visualization packages.
 
-.. _vtk: http://www.vtk.org
+.. _vtk: https://www.vtk.org
 
-.. _paraview: http://www.paraview.org
+.. _paraview: https://www.paraview.org
 
 To use this package you must have VTK library available on your
 system.
@@ -2941,11 +2963,13 @@ which discuss the `QuickFF <quickff_>`_ methodology.
 
 .. _vanduyfhuys2015: https://doi.org/10.1002/jcc.23877
 .. _vanduyfhuys2018: https://doi.org/10.1002/jcc.25173
-.. _quickff: http://molmod.github.io/QuickFF
+.. _quickff: https://molmod.github.io/QuickFF
 .. _yaff: https://github.com/molmod/yaff
 
 **Author:** Steven Vandenbrande.
 
+.. versionadded:: 1Feb2019
+
 **Supporting info:**
 
 * src/YAFF/README

doc/src/Python_examples.rst

@@ -43,26 +43,18 @@ Note that for AtomEye, you need version 3, and there is a line in the
 scripts that specifies the path and name of the executable.  See the
 AtomEye web pages for more details:
 
-* `http://li.mit.edu/Archive/Graphics/A/ <atomeye_>`_
+* `http://li.mit.edu/Archive/Graphics/A/ <http://li.mit.edu/Archive/Graphics/A/>`_
-* `http://li.mit.edu/Archive/Graphics/A3/A3.html <atomeye3_>`_
+* `http://li.mit.edu/Archive/Graphics/A3/A3.html <http://li.mit.edu/Archive/Graphics/A3/A3.html>`_
 
-.. _atomeye: http://li.mit.edu/Archive/Graphics/A/
+The latter link is to AtomEye 3 which has the scripting capability
-
+needed by these Python scripts.
-.. _atomeye3: http://li.mit.edu/Archive/Graphics/A3/A3.html
-
-The latter link is to AtomEye 3 which has the scripting
-capability needed by these Python scripts.
 
 Note that for PyMol, you need to have built and installed the
 open-source version of PyMol in your Python, so that you can import it
 from a Python script.  See the PyMol web pages for more details:
 
- * `https://www.pymol.org <pymolhome_>`_
+ * `https://www.pymol.org <https://www.pymol.org>`_
- * `https://github.com/schrodinger/pymol-open-source <pymolopen_>`_
+ * `https://github.com/schrodinger/pymol-open-source <https://github.com/schrodinger/pymol-open-source>`_
-
-.. _pymolhome: https://www.pymol.org
-
-.. _pymolopen: https://github.com/schrodinger/pymol-open-source
 
 The latter link is to the open-source version.
 

doc/src/Python_head.rst

@@ -18,17 +18,17 @@ together.
    Python_error
    Python_trouble
 
-If you are not familiar with `Python <http://www.python.org>`_, it is a
+If you are not familiar with `Python <https://www.python.org>`_, it is a
 powerful scripting and programming language which can do almost
 everything that compiled languages like C, C++, or Fortran can do in
 fewer lines of code. It also comes with a large collection of add-on
 modules for many purposes (either bundled or easily installed from
 Python code repositories).  The major drawback is slower execution speed
 of the script code compared to compiled programming languages.  But when
-the script code is interfaced to optimized compiled code, performance can
+the script code is interfaced to optimized compiled code, performance
-be on par with a standalone executable, for as long as the scripting is
+can be on par with a standalone executable, for as long as the scripting
-restricted to high-level operations.  Thus Python is also convenient to
+is restricted to high-level operations.  Thus Python is also convenient
-use as a "glue" language to "drive" a program through its library
+to use as a "glue" language to "drive" a program through its library
 interface, or to hook multiple pieces of software together, such as a
 simulation code and a visualization tool, or to run a coupled
 multi-scale or multi-physics model.

doc/src/Python_neighbor.rst

@@ -38,6 +38,40 @@ using the NumPy access method.
            for n in np.nditer(nlist):
                print("  atom {} with ID {}".format(n,tags[n]))
 
+Another example for extracting a full neighbor list without evaluating a
+potential is shown below.
+
+.. code-block:: python
+
+    from lammps import lammps
+    import numpy as np
+
+    lmp = lammps()
+    lmp.commands_string("""
+    newton off
+    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 zero 1.0 full
+    pair_coeff * *
+    run 0 post no""")
+
+    # look up the neighbor list
+    nlidx = lmp.find_pair_neighlist('zero')
+    nl = lmp.numpy.get_neighlist(nlidx)
+    tags = lmp.extract_atom('id')
+    print("full 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):
+                pass
+                print("  atom {} with ID {}".format(n,tags[n]))
+
 **Methods:**
 
 * :py:meth:`lammps.get_neighlist() <lammps.lammps.get_neighlist()>`: Get neighbor list for given index

doc/src/Run_basics.rst

@@ -30,12 +30,13 @@ executable itself can be placed elsewhere.
 
 .. note::
 
-   The redirection operator "<" will not always work when running
+   The redirection operator "<" will not always work when running in
-   in parallel with mpirun or mpiexec; for those systems the -in form is required.
+   parallel with ``mpirun`` or ``mpiexec``; for those systems the -in
+   form is required.
 
 As LAMMPS runs it prints info to the screen and a logfile named
-*log.lammps*\ .  More info about output is given on the
+*log.lammps*\ .  More info about output is given on the :doc:`screen and
-:doc:`screen and logfile output <Run_output>` page.
+logfile output <Run_output>` page.
 
 If LAMMPS encounters errors in the input script or while running a
 simulation it will print an ERROR message and stop or a WARNING

doc/src/Run_options.rst

@@ -93,13 +93,13 @@ switch is not set (the default), LAMMPS will operate as if the KOKKOS
 package were not installed; i.e. you can run standard LAMMPS or with
 the GPU or OPENMP packages, for testing or benchmarking purposes.
 
-Additional optional keyword/value pairs can be specified which
+Additional optional keyword/value pairs can be specified which determine
-determine how Kokkos will use the underlying hardware on your
+how Kokkos will use the underlying hardware on your platform.  These
-platform.  These settings apply to each MPI task you launch via the
+settings apply to each MPI task you launch via the ``mpirun`` or
-"mpirun" or "mpiexec" command.  You may choose to run one or more MPI
+``mpiexec`` command.  You may choose to run one or more MPI tasks per
-tasks per physical node.  Note that if you are running on a desktop
+physical node.  Note that if you are running on a desktop machine, you
-machine, you typically have one physical node.  On a cluster or
+typically have one physical node.  On a cluster or supercomputer there
-supercomputer there may be dozens or 1000s of physical nodes.
+may be dozens or 1000s of physical nodes.
 
 Either the full word or an abbreviation can be used for the keywords.
 Note that the keywords do not use a leading minus sign.  I.e. the
@@ -148,9 +148,9 @@ one of these 4 environment variables
    MV2_COMM_WORLD_LOCAL_RANK (Mvapich)
    OMPI_COMM_WORLD_LOCAL_RANK (OpenMPI)
 
-which are initialized by the "srun", "mpirun" or "mpiexec" commands.
+which are initialized by the ``srun``, ``mpirun``, or ``mpiexec``
-The environment variable setting for each MPI rank is used to assign a
+commands.  The environment variable setting for each MPI rank is used to
-unique GPU ID to the MPI task.
+assign a unique GPU ID to the MPI task.
 
 .. parsed-literal::
 

doc/src/Run_output.rst

@@ -16,46 +16,47 @@ simulation.  An example set of statistics is shown here:
 
 .. parsed-literal::
 
-   Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
+   Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms
 
-   Performance: 18.436 ns/day  1.302 hours/ns  106.689 timesteps/s
+   Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s
-   97.0% CPU use with 4 MPI tasks x no OpenMP threads
+   195.2% CPU use with 2 MPI tasks x 2 OpenMP threads
 
-   MPI task timings breakdown:
+   MPI task timing breakdown:
    Section \|  min time  \|  avg time  \|  max time  \|%varavg\| %total
    ---------------------------------------------------------------
-   Pair    \| 1.9808     \| 2.0134     \| 2.0318     \|   1.4 \| 71.60
+   Pair    \| 0.61419    \| 0.62872    \| 0.64325    \|   1.8 \| 66.69
-   Bond    \| 0.0021894  \| 0.0060319  \| 0.010058   \|   4.7 \|  0.21
+   Bond    \| 0.0028608  \| 0.0028899  \| 0.002919   \|   0.1 \|  0.31
-   Kspace  \| 0.3207     \| 0.3366     \| 0.36616    \|   3.1 \| 11.97
+   Kspace  \| 0.12652    \| 0.14048    \| 0.15444    \|   3.7 \| 14.90
-   Neigh   \| 0.28411    \| 0.28464    \| 0.28516    \|   0.1 \| 10.12
+   Neigh   \| 0.10242    \| 0.10242    \| 0.10242    \|   0.0 \| 10.86
-   Comm    \| 0.075732   \| 0.077018   \| 0.07883    \|   0.4 \|  2.74
+   Comm    \| 0.026753   \| 0.027593   \| 0.028434   \|   0.5 \|  2.93
-   Output  \| 0.00030518 \| 0.00042665 \| 0.00078821 \|   1.0 \|  0.02
+   Output  \| 0.00018341 \| 0.00030942 \| 0.00043542 \|   0.0 \|  0.03
-   Modify  \| 0.086606   \| 0.086631   \| 0.086668   \|   0.0 \|  3.08
+   Modify  \| 0.039117   \| 0.039348   \| 0.039579   \|   0.1 \|  4.17
-   Other   \|            \| 0.007178   \|            \|       \|  0.26
+   Other   \|            \| 0.001041   \|            \|       \|  0.11
 
-   Nlocal:    501 ave 508 max 490 min
+   Nlocal:           1002 ave        1006 max         998 min
-   Histogram: 1 0 0 0 0 0 1 1 0 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
-   Nghost:    6586.25 ave 6628 max 6548 min
+   Nghost:         8670.5 ave        8691 max        8650 min
-   Histogram: 1 0 1 0 0 0 1 0 0 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
-   Neighs:    177007 ave 180562 max 170212 min
+   Neighs:         354010 ave      357257 max      350763 min
-   Histogram: 1 0 0 0 0 0 0 1 1 1
+   Histogram: 1 0 0 0 0 0 0 0 0 1
 
-   Total # of neighbors = 708028
+   Total # of neighbors = 708020
-   Ave neighs/atom = 353.307
+   Ave neighs/atom = 353.30339
-   Ave special neighs/atom = 2.34032
+   Ave special neighs/atom = 2.3403194
    Neighbor list builds = 26
    Dangerous builds = 0
 
 ----------
 
-The first section provides a global loop timing summary. The *loop
+The first section provides a global loop timing summary. The *loop time*
-time* is the total wall-clock time for the simulation to run.  The
+is the total wall-clock time for the simulation to run.  The
-*Performance* line is provided for convenience to help predict how
+*Performance* line is provided for convenience to help predict how long
-long it will take to run a desired physical simulation.  The *CPU use*
+it will take to run a desired physical simulation and to have numbers
-line provides the CPU utilization per MPI task; it should be close to
+useful for performance comparison between different simulation settings
-100% times the number of OpenMP threads (or 1 of not using OpenMP).
+or system sizes.  The *CPU use* line provides the CPU utilization per
-Lower numbers correspond to delays due to file I/O or insufficient
+MPI task; it should be close to 100% times the number of OpenMP threads
-thread utilization.
+(or 1 of not using OpenMP).  Lower numbers correspond to delays due to
+file I/O or insufficient thread utilization.
 
 ----------
 

doc/src/Run_windows.rst

@@ -25,8 +25,8 @@ in parallel, follow these steps.
 
 Download and install a compatible MPI library binary package:
 
-* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
+* for 32-bit Windows: `mpich2-1.4.1p1-win-ia32.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-ia32.msi>`_
-* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <http://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
+* for 64-bit Windows: `mpich2-1.4.1p1-win-x86-64.msi <https://download.lammps.org/thirdparty/mpich2-1.4.1p1-win-x86-64.msi>`_
 
 The LAMMPS Windows installer packages will automatically adjust your
 path for the default location of this MPI package. After the

doc/src/Speed_gpu.rst

@@ -39,7 +39,7 @@ toolkit software on your system (this is only tested on Linux
 and unsupported on Windows):
 
 * Check if you have an NVIDIA GPU: cat /proc/driver/nvidia/gpus/\*/information
-* Go to http://www.nvidia.com/object/cuda_get.html
+* Go to https://developer.nvidia.com/cuda-downloads
 * Install a driver and toolkit appropriate for your system (SDK is not necessary)
 * Run lammps/lib/gpu/nvc_get_devices (after building the GPU library, see below) to
   list supported devices and properties
@@ -76,10 +76,11 @@ instructions.
 
 **Run with the GPU package from the command line:**
 
-The mpirun or mpiexec command sets the total number of MPI tasks used
+The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
-by LAMMPS (one or multiple per compute node) and the number of MPI
+used by LAMMPS (one or multiple per compute node) and the number of MPI
-tasks used per node.  E.g. the mpirun command in MPICH does this via
+tasks used per node.  E.g. the ``mpirun`` command in MPICH does this via
-its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
+its ``-np`` and ``-ppn`` switches.  Ditto for OpenMPI via ``-np`` and
+``-npernode``.
 
 When using the GPU package, you cannot assign more than one GPU to a
 single MPI task.  However multiple MPI tasks can share the same GPU,
@@ -129,8 +130,8 @@ GPU package pair styles.
 
 **Or run with the GPU package by editing an input script:**
 
-The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
-and use of multiple MPI tasks/GPU is the same.
+tasks/node, and use of multiple MPI tasks/GPU is the same.
 
 Use the :doc:`suffix gpu <suffix>` command, or you can explicitly add an
 "gpu" suffix to individual styles in your input script, e.g.

doc/src/Speed_intel.rst

@@ -537,5 +537,5 @@ References
 """"""""""
 
 * Brown, W.M., Carrillo, J.-M.Y., Mishra, B., Gavhane, N., Thakkar, F.M., De Kraker, A.R., Yamada, M., Ang, J.A., Plimpton, S.J., "Optimizing Classical Molecular Dynamics in LAMMPS", in Intel Xeon Phi Processor High Performance Programming: Knights Landing Edition, J. Jeffers, J. Reinders, A. Sodani, Eds. Morgan Kaufmann.
-* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <http://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
+* Brown, W. M., Semin, A., Hebenstreit, M., Khvostov, S., Raman, K., Plimpton, S.J. `Increasing Molecular Dynamics Simulation Rates with an 8-Fold Increase in Electrical Power Efficiency. <https://dl.acm.org/citation.cfm?id=3014915>`_ 2016 High Performance Computing, Networking, Storage and Analysis, SC16: International Conference (pp. 82-95).
 * Brown, W.M., Carrillo, J.-M.Y., Gavhane, N., Thakkar, F.M., Plimpton, S.J. Optimizing Legacy Molecular Dynamics Software with Directive-Based Offload. Computer Physics Communications. 2015. 195: p. 95-101.

doc/src/Speed_kokkos.rst

@@ -72,12 +72,12 @@ See the :ref:`Build extras <kokkos>` page for instructions.
 Running LAMMPS with the KOKKOS package
 """"""""""""""""""""""""""""""""""""""
 
-All Kokkos operations occur within the context of an individual MPI
+All Kokkos operations occur within the context of an individual MPI task
-task running on a single node of the machine. The total number of MPI
+running on a single node of the machine. The total number of MPI tasks
-tasks used by LAMMPS (one or multiple per compute node) is set in the
+used by LAMMPS (one or multiple per compute node) is set in the usual
-usual manner via the mpirun or mpiexec commands, and is independent of
+manner via the ``mpirun`` or ``mpiexec`` commands, and is independent of
-Kokkos. E.g. the mpirun command in OpenMPI does this via its -np and
+Kokkos. E.g. the mpirun command in OpenMPI does this via its ``-np`` and
--npernode switches. Ditto for MPICH via -np and -ppn.
+``-npernode`` switches. Ditto for MPICH via ``-np`` and ``-ppn``.
 
 Running on a multi-core CPU
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -168,7 +168,7 @@ for your MPI installation), binding can be forced with these flags:
 
 .. parsed-literal::
 
-   OpenMPI 1.8: mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
+   OpenMPI 1.8:  mpirun -np 2 --bind-to socket --map-by socket ./lmp_openmpi ...
    Mvapich2 2.0: mpiexec -np 2 --bind-to socket --map-by socket ./lmp_mvapich ...
 
 For binding threads with KOKKOS OpenMP, use thread affinity environment
@@ -310,7 +310,8 @@ Alternatively the effect of the "-sf" or "-pk" switches can be
 duplicated by adding the :doc:`package kokkos <package>` or :doc:`suffix kk <suffix>` commands to your input script.
 
 The discussion above for building LAMMPS with the KOKKOS package, the
-mpirun/mpiexec command, and setting appropriate thread are the same.
+``mpirun`` or ``mpiexec`` command, and setting appropriate thread
+properties are the same.
 
 You must still use the "-k on" :doc:`command-line switch <Run_options>`
 to enable the KOKKOS package, and specify its additional arguments for

doc/src/Speed_omp.rst

@@ -33,8 +33,8 @@ These examples assume one or more 16-core nodes.
    mpirun -np 4 lmp_omp -sf omp -pk omp 4 -in in.script           # 4 MPI tasks, 4 threads/task
    mpirun -np 32 -ppn 4 lmp_omp -sf omp -pk omp 4 -in in.script   # 8 nodes, 4 MPI tasks/node, 4 threads/task
 
-The mpirun or mpiexec command sets the total number of MPI tasks used
+The ``mpirun`` or ``mpiexec`` command sets the total number of MPI tasks
-by LAMMPS (one or multiple per compute node) and the number of MPI
+used by LAMMPS (one or multiple per compute node) and the number of MPI
 tasks used per node.  E.g. the mpirun command in MPICH does this via
 its -np and -ppn switches.  Ditto for OpenMPI via -np and -npernode.
 
@@ -58,8 +58,8 @@ OMP_NUM_THREADS environment variable.
 Or run with the OPENMP package by editing an input script
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-The discussion above for the mpirun/mpiexec command, MPI tasks/node,
+The discussion above for the ``mpirun`` or ``mpiexec`` command, MPI
-and threads/MPI task is the same.
+tasks/node, and threads/MPI task is the same.
 
 Use the :doc:`suffix omp <suffix>` command, or you can explicitly add an
 "omp" suffix to individual styles in your input script, e.g.
@@ -97,7 +97,7 @@ sub-section.
 
 A description of the multi-threading strategy used in the OPENMP
 package and some performance examples are
-`presented here <http://sites.google.com/site/akohlmey/software/lammps-icms/lammps-icms-tms2011-talk.pdf?attredirects=0&d=1>`_.
+`presented here <https://drive.google.com/file/d/1d1gLK6Ru6aPYB50Ld2tO10Li8zgPVNB8/view?usp=sharing>`_.
 
 Guidelines for best performance
 """""""""""""""""""""""""""""""

doc/src/Speed_packages.rst

@@ -117,33 +117,15 @@ script.
    with all its accelerator packages installed.  Note however that the
    INTEL and KOKKOS packages require you to choose one of their
    hardware options when building for a specific platform.  I.e. CPU or
-   Phi option for the INTEL package.  Or the OpenMP, Cuda, or Phi
+   Phi option for the INTEL package.  Or the OpenMP, CUDA, HIP, SYCL,
-   option for the KOKKOS package.
+   or Phi option for the KOKKOS package.  Or the OpenCL, HIP, or CUDA
+   option for the GPU package.
 
 These are the exceptions.  You cannot build a single executable with:
 
 * both the INTEL Phi and KOKKOS Phi options
 * the INTEL Phi or Kokkos Phi option, and the GPU package
 
-See the examples/accelerate/README and make.list files for sample
-Make.py commands that build LAMMPS with any or all of the accelerator
-packages.  As an example, here is a command that builds with all the
-GPU related packages installed (GPU, KOKKOS with Cuda), including
-settings to build the needed auxiliary GPU libraries for Kepler GPUs:
-
-.. code-block:: bash
-
-   Make.py -j 16 -p omp gpu kokkos -cc nvcc wrap=mpi   -gpu mode=double arch=35 -kokkos cuda arch=35 lib-all file mpi
-
-The examples/accelerate directory also has input scripts that can be
-used with all of the accelerator packages.  See its README file for
-details.
-
-Likewise, the bench directory has FERMI and KEPLER and PHI
-sub-directories with Make.py commands and input scripts for using all
-the accelerator packages on various machines.  See the README files in
-those directories.
-
 As mentioned above, the `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS website gives
 performance results for the various accelerator packages for several
 of the standard LAMMPS benchmark problems, as a function of problem

doc/src/Tools.rst

@@ -205,6 +205,7 @@ scripts are available:
    whitespace.py    # detects TAB characters and trailing whitespace
    homepage.py      # detects outdated LAMMPS homepage URLs (pointing to sandia.gov instead of lammps.org)
    errordocs.py     # detects deprecated error docs in header files
+   versiontags.py   # detects .. versionadded:: or .. versionchanged:: with pending version date
 
 The tools need to be given the main folder of the LAMMPS distribution
 or individual file names as argument and will by default check them
@@ -397,7 +398,7 @@ ipp tool
 ------------------
 
 The tools/ipp directory contains a Perl script ipp which can be used
-to facilitate the creation of a complicated file (say, a lammps input
+to facilitate the creation of a complicated file (say, a LAMMPS input
 script or tools/createatoms input file) using a template file.
 
 ipp was created and is maintained by Reese Jones (Sandia), rjones at
@@ -512,8 +513,8 @@ with an ``.inputrc`` file in the home directory.  For application
 specific customization, the LAMMPS shell uses the name "lammps-shell".
 For more information about using and customizing an application using
 readline, please see the available documentation at:
-`http://www.gnu.org/s/readline/#Documentation
+https://www.gnu.org/software/readline/
-<http://www.gnu.org/s/readline/#Documentation>`_
+
 
 Additional commands
 ^^^^^^^^^^^^^^^^^^^
@@ -715,7 +716,7 @@ See the README.pdf file for more information.
 These scripts were written by Arun Subramaniyan at Purdue Univ
 (asubrama at purdue.edu).
 
-.. _matlabhome: http://www.mathworks.com
+.. _matlabhome: https://www.mathworks.com
 
 ----------
 
@@ -1046,7 +1047,7 @@ the binary file.  This usually is a so-called little endian hardware
 SWIG interface
 --------------
 
-The `SWIG tool <http://swig.org>`_ offers a mostly automated way to
+The `SWIG tool <https://swig.org>`_ offers a mostly automated way to
 incorporate compiled code modules into scripting languages.  It
 processes the function prototypes in C and generates wrappers for a wide
 variety of scripting languages from it.  Thus it can also be applied to
@@ -1126,7 +1127,7 @@ data passed or returned as pointers are included in the ``lammps.i``
 file.  So most of the functionality of the library interface should be
 accessible.  What works and what does not depends a bit on the
 individual language for which the wrappers are built and how well SWIG
-supports those.  The `SWIG documentation <http://swig.org/doc.html>`_
+supports those.  The `SWIG documentation <https://swig.org/doc.html>`_
 has very detailed instructions and recommendations.
 
 Usage examples

doc/src/atom_style.rst

@@ -91,7 +91,7 @@ quantities.
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *charge*     | charge                                              | atomic system with charges           |
 +--------------+-----------------------------------------------------+--------------------------------------+
-| *dielectric* | dipole, area, curvature                             | system with surface polarization     |
+| *dielectric* | normx normy normz area/patch ed em epsilon curv     | system with surface polarization     |
 +--------------+-----------------------------------------------------+--------------------------------------+
 | *dipole*     | charge and dipole moment                            | system with dipolar particles        |
 +--------------+-----------------------------------------------------+--------------------------------------+
@@ -180,16 +180,21 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
 with its orientation.
 
 For the *dielectric* style, each particle can be either a physical
-particle (e.g. an ion), or an interface particle representing a
+particle (e.g. an ion), or an interface particle representing a boundary
-boundary element. For physical particles, the per-particle properties
+element between two regions of different dielectric constant. For
-are the same as atom_style full.  For interface particles, in addition
+interface particles, in addition to the properties associated with
-to these properties, each particle also has an area, a normal unit
+atom_style full, each particle also should be assigned a normal unit
-vector, a mean local curvature, the mean and difference of the
+vector (defined by normx, normy, normz), an area (area/patch), the
-dielectric constants of two sides of the interface, and the local
+difference and mean of the dielectric constants of two sides of the
-dielectric constant at the boundary element.  The distinction between
+interface along the direction of the normal vector (ed and em), the
-the physical and interface particles is only meaningful when :doc:`fix
+local dielectric constant at the boundary element (epsilon), and a mean
-polarize <fix_polarize>` commands are applied to the interface
+local curvature (curv).  Physical particles must be assigned these
-particles.
+values, as well, but only their local dielectric constants will be used;
+see documentation for associated :doc:`pair styles <pair_dielectric>`
+and :doc:`fixes <fix_polarize>`.  The distinction between the physical
+and interface particles is only meaningful when :doc:`fix polarize
+<fix_polarize>` commands are applied to the interface particles. This
+style is part of the DIELECTRIC package.
 
 For the *dipole* style, a point dipole is defined for each point
 particle.  Note that if you wish the particles to be finite-size

doc/src/bond_bpm_rotational.rst

@@ -138,15 +138,14 @@ the *overlay/pair* keyword. These settings require specific
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
-If the *store/local* keyword is used, this fix will track bonds that
+If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
-local data to be accessed by other LAMMPS commands.
+local data to be accessed by other LAMMPS commands. Following this optional
-Following any optional keyword/value arguments, a list of one or more
+keyword, a list of one or more attributes is specified.  These include the
-attributes is specified.  These include the IDs of the two atoms in
+IDs of the two atoms in the bond. The other attributes for the two atoms
-the bond. The other attributes for the two atoms include the timestep
+include the timestep during which the bond broke and the current/initial
-during which the bond broke and the current/initial center of mass
+center of mass position of the two atoms.
-position of the two atoms.
 
 Data is continuously accumulated over intervals of *N*
 timesteps. At the end of each interval, all of the saved accumulated
@@ -177,29 +176,38 @@ Restart and other info
 
 This bond style writes the reference state of each bond to
 :doc:`binary restart files <restart>`. Loading a restart file will
-properly resume bonds.
+properly resume bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
 
-The single() function of these pair styles returns 0.0 for the energy
+If the *store/local* option is used, an internal fix will calculate
-of a pairwise interaction, since energy is not conserved in these
+a local vector or local array depending on the number of input values.
-dissipative potentials.  It also returns only the normal component of
+The length of the vector or number of rows in the array is the number
-the pairwise interaction force.
+of recorded, broken bonds.  If a single input is specified, a local
-
+vector is produced. If two or more inputs are specified, a local array
-The accumulated data is not written to restart files and should be
+is produced where the number of columns = the number of inputs.  The
-output before a restart file is written to avoid missing data.
+vector or array can be accessed by any command that uses local values
-
+from a compute as input. See the :doc:`Howto output <Howto_output>` page
-The internal fix calculates a local vector or local array depending on the
+for an overview of LAMMPS output options.
-number of input values.  The length of the vector or number of rows in
-the array is the number of recorded, lost interactions.  If a single
-input is specified, a local vector is produced.  If two or more inputs
-are specified, a local array is produced where the number of columns =
-the number of inputs.  The vector or array can be accessed by any
-command that uses local values from a compute as input.  See the
-:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
-output options.
 
 The vector or array will be floating point values that correspond to
 the specified attribute.
 
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  It also returns only the normal component of
+the bonded interaction force.  However, the single() function also
+calculates 7 extra bond quantities.  The first 4 are data from the
+reference state of the bond including the initial distance between particles
+:math:`r_0` followed by the :math:`x`, :math:`y`, and :math:`z` components
+of the initial unit vector pointing to particle I from particle J. The next 3
+quantities (5-7) are the  :math:`x`, :math:`y`, and :math:`z` components
+of the total force, including normal and tangential contributions, acting
+on particle I.
+
+These extra quantities can be accessed by the :doc:`compute bond/local <compute_bond_local>`
+command, as *b1*, *b2*, ..., *b7*\ .
+
 Restrictions
 """"""""""""
 

doc/src/bond_bpm_spring.rst

@@ -103,15 +103,14 @@ the *overlay/pair* keyword. These settings require specific
 restrictions.  Further details can be found in the `:doc: how to
 <Howto_BPM>` page on BPMs.
 
-If the *store/local* keyword is used, this fix will track bonds that
+If the *store/local* keyword is used, an internal fix will track bonds that
 break during the simulation. Whenever a bond breaks, data is processed
 and transferred to an internal fix labeled *fix_ID*. This allows the
-local data to be accessed by other LAMMPS commands.
+local data to be accessed by other LAMMPS commands. Following this optional
-Following any optional keyword/value arguments, a list of one or more
+keyword, a list of one or more attributes is specified.  These include the
-attributes is specified.  These include the IDs of the two atoms in
+IDs of the two atoms in the bond. The other attributes for the two atoms
-the bond. The other attributes for the two atoms include the timestep
+include the timestep during which the bond broke and the current/initial
-during which the bond broke and the current/initial center of mass
+center of mass position of the two atoms.
-position of the two atoms.
 
 Data is continuously accumulated over intervals of *N*
 timesteps. At the end of each interval, all of the saved accumulated
@@ -141,28 +140,30 @@ Restart and other info
 
 This bond style writes the reference state of each bond to
 :doc:`binary restart files <restart>`. Loading a restart
-file will properly resume bonds.
+file will properly restore bonds. However, the reference state is NOT
+written to data files. Therefore reading a data file will not
+restore bonds and will cause their reference states to be redefined.
 
-The single() function of these pair styles returns 0.0 for the energy
+If the *store/local* option is used, an internal fix will calculate
-of a pairwise interaction, since energy is not conserved in these
+a local vector or local array depending on the number of input values.
-dissipative potentials.
+The length of the vector or number of rows in the array is the number
-
+of recorded, broken bonds.  If a single input is specified, a local
-The accumulated data is not written to restart files and should be
+vector is produced. If two or more inputs are specified, a local array
-output before a restart file is written to avoid missing data.
+is produced where the number of columns = the number of inputs.  The
-
+vector or array can be accessed by any command that uses local values
-The internal fix calculates a local vector or local array depending on the
+from a compute as input. See the :doc:`Howto output <Howto_output>` page
-number of input values.  The length of the vector or number of rows in
+for an overview of LAMMPS output options.
-the array is the number of recorded, lost interactions.  If a single
-input is specified, a local vector is produced.  If two or more inputs
-are specified, a local array is produced where the number of columns =
-the number of inputs.  The vector or array can be accessed by any
-command that uses local values from a compute as input.  See the
-:doc:`Howto output <Howto_output>` page for an overview of LAMMPS
-output options.
 
 The vector or array will be floating point values that correspond to
 the specified attribute.
 
+The single() function of this bond style returns 0.0 for the energy
+of a bonded interaction, since energy is not conserved in these
+dissipative potentials.  The single() function also calculates an
+extra bond quantity, the initial distance :math:`r_0`. This
+extra quantity can be accessed by the
+:doc:`compute bond/local <compute_bond_local>` command as *b1*\ .
+
 Restrictions
 """"""""""""
 

doc/src/bond_coeff.rst

@@ -21,7 +21,7 @@ Examples
    bond_coeff 5 80.0 1.2
    bond_coeff * 30.0 1.5 1.0 1.0
    bond_coeff 1*4 30.0 1.5 1.0 1.0
-   bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
+   bond_coeff 1 harmonic 200.0 1.0 # (for bond_style hybrid)
 
    labelmap bond 5 carbonyl
    bond_coeff carbonyl 80.0 1.2

doc/src/bond_mm3.rst

@@ -26,14 +26,14 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>`
 
 .. math::
 
-   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + (7/12) 2.55^2(r-r_0)^2 \right]
+   E = K (r - r_0)^2 \left[ 1 - 2.55(r-r_0) + \frac{7}{12} 2.55^2(r-r_0)^2 \right]
 
 where :math:`r_0` is the equilibrium value of the bond, and :math:`K` is a
-prefactor. The anharmonic prefactors have units angstrom\^(-n):
+prefactor. The anharmonic prefactors have units :math:`\AA^{-n}`:
--2.55 angstrom\^(-1) and (7/12)2.55\^2 angstrom\^(-2). The code takes
+:math:`-2.55 \AA^{-1}` and :math:`\frac{7}{12} 2.55^2 \AA^{-2}`. The code takes
 care of the necessary unit conversion for these factors internally.
-Note that the MM3 papers contains an error in Eq (1):
+Note that the MM3 papers contain an error in Eq (1):
-(7/12)2.55 should be replaced with (7/12)2.55\^2
+:math:`\frac{7}{12} 2.55` should be replaced with :math:`\frac{7}{12} 2.55^2`
 
 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

doc/src/bond_quartic.rst

@@ -28,11 +28,18 @@ The *quartic* bond style uses the potential
 
 .. math::
 
-   E = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 + 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon
+   E      & = E_q + E_{LJ} \\
+   E_q    & = K (r - R_c)^ 2 (r - R_c - B_1) (r - R_c - B_2) + U_0 \\
+   E_{LJ} & = \left\{ \begin{array} {l@{\quad:\quad}l}
+   4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^6 \right] + \epsilon & r < 2^{\frac{1}{6}}, \epsilon = 1, \sigma = 1 \\
+                                                  0 & r >= 2^{\frac{1}{6}}
+                         \end{array} \right.
 
 to define a bond that can be broken as the simulation proceeds (e.g.
-due to a polymer being stretched).  The :math:`\sigma` and :math:`\epsilon` used in the
+due to a polymer being stretched).  The :math:`\sigma` and
-LJ portion of the formula are both set equal to 1.0 by LAMMPS.
+:math:`\epsilon` used in the LJ portion of the formula are both set
+equal to 1.0 by LAMMPS and the LJ portion is cut off at its minimum,
+i.e. at :math:`r_c = 2^{\frac{1}{6}}`.
 
 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
@@ -46,9 +53,9 @@ or :doc:`read_restart <read_restart>` commands:
 * :math:`U_0` (energy)
 
 This potential was constructed to mimic the FENE bond potential for
-coarse-grained polymer chains.  When monomers with :math:`\sigma = \epsilon = 1.0`
+coarse-grained polymer chains.  When monomers with :math:`\sigma =
-are used, the following choice of parameters gives a quartic potential that
+\epsilon = 1.0` are used, the following choice of parameters gives a
-looks nearly like the FENE potential:
+quartic potential that looks nearly like the FENE potential:
 
 .. math::
 

doc/src/clear.rst

@@ -23,15 +23,16 @@ Description
 """""""""""
 
 This command deletes all atoms, restores all settings to their default
-values, and frees all memory allocated by LAMMPS.  Once a clear
+values, and frees all memory allocated by LAMMPS.  Once a clear command
-command has been executed, it is almost as if LAMMPS were starting
+has been executed, it is almost as if LAMMPS were starting over, with
-over, with only the exceptions noted below.  This command enables
+only the exceptions noted below.  This command enables multiple jobs to
-multiple jobs to be run sequentially from one input script.
+be run sequentially from one input script.
 
 These settings are not affected by a clear command: the working
-directory (:doc:`shell <shell>` command), log file status
+directory (:doc:`shell <shell>` command), log file status (:doc:`log
-(:doc:`log <log>` command), echo status (:doc:`echo <echo>` command), and
+<log>` command), echo status (:doc:`echo <echo>` command), and input
-input script variables (:doc:`variable <variable>` command).
+script variables except for *atomfile* style variables (:doc:`variable
+<variable>` command).
 
 Restrictions
 """"""""""""

doc/src/compute_ave_sphere_atom.rst

@@ -35,6 +35,8 @@ Examples
 Description
 """""""""""
 
+.. versionadded:: 7Jan2022
+
 Define a computation that calculates the local mass density and
 temperature for each atom based on its neighbors inside a spherical
 cutoff.  If an atom has :math:`M` neighbors, then its local mass density is

doc/src/compute_bond_local.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * bond/local = style name of this compute command
 * one or more values may be appended
-* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name*
+* value = *dist* or *dx* or *dy* or *dz* or *engpot* or *force* or *fx* or *fy* or *fz* or *engvib* or *engrot* or *engtrans* or *omega* or *velvib* or *v_name* or *bN*
 
 .. parsed-literal::
 
@@ -29,6 +29,7 @@ Syntax
      *omega* = magnitude of bond angular velocity
      *velvib* = vibrational velocity along the bond length
      *v_name* = equal-style variable with name (see below)
+     *bN* = bond style specific quantities for allowed N values
 
 * zero or more keyword/args pairs may be appended
 * keyword = *set*
@@ -47,7 +48,7 @@ Examples
    compute 1 all bond/local engpot
    compute 1 all bond/local dist engpot force
 
-   compute 1 all bond/local dist fx fy fz
+   compute 1 all bond/local dist fx fy fz b1 b2
 
    compute 1 all bond/local dist v_distsq set dist d
 
@@ -147,6 +148,19 @@ those quantities via the :doc:`compute reduce <compute_reduce>` command
 with thermo output, and the :doc:`fix ave/histo <fix_ave_histo>`
 command will histogram the length\ :math:`^2` values and write them to a file.
 
+A bond style may define additional bond quantities which can be
+accessed as *b1* to *bN*, where N is defined by the bond style.  Most
+bond styles do not define any additional quantities, so N = 0.  An
+example of ones that do are the :doc:`BPM bond styles <Howto_bpm>`
+which store the reference state between two particles. See
+individual bond styles for details.
+
+When using *bN* with bond style *hybrid*, the output will be the Nth
+quantity from the sub-style that computes the bonded interaction
+(based on bond type).  If that sub-style does not define a *bN*,
+the output will be 0.0.  The maximum allowed N is the maximum number
+of quantities provided by any sub-style.
+
 ----------
 
 The local data stored by this command is generated by looping over all

doc/src/compute_chunk_atom.rst

@@ -602,8 +602,7 @@ be used.  For non-orthogonal (triclinic) simulation boxes, only the
 *reduced* option may be used.
 
 A *box* value selects standard distance units as defined by the
-:doc:`units <units>` command (e.g., :math:`\mathrm{\mathring A}`
+:doc:`units <units>` command (e.g., :math:`\AA` for units = *real* or *metal*).
-for units = *real* or *metal*).
 A *lattice* value means the distance units are in lattice spacings.
 The :doc:`lattice <lattice>` command must have been previously used to
 define the lattice spacing.  A *reduced* value means normalized

doc/src/compute_damage_atom.rst

@@ -24,16 +24,17 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom damage for each atom
-in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+in a group.  This is a quantity relevant for :doc:`Peridynamics models
-for an overview of LAMMPS commands for Peridynamics modeling.
+<pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_ for an
+overview of LAMMPS commands for Peridynamics modeling.
 
 The "damage" of a Peridynamics particles is based on the bond breakage
 between the particle and its neighbors.  If all the bonds are broken
 the particle is considered to be fully damaged.
 
-See the `PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for a formal
+See the :doc:`Peridynamics Howto <Howto_peri>` for a formal definition
-definition of "damage" and more details about Peridynamics as it is
+of "damage" and more details about Peridynamics as it is implemented in
-implemented in LAMMPS.
+LAMMPS.
 
 This command can be used with all the Peridynamic pair styles.
 
@@ -53,8 +54,9 @@ The per-atom vector values are unitless numbers (damage) :math:`\ge 0.0`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_dilatation_atom.rst

@@ -24,7 +24,8 @@ Description
 """""""""""
 
 Define a computation that calculates the per-atom dilatation for each
-atom in a group.  This is a quantity relevant for :doc:`Peridynamics models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
+atom in a group.  This is a quantity relevant for :doc:`Peridynamics
+models <pair_peri>`.  See `this document <PDF/PDLammps_overview.pdf>`_
 for an overview of LAMMPS commands for Peridynamics modeling.
 
 For small deformation, dilatation of is the measure of the volumetric
@@ -32,13 +33,14 @@ strain.
 
 The dilatation :math:`\theta` for each peridynamic particle :math:`i` is
 calculated as a sum over its neighbors with unbroken bonds, where the
-contribution of the :math:`ij` pair is a function of the change in bond length
+contribution of the :math:`ij` pair is a function of the change in bond
-(versus the initial length in the reference state), the volume
+length (versus the initial length in the reference state), the volume
 fraction of the particles and an influence function.  See the
-`PDLAMMPS user guide <http://www.sandia.gov/~mlparks/papers/PDLAMMPS.pdf>`_ for
+:doc:`Peridynamics Howto <Howto_peri>` for a formal definition of
-a formal definition of dilatation.
+dilatation.
 
-This command can only be used with a subset of the Peridynamic :doc:`pair styles <pair_peri>`: peri/lps, peri/ves and peri/eps.
+This command can only be used with a subset of the Peridynamic
+:doc:`pair styles <pair_peri>`: *peri/lps*, *peri/ves*, and *peri/eps*.
 
 The dilatation value will be 0.0 for atoms not in the specified
 compute group.
@@ -56,9 +58,9 @@ The per-atom vector values are unitless numbers :math:`(\theta \ge 0.0)`.
 Restrictions
 """"""""""""
 
-This compute is part of the PERI package.  It is only enabled if
+This compute is part of the PERI package.  It is only enabled if LAMMPS
-LAMMPS was built with that package.  See the
+was built with that package.  See the :doc:`Build package
-:doc:`Build package <Build_package>` page for more info.
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/compute_displace_atom.rst

@@ -17,7 +17,7 @@ Syntax
 
   .. parsed-literal::
 
-       *replace* arg = name of per-atom variable
+       *refresh* arg = name of per-atom variable
 
 Examples
 """"""""
@@ -95,7 +95,7 @@ something like the following commands:
                    refresh c_dsp delay 100
 
 The :doc:`dump_modify thresh <dump_modify>` command will only output
-atoms that have displaced more than :math:`0.6~\mathrm{\mathring A}` on each
+atoms that have displaced more than :math:`0.6~\AA` on each
 snapshot (assuming metal units).  The dump_modify *refresh* option triggers a
 call to this compute at the end of every dump.
 

doc/src/compute_entropy_atom.rst

@@ -97,13 +97,13 @@ by the corresponding volume. This option can be useful when dealing with
 inhomogeneous systems such as those that have surfaces.
 
 Here are typical input parameters for fcc aluminum (lattice
-constant :math:`4.05~\mathrm{\mathring A}`),
+constant :math:`4.05~\AA`),
 
 .. parsed-literal::
 
    compute 1 all entropy/atom 0.25 5.7 avg yes 3.7
 
-and for bcc sodium (lattice constant 4.23 Angstroms),
+and for bcc sodium (lattice constant :math:`4.23~\AA`),
 
 .. parsed-literal::
 

doc/src/compute_fep_ta.rst

@@ -34,6 +34,8 @@ Examples
 Description
 """""""""""
 
+.. versionadded:: 4May2022
+
 Define a computation that calculates the change in the free energy due
 to a test-area (TA) perturbation :ref:`(Gloor) <Gloor>`. The test-area
 approach can be used to determine the interfacial tension of the system

doc/src/compute_rigid_local.rst

@@ -6,7 +6,7 @@ compute rigid/local command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    compute ID group-ID rigid/local rigidID input1 input2 ...
 
@@ -25,6 +25,9 @@ Syntax
                              quatw, quati, quatj, quatk,
                              tqx, tqy, tqz,
                              inertiax, inertiay, inertiaz
+
+  .. parsed-literal::
+
            id = atom ID of atom within body which owns body properties
            mol = molecule ID used to define body in :doc:`fix rigid/small <fix_rigid>` command
            mass = total mass of body
@@ -69,8 +72,8 @@ the atoms owned on a processor.  If the atom is not in the specified
 the atom within a body that is assigned to store the body information
 it is skipped (only one atom per body is so assigned).  If it is the
 assigned atom, then the info for that body is output.  This means that
-information for N bodies is generated.  N may be less than the # of
+information for :math:`N` bodies is generated.  :math:`N` may be less than the
-bodies defined by the fix rigid command, if the atoms in some bodies
+number of bodies defined by the fix rigid command, if the atoms in some bodies
 are not in the *group-ID*\ .
 
 .. note::
@@ -109,8 +112,7 @@ The *mass* attribute is the total mass of the rigid body.
 There are two options for outputting the coordinates of the center of
 mass (COM) of the body.  The *x*, *y*, *z* attributes write the COM
 "unscaled", in the appropriate distance :doc:`units <units>`
-(:math:`\mathrm{\mathring A}`,
+(:math:`\AA`, :math:`\sigma`, etc).  Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
-sigma, etc).  Use *xu*, *yu*, *zu* if you want the COM "unwrapped" by
 the image flags for each body.  Unwrapped means that if the body
 COM has passed through a periodic boundary one or more times, the value
 is generated what the COM coordinate would be if it had not been
@@ -120,7 +122,7 @@ The image flags for the body can be generated directly using the *ix*,
 *iy*, *iz* attributes.  For periodic dimensions, they specify which
 image of the simulation box the COM is considered to be in.  An image
 of 0 means it is inside the box as defined.  A value of 2 means add 2
-box lengths to get the true value.  A value of -1 means subtract 1 box
+box lengths to get the true value.  A value of :math:`-1` means subtract 1 box
 length to get the true value.  LAMMPS updates these flags as the rigid
 body COMs cross periodic boundaries during the simulation.
 
@@ -142,8 +144,8 @@ The *tqx*, *tqy*, *tqz* attributes are components of the torque acting
 on the body around its COM.
 
 The *inertiax*, *inertiay*, *inertiaz* attributes are components of
-diagonalized inertia tensor for the body, i.e the 3 moments of inertia
+diagonalized inertia tensor for the body (i.e., the three moments of inertia
-for the body around its principal axes, as computed internally by
+for the body around its principal axes), as computed internally by
 LAMMPS.
 
 ----------
@@ -170,10 +172,10 @@ corresponding attribute is in:
 * vx,vy,vz = velocity units
 * fx,fy,fz = force units
 * omegax,omegay,omegaz = radians/time units
-* angmomx,angmomy,angmomz = mass\*distance\^2/time units
+* angmomx,angmomy,angmomz = mass\*distance\ :math:`^2`\ /time units
 * quatw,quati,quatj,quatk = unitless
 * tqx,tqy,tqz = torque units
-* inertiax,inertiay,inertiaz = mass\*distance\^2 units
+* inertiax,inertiay,inertiaz = mass\*distance\ :math:`^2` units
 
 Restrictions
 """"""""""""

doc/src/compute_saed.rst

@@ -86,7 +86,7 @@ will defined using the *c* values for the spacing along each reciprocal
 lattice axis. Note that manual mapping of the reciprocal space mesh is
 good for comparing diffraction results from  multiple simulations; however
 it can reduce the likelihood that Bragg reflections will be satisfied
-unless small spacing parameters (:math:`<0.05~\mathrm{\mathring A}^-1`)
+unless small spacing parameters (:math:`<0.05~\AA^-1`)
 are implemented.  Meshes with manual spacing do not require a periodic
 boundary.
 

doc/src/compute_sna_atom.rst

@@ -228,18 +228,20 @@ command:
 See section below on output for a detailed explanation of the data
 layout in the global array.
 
+.. versionadded:: 3Aug2022
+
 The compute *sna/grid* and *sna/grid/local* commands calculate
-bispectrum components for a regular grid of points.
+bispectrum components for a regular grid of points.  These are
-These are calculated from the local density of nearby atoms *i'*
+calculated from the local density of nearby atoms *i'* around each grid
-around each grid point, as if there was a central atom *i*
+point, as if there was a central atom *i* at the grid point. This is
-at the grid point. This is useful for characterizing fine-scale
+useful for characterizing fine-scale structure in a configuration of
-structure in a configuration of atoms, and it is used
+atoms, and it is used in the `MALA package
-in the `MALA package <https://github.com/casus/mala>`_
+<https://github.com/casus/mala>`_ to build machine-learning surrogates
-to build machine-learning surrogates for finite-temperature Kohn-Sham
+for finite-temperature Kohn-Sham density functional theory (:ref:`Ellis
-density functional theory (:ref:`Ellis et al. <Ellis2021>`)
+et al. <Ellis2021>`) Neighbor atoms not in the group do not contribute
-Neighbor atoms not in the group do not contribute to the
+to the bispectrum components of the grid points. The distance cutoff
-bispectrum components of the grid points. The distance cutoff :math:`R_{ii'}`
+:math:`R_{ii'}` assumes that *i* has the same type as the neighbor atom
-assumes that *i* has the same type as the neighbor atom *i'*.
+*i'*.
 
 Compute *sna/grid* calculates a global array containing bispectrum
 components for a regular grid of points.

doc/src/compute_temp_cs.rst

@@ -29,7 +29,7 @@ Description
 Define a computation that calculates the temperature of a system based
 on the center-of-mass velocity of atom pairs that are bonded to each
 other.  This compute is designed to be used with the adiabatic
-core/shell model of :ref:`(Mitchell and Finchham) <MitchellFinchham1>`.
+core/shell model of :ref:`(Mitchell and Fincham) <MitchellFincham1>`.
 See the :doc:`Howto coreshell <Howto_coreshell>` page for an overview of
 the model as implemented in LAMMPS.  Specifically, this compute
 enables correct temperature calculation and thermostatting of
@@ -127,7 +127,7 @@ none
 
 ----------
 
-.. _MitchellFinchham1:
+.. _MitchellFincham1:
 
-**(Mitchell and Finchham)** Mitchell, Finchham, J Phys Condensed Matter,
+**(Mitchell and Fincham)** Mitchell, Fincham, J Phys Condensed Matter,
 5, 1031-1038 (1993).

doc/src/compute_temp_ramp.rst

@@ -58,7 +58,7 @@ constant, and :math:`T` is the absolute temperature.
 The *units* keyword determines the meaning of the distance units used
 for coordinates (*clo*, *chi*) and velocities (*vlo*, *vhi*).  A *box* value
 selects standard distance units as defined by the :doc:`units <units>`
-command (e.g., :math:`\mathrm{\mathring{A}}` for units = real or metal).  A
+command (e.g., :math:`\AA` for units = real or metal).  A
 *lattice* value means the distance units are in lattice spacings (i.e.,
 velocity in lattice spacings per unit time).  The :doc:`lattice <lattice>`
 command must have been previously used to define the lattice spacing.

doc/src/compute_voronoi_atom.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`compute <compute>` command
 * voronoi/atom = style name of this compute command
 * zero or more keyword/value pairs may be appended
-* keyword = *only_group* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
+* keyword = *only_group* or *occupation* or *surface* or *radius* or *edge_histo* or *edge_threshold* or *face_threshold* or *neighbors* or *peratom*
 
   .. parsed-literal::
 
@@ -154,25 +154,25 @@ which must be installed on your system when building LAMMPS for use
 with this compute.  See instructions on obtaining and installing the
 Voro++ software in the src/VORONOI/README file.
 
-.. _voronoi: http://math.lbl.gov/voro++/
+.. _voronoi: https://math.lbl.gov/voro++/
 
 .. note::
 
-   The calculation of Voronoi volumes is performed by each
+   The calculation of Voronoi volumes is performed by each processor for
-   processor for the atoms it owns, and includes the effect of ghost
+   the atoms it owns, and includes the effect of ghost atoms stored by
-   atoms stored by the processor.  This assumes that the Voronoi cells of
+   the processor.  This assumes that the Voronoi cells of owned atoms
-   owned atoms are not affected by atoms beyond the ghost atom cut-off
+   are not affected by atoms beyond the ghost atom cut-off distance.
-   distance.  This is usually a good assumption for liquid and solid
+   This is usually a good assumption for liquid and solid systems, but
-   systems, but may lead to underestimation of Voronoi volumes in low
+   may lead to underestimation of Voronoi volumes in low density
-   density systems.  By default, the set of ghost atoms stored by each
+   systems.  By default, the set of ghost atoms stored by each processor
-   processor is determined by the cutoff used for
+   is determined by the cutoff used for :doc:`pair_style <pair_style>`
-   :doc:`pair_style <pair_style>` interactions.  The cutoff can be set
+   interactions.  The cutoff can be set explicitly via the
-   explicitly via the :doc:`comm_modify cutoff <comm_modify>` command.  The
+   :doc:`comm_modify cutoff <comm_modify>` command.  The Voronoi cells
-   Voronoi cells for atoms adjacent to empty regions will extend into
+   for atoms adjacent to empty regions will extend into those regions up
-   those regions up to the communication cutoff in :math:`x`, :math:`y`, or
+   to the communication cutoff in :math:`x`, :math:`y`, or :math:`z`.
-   :math:`z`.  In that situation, an exterior face is created at the cutoff
+   In that situation, an exterior face is created at the cutoff distance
-   distance normal to the :math:`x`, :math:`y`, or :math:`z` direction.
+   normal to the :math:`x`, :math:`y`, or :math:`z` direction.  For
-   For triclinic systems, the exterior face is parallel to the corresponding
+   triclinic systems, the exterior face is parallel to the corresponding
    reciprocal lattice vector.
 
 .. note::

doc/src/compute_xrd.rst

@@ -91,7 +91,7 @@ reciprocal lattice axis. Note that manual mapping of the reciprocal
 space mesh is good for comparing diffraction results from multiple
 simulations; however, it can reduce the likelihood that Bragg
 reflections will be satisfied unless small spacing parameters
-(:math:`< 0.05~\mathrm{\mathring{A}}^{-1}`) are implemented.
+(:math:`< 0.05~\AA^{-1}`) are implemented.
 Meshes with manual spacing do not require a periodic boundary.
 
 The limits of the reciprocal lattice mesh are determined by range of