merged in current master

.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:

cmake/CMakeLists.txt

@@ -7,6 +7,10 @@ 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)
@@ -385,9 +389,9 @@ 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()
@@ -396,8 +400,8 @@ 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 +731,17 @@ 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 +750,14 @@ 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)
@@ -969,9 +980,6 @@ 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()
@@ -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/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()

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,6 +1,6 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2022.09.27.fix10Oct.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 "766cebcc0e5c4b8430c2f3cd202d9905" 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)
 

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/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/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 ;\
@@ -163,6 +167,8 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 	@if [ "$(HAS_PDFLATEX)" == "NO" ] ; then echo "PDFLaTeX or latexmk were not found! Please check README for further instructions" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
+		sphinx-build -E $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
+		touch $(RSTDIR)/Fortran.rst ;\
 		sphinx-build  $(SPHINXEXTRA) -b latex -c $(SPHINXCONFIG) -d $(BUILDDIR)/doctrees $(RSTDIR) latex ;\
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ;\

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/Build_development.rst

@@ -147,6 +147,16 @@ 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
@@ -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
@@ -954,7 +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
@@ -1011,7 +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
@@ -1100,7 +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
@@ -1179,7 +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
@@ -1230,7 +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
@@ -1293,7 +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
@@ -1334,20 +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
 
@@ -1356,6 +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:
@@ -1555,7 +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
@@ -1611,7 +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
 
@@ -1748,7 +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
@@ -1917,7 +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
@@ -2025,7 +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
@@ -2069,7 +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/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>`
@@ -295,6 +295,7 @@ 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/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
@@ -87,15 +97,16 @@ 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 <https://en.wikipedia.org/wiki/Water_model>`_.
 

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/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

@@ -200,6 +200,7 @@ 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
@@ -1736,8 +1737,6 @@ must be installed.
 
 .. versionadded:: 30Jun2020
 
-   .. versionadded:: 30Jun2020
-
 **Supporting info:**
 
 * src/ML-IAP: filenames -> commands

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/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/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_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
 """"""""

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::
@@ -119,7 +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.
 
@@ -141,8 +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.
 
 ----------
@@ -169,10 +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_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::
 

doc/src/create_atoms.rst

@@ -28,7 +28,7 @@ Syntax
          region-ID = create atoms within this region, use NULL for entire simulation box
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *overlap* or *maxtry* or *units*
+* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *radscale* or *meshmode* or *rotate* or *overlap* or *maxtry* or *units*
 
   .. parsed-literal::
 

doc/src/delete_bonds.rst

@@ -26,6 +26,13 @@ Syntax
 * zero or more keywords may be appended
 * keyword = *any* or *undo* or *remove* or *special*
 
+  .. parsed-literal::
+
+       *any* arg = none = turn off interactions if any atoms are in the group (or on if *undo* is also used)
+       *undo* arg = none = turn specified bonds on instead of off
+       *remove* arg = permanently remove bonds that have been turned off
+       *special* arg = recompute pairwise 1-2, 1-3, and 1-4 lists
+
 Examples
 """"""""
 
@@ -101,13 +108,13 @@ Several keywords can be appended to the argument list to alter the
 default behaviors.
 
 The *any* keyword changes the requirement that all atoms in the bond
-(angle, etc) must be in the specified group in order to turn off the
+(angle, etc.) must be in the specified group in order to turn off the
 interaction.  Instead, if any of the atoms in the interaction are in
 the specified group, it will be turned off (or on if the *undo*
 keyword is used).
 
 The *undo* keyword inverts the delete_bonds command so that the
-specified bonds, angles, etc are turned on if they are currently
+specified bonds, angles, etc. are turned on if they are currently
 turned off.  This means a negative value is toggled to positive.  For
 example, for style *angle*, if *type* is specified as 2, then all
 angles with current type = :math:`-2` are reset to type = :math:`2`.

doc/src/dump.rst

@@ -216,7 +216,7 @@ or multiple smaller files).
    to a dump file may be slightly outside the simulation box.
    Re-neighbor timesteps will not typically coincide with the
    timesteps dump snapshots are written.  See the :doc:`dump_modify
-   pbc <dump_modify>` command if you with to force coordinates to be
+   pbc <dump_modify>` command if you wish to force coordinates to be
    strictly inside the simulation box.
 
 .. note::

doc/src/fix_ave_chunk.rst

@@ -31,7 +31,7 @@ Syntax
        v_name = per-atom vector calculated by an atom-style variable with name
 
 * zero or more keyword/arg pairs may be appended
-* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *title1* or *title2* or *title3*
+* keyword = *norm* or *ave* or *bias* or *adof* or *cdof* or *file* or *overwrite* or *format* or *title1* or *title2* or *title3*
 
   .. parsed-literal::
 

doc/src/fix_ave_histo.rst

@@ -35,7 +35,7 @@ Syntax
        v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
 
 * zero or more keyword/arg pairs may be appended
-* keyword = *mode* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
+* keyword = *mode* or *kind* or *file* or *ave* or *start* or *beyond* or *overwrite* or *title1* or *title2* or *title3*
 
   .. parsed-literal::
 

doc/src/fix_ave_time.rst

@@ -28,7 +28,7 @@ Syntax
        v_name[I] = value calculated by a vector-style variable with name, I can include wildcard (see below)
 
 * zero or more keyword/arg pairs may be appended
-* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *title1* or *title2* or *title3*
+* keyword = *mode* or *file* or *ave* or *start* or *off* or *overwrite* or *format* or *title1* or *title2* or *title3*
 
   .. parsed-literal::
 

doc/src/fix_bocs.rst

@@ -6,17 +6,28 @@ fix bocs command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID bocs keyword values ...
 
-   keyword = *temp* or *cgiso* or *analytic* or *linear_spline* or *cubic_spline*
+* ID, group-ID are documented in :doc:`fix <fix>` command
+* bocs = style name of this fix command
+* two or more keyword/value pairs may be appended
+* keyword = *temp* or *cgiso* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop*
+
+  .. parsed-literal::
+
      *temp* values = Tstart Tstop Tdamp
-     *cgiso* values = Pstart Pstop Pdamp
+     *cgiso* values = Pstart Pstop Pdamp basis_set args
-     *basis set*
+       basis_set = *analytic* or *linear_spline* or *cubic_spline*
-       *analytic* values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
+         *analytic* args = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
-       *linear_spline* values = input_filename
+         *linear_spline* args = input_filename
-       *cubic_spline* values = input_filename
+         *cubic_spline* args = input_filename
+     *tchain* value = N = length of thermostat chain (1 = single thermostat)
+     *pchain* value = N = length of thermostat on barostat (0 = no thermostat)
+     *mtk* value = *yes* or *no* = add MTK adjustment term or not
+     *tloop* value = M = number of sub-cycles to perform on thermostat
+     *ploop* value = M = number of sub-cycles to perform on barostat
 
 Examples
 """"""""
@@ -24,25 +35,24 @@ Examples
 .. code-block:: LAMMPS
 
    fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
-
    fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat
-
    thermo_modify press 1_press
 
 Description
 """""""""""
 
 These commands incorporate a pressure correction as described by
-Dunn and Noid in :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTTK
+Dunn and Noid :ref:`(Dunn1) <bocs-Dunn1>` to the standard MTK
-barostat by Martyna et. al. in :ref:`(Martyna) <bocs-Martyna>` .
+barostat by Martyna et al. :ref:`(Martyna) <bocs-Martyna>`.
-The first half of the command mimics a standard fix npt command:
+The first half of the command mimics a standard :doc:`fix npt <fix_nh>`
+command:
 
 .. code-block:: LAMMPS
 
    fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp
 
 The two differences are replacing *npt* with *bocs*, and replacing
-*iso*\ /\ *aniso*\ /\ *etc* with *cgiso*\ .
+*iso*\ /\ *aniso*\ /\ etc. with *cgiso*\ .
 The rest of the command details what form you would like to use for
 the pressure correction equation. The choices are: *analytic*, *linear_spline*,
 or *cubic_spline*.
@@ -58,9 +68,9 @@ as a function of volume. The file must be formatted so each line has:
 Note both the COMMA and the SPACE separating the volume's
 value and its corresponding pressure correction. The volumes in the file
 must be uniformly spaced. Both the volumes and the pressure corrections
-should be provided in the proper units, e.g. if you are using *units real*,
+should be provided in the proper units (e.g., if you are using *units real*,
-the volumes should all be in cubic Angstroms, and the pressure corrections
+the volumes should all be in :math:`\mathrm{\mathring{A}}^3` and the pressure
-should all be in atmospheres. Furthermore, the table should start/end at a
+corrections should all be in atm). Furthermore, the table should start/end at a
 volume considerably smaller/larger than you expect your system to sample
 during the simulation. If the system ever reaches a volume outside of the
 range provided, the simulation will stop.
@@ -71,9 +81,10 @@ With the *analytic* option, the arguments are as follows:
 
    ... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
 
-Note that *V_avg* and *Coeff_i* should all be in the proper units, e.g. if you
+Note that *V_avg* and *Coeff_i* should all be in the proper units (e.g., if you
-are using *units real*, *V_avg* should be in cubic Angstroms, and the
+are using *units real*, *V_avg* should be in :math:`\mathrm{\mathring{A}^3}`
-coefficients should all be in atmospheres \* cubic Angstroms.
+and the coefficients should all be in
+:math:`\mathrm{atm}\cdot\mathrm{\mathring{A}^3}`\ ).
 
 ----------
 
@@ -122,7 +133,7 @@ are written to a file every so often. In order to have LAMMPS report the
 modified pressure, you must include the *thermo_modify* command given in
 the examples. For the last argument in the command, you should put
 XXXX_press, where XXXX is the ID given to the fix bocs command (in the
-example, the ID of the fix bocs command is 1 ).
+example, the ID of the fix bocs command is 1).
 
 This fix is part of the BOCS package.  It is only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
@@ -132,7 +143,7 @@ Further information
 
 For more details about the pressure correction and the entire BOCS software
 package, visit the `BOCS package on GitHub <bocsgithub_>`_ and read the release
-paper by Dunn et. al. :ref:`(Dunn2) <bocs-Dunn2>` .
+paper by Dunn et al. :ref:`(Dunn2) <bocs-Dunn2>` .
 
 .. _bocsgithub: https://github.com/noid-group/BOCS
 

doc/src/fix_bond_break.rst

@@ -6,7 +6,7 @@ fix bond/break command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID bond/break Nevery bondtype Rmax keyword values ...
 
@@ -15,7 +15,7 @@ Syntax
 * Nevery = attempt bond breaking every this many steps
 * bondtype = type of bonds to break
 * Rmax = bond longer than Rmax can break (distance units)
-* zero or more keyword/value pairs may be appended to args
+* zero or more keyword/value pairs may be appended
 * keyword = *prob*
 
   .. parsed-literal::
@@ -43,42 +43,42 @@ pair of atoms computed by the :doc:`bond_style <bond_style>` command.
 Once the bond is broken it will be permanently deleted, as will all
 angle, dihedral, and improper interactions that bond is part of.
 
-This is different than a :doc:`pairwise <pair_style>` bond-order
+This is different than a :doc:`pair-wise <pair_style>` bond-order
 potential such as Tersoff or AIREBO which infers bonds and many-body
 interactions based on the current geometry of a small cluster of atoms
 and effectively creates and destroys bonds and higher-order many-body
 interactions from timestep to timestep as atoms move.
 
 A check for possible bond breakage is performed every *Nevery*
-timesteps.  If two bonded atoms I,J are further than a distance *Rmax*
+timesteps.  If two bonded atoms :math:`i` and :math:`j` are farther than the
-of each other, if the bond is of type *bondtype*, and if both I and J
+distance *Rmax* from each other, the bond is of type *bondtype*, and both
-are in the specified fix group, then I,J is labeled as a "possible"
+:math:`i` and :math:`j` are in the specified fix group, then the bond between
-bond to break.
+:math:`i` and :math:`j` is labeled as a "possible" bond to break.
 
 If several bonds involving an atom are stretched, it may have multiple
 possible bonds to break.  Every atom checks its list of possible bonds
 to break and labels the longest such bond as its "sole" bond to break.
-After this is done, if atom I is bonded to atom J in its sole bond,
+After this is done, if atom :math:`i` is bonded to atom :math:`j` in its sole
-and atom J is bonded to atom I in its sole bond, then the I,J bond is
+bond, and atom :math:`j` is bonded to atom :math:`j` in its sole bond, then the
-"eligible" to be broken.
+bond between :math:`i` and :math:`j` is "eligible" to be broken.
 
 Note that these rules mean an atom will only be part of at most one
-broken bond on a given timestep.  It also means that if atom I chooses
+broken bond on a given time step.  It also means that if atom :math:`i` chooses
-atom J as its sole partner, but atom J chooses atom K is its sole
+atom :math:`j` as its sole partner, but atom :math:`j` chooses atom :math:`k`
-partner (due to Rjk > Rij), then this means atom I will not be part of
+as its sole partner (because :math:`R_{jk} > R_{ij}`), then this means atom
-a broken bond on this timestep, even if it has other possible bond
+:math:`i` will not be part of a broken bond on this time step, even if it has
-partners.
+other possible bond partners.
 
 The *prob* keyword can effect whether an eligible bond is actually
 broken.  The *fraction* setting must be a value between 0.0 and 1.0.
 A uniform random number between 0.0 and 1.0 is generated and the
-eligible bond is only broken if the random number < fraction.
+eligible bond is only broken if the random number is less than *fraction*.
 
 When a bond is broken, data structures within LAMMPS that store bond
-topology are updated to reflect the breakage.  Likewise, if the bond
+topologies are updated to reflect the breakage.  Likewise, if the bond
 is part of a 3-body (angle) or 4-body (dihedral, improper)
 interaction, that interaction is removed as well.  These changes
-typically affect pairwise interactions between atoms that used to be
+typically affect pair-wise interactions between atoms that used to be
 part of bonds, angles, etc.
 
 .. note::
@@ -88,17 +88,17 @@ part of bonds, angles, etc.
    becomes two molecules due to the broken bond, all atoms in both new
    molecules retain their original molecule IDs.
 
-Computationally, each timestep this fix operates, it loops over all
+Computationally, each time step this fix is invoked, it loops over all
 the bonds in the system and computes distances between pairs of bonded
 atoms.  It also communicates between neighboring processors to
 coordinate which bonds are broken.  Moreover, if any bonds are broken,
-neighbor lists must be immediately updated on the same timestep.  This
+neighbor lists must be immediately updated on the same time step.  This
-is to insure that any pairwise interactions that should be turned "on"
+is to ensure that any pair-wise interactions that should be turned "on"
 due to a bond breaking, because they are no longer excluded by the
 presence of the bond and the settings of the
 :doc:`special_bonds <special_bonds>` command, will be immediately
-recognized.  All of these operations increase the cost of a timestep.
+recognized.  All of these operations increase the cost of a time step.
-Thus you should be cautious about invoking this fix too frequently.
+Thus, you should be cautious about invoking this fix too frequently.
 
 You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
 
@@ -107,11 +107,11 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
    Breaking a bond typically alters the energy of a system.  You
    should be careful not to choose bond breaking criteria that induce a
    dramatic change in energy.  For example, if you define a very stiff
-   harmonic bond and break it when 2 atoms are separated by a distance
+   harmonic bond and break it when two atoms are separated by a distance
-   far from the equilibrium bond length, then the 2 atoms will be
+   far from the equilibrium bond length, then the two atoms will be
    dramatically released when the bond is broken.  More generally, you
    may need to thermostat your system to compensate for energy changes
-   resulting from broken bonds (and angles, dihedrals, impropers).
+   resulting from broken bonds (as well as angles, dihedrals, and impropers).
 
 See the :doc:`Howto <Howto_broken_bonds>` page on broken bonds for more
 information on related features in LAMMPS.
@@ -124,14 +124,14 @@ Restart, fix_modify, output, run start/stop, minimize info
 No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
 are relevant to this fix.
 
-This fix computes two statistics which it stores in a global vector of
+This fix computes two statistics, which it stores in a global vector of
-length 2, which can be accessed by various :doc:`output commands <Howto_output>`.  The vector values calculated by this fix
+length 2. This vector can be accessed by various :doc:`output commands
-are "intensive".
+<Howto_output>`.  The vector values calculated by this fix are "intensive".
 
-These are the 2 quantities:
+The two quantities in the global vector are
 
-* (1) # of bonds broken on the most recent breakage timestep
+  (1) number of bonds broken on the most recent breakage time step
-* (2) cumulative # of bonds broken
+  (2) cumulative number of bonds broken
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.

doc/src/fix_bond_create.rst

@@ -10,7 +10,7 @@ fix bond/create/angle command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID bond/create Nevery itype jtype Rmin bondtype keyword values ...
 
@@ -58,83 +58,84 @@ Description
 """""""""""
 
 Create bonds between pairs of atoms as a simulation runs according to
-specified criteria.  This can be used to model cross-linking of
+specified criteria.  This can be used to model the cross-linking of
 polymers, the formation of a percolation network, etc.  In this
 context, a bond means an interaction between a pair of atoms computed
 by the :doc:`bond_style <bond_style>` command.  Once the bond is created
 it will be permanently in place.  Optionally, the creation of a bond
-can also create angle, dihedral, and improper interactions that bond
+can also create angle, dihedral, and improper interactions that the bond
 is part of.  See the discussion of the *atype*, *dtype*, and *itype*
 keywords below.
 
-This is different than a :doc:`pairwise <pair_style>` bond-order
+This process is different than a :doc:`pair-wise <pair_style>` bond-order
-potential such as Tersoff or AIREBO which infers bonds and many-body
+potential such as Tersoff or AIREBO, which infer bonds and many-body
 interactions based on the current geometry of a small cluster of atoms
-and effectively creates and destroys bonds and higher-order many-body
+and effectively create and destroy bonds and higher-order many-body
-interactions from timestep to timestep as atoms move.
+interactions from time step to time step as the atoms move.
 
-A check for possible new bonds is performed every *Nevery* timesteps.
+A check for possible new bonds is performed every *Nevery* time steps.
-If two atoms I,J are within a distance *Rmin* of each other, if I is
+If two atoms :math:`i` and :math:`j` are within a distance *Rmin* of each
-of atom type *itype*, if J is of atom type *jtype*, if both I and J
+other, atom :math:`i` is of type *itype*, atom :math:`j` is of type *jtype*,
-are in the specified fix group, if a bond does not already exist
+and both :math:`i` and :math:`j` are in the specified fix group, then if a bond
-between I and J, and if both I and J meet their respective *maxbond*
+does not already exist between atoms :math:`i` and :math:`j`, and if both
-requirement (explained below), then I,J is labeled as a "possible"
+:math:`i` and :math:`j` meet their respective *maxbond* requirements (explained
-bond pair.
+below), then :math:`i` and :math:`j` are labeled as a "possible" bond pair.
 
 If several atoms are close to an atom, it may have multiple possible
 bond partners.  Every atom checks its list of possible bond partners
 and labels the closest such partner as its "sole" bond partner.  After
-this is done, if atom I has atom J as its sole partner, and atom J has
+this is done, if atom :math:`i` has atom :math:`j` as its sole partner and
-atom I as its sole partner, then the I,J bond is "eligible" to be
+atom :math:`j` has atom :math:`i` as its sole partner, then the
-formed.
+:math:`i,j` bond is "eligible" to be formed.
 
-Note that these rules mean an atom will only be part of at most one
+Note that these rules mean that an atom will only be part of at most one
-created bond on a given timestep.  It also means that if atom I
+created bond on a given time step.  It also means that if atom :math:`i`
-chooses atom J as its sole partner, but atom J chooses atom K is its
+chooses atom :math:`j` as its sole partner, but atom :math:`j` chooses atom
-sole partner (due to Rjk < Rij), then this means atom I will not form
+:math:`k` as its sole partner (because :math:`R_{jk} < R_{ij}`), then atom
-a bond on this timestep, even if it has other possible bond partners.
+:math:`i` will not form a bond on this time step, even if it has other possible
+bond partners.
 
-It is permissible to have *itype* = *jtype*\ .  *Rmin* must be <= the
+It is permissible to have *itype* = *jtype*\ .  *Rmin* must be :math:`\leq` the
-pairwise cutoff distance between *itype* and *jtype* atoms, as defined
+pair-wise cutoff distance between *itype* and *jtype* atoms, as defined
 by the :doc:`pair_style <pair_style>` command.
 
 The *iparam* and *jparam* keywords can be used to limit the bonding
 functionality of the participating atoms.  Each atom keeps track of
-how many bonds of *bondtype* it already has.  If atom I of
+how many bonds of *bondtype* it already has.  If atom :math:`i` of type
-itype already has *maxbond* bonds (as set by the *iparam*
+*itype* already has *maxbond* bonds (as set by the *iparam*
-keyword), then it will not form any more.  Likewise for atom J.  If
+keyword), then it will not form any more, and likewise for atom :math:`j`.
-*maxbond* is set to 0, then there is no limit on the number of bonds
+If *maxbond* is set to 0, then there is no limit on the number of bonds
 that can be formed with that atom.
 
 The *newtype* value for *iparam* and *jparam* can be used to change
-the atom type of atom I or J when it reaches *maxbond* number of bonds
+the atom type of atom :math:`i` or :math:`j` when it reaches *maxbond* number
-of type *bondtype*\ .  This means it can now interact in a pairwise
+of bonds of type *bondtype*\ .  This means it can now interact in a pair-wise
 fashion with other atoms in a different way by specifying different
 :doc:`pair_coeff <pair_coeff>` coefficients.  If you do not wish the
 atom type to change, simply specify *newtype* as *itype* or *jtype*\ .
 
-The *prob* keyword can also effect whether an eligible bond is
+The *prob* keyword can also affect whether an eligible bond is
 actually created.  The *fraction* setting must be a value between 0.0
 and 1.0.  A uniform random number between 0.0 and 1.0 is generated and
-the eligible bond is only created if the random number < fraction.
+the eligible bond is only created if the random number is less than *fraction*.
 
 The *aconstrain* keyword is only available with the fix
-bond/create/angle command.  It allows to specify a minimal and maximal
+bond/create/angle command.  It allows one to specify minimum and maximum
-angle *amin* and *amax* between the two prospective bonding partners and
+angles *amin* and *amax*, respectively, between the two prospective bonding
-a third particle that is already bonded to one of the two partners.
+partners and a third particle that is already bonded to one of the two
-Such a criterion can be important when new angles are defined together
+partners. Such a criterion can be important when new angles are defined
-with the formation of a new bond.  Without a restriction on the
+together with the formation of a new bond.  Without a restriction on the
 permissible angle, and for stiffer angle potentials, very large energies
-can arise and lead to uncontrolled behavior.
+can arise and lead to unphysical behavior.
 
 Any bond that is created is assigned a bond type of *bondtype*.
 
 When a bond is created, data structures within LAMMPS that store bond
-topology are updated to reflect the creation.  If the bond is part of
+topologies are updated to reflect the creation.  If the bond is part of
 new 3-body (angle) or 4-body (dihedral, improper) interactions, you
-can choose to create new angles, dihedrals, impropers as well, using
+can choose to create new angles, dihedrals, and impropers as well using
 the *atype*, *dtype*, and *itype* keywords.  All of these changes
-typically affect pairwise interactions between atoms that are now part
+typically affect pair-wise interactions between atoms that are now part
 of new bonds, angles, etc.
 
 .. note::
@@ -165,19 +166,19 @@ of type *angletype*, with parameters assigned by the corresponding
    when bonds are created.  See the :doc:`read_data <read_data>` or
    :doc:`create_box <create_box>` command for more details.  Note that a
    data file with no atoms can be used if you wish to add non-bonded
-   atoms via the :doc:`create atoms <create_atoms>` command, e.g. for a
+   atoms via the :doc:`create atoms <create_atoms>` command (e.g., for a
-   percolation simulation.
+   percolation simulation).
 
 .. note::
 
    LAMMPS stores and maintains a data structure with a list of the
    first, second, and third neighbors of each atom (within the bond topology of
-   the system) for use in weighting pairwise interactions for bonded
+   the system) for use in weighting pair-wise interactions for bonded
    atoms.  Note that adding a single bond always adds a new first neighbor
-   but may also induce \*many\* new second and third neighbors, depending on the
+   but may also induce **many** new second and third neighbors, depending on the
    molecular topology of your system.  The "extra special per atom"
    parameter must typically be set to allow for the new maximum total
-   size (first + second + third neighbors) of this per-atom list.  There are 2
+   size (first + second + third neighbors) of this per-atom list.  There are two
    ways to do this.  See the :doc:`read_data <read_data>` or
    :doc:`create_box <create_box>` commands for details.
 
@@ -186,15 +187,16 @@ of type *angletype*, with parameters assigned by the corresponding
    Even if you do not use the *atype*, *dtype*, or *itype*
    keywords, the list of topological neighbors is updated for atoms
    affected by the new bond.  This in turn affects which neighbors are
-   considered for pairwise interactions, using the weighting rules set by
+   considered for pair-wise interactions, using the weighting rules set by
    the :doc:`special_bonds <special_bonds>` command.  Consider a new bond
-   created between atoms I,J.  If J has a bonded neighbor K, then K
+   created between atoms :math:`i` and :math:`j`.  If :math:`j` has a bonded
-   becomes a second neighbor of I.  Even if the *atype* keyword is not used
+   neighbor :math:`k`, then :math:`k` becomes a second neighbor of :math:`i`.
-   to create angle I-J-K, the pairwise interaction between I and K will
+   Even if the *atype* keyword is not used to create angle :math:`\angle ijk`,
-   be potentially turned off or weighted by the 1-3 weighting specified
+   the pair-wise interaction between :math:`i` and :math:`k` could potentially
+   be turned off or weighted by the 1--3 weighting specified
    by the :doc:`special_bonds <special_bonds>` command.  This is the case
    even if the "angle yes" option was used with that command.  The same
-   is true for third neighbors (1-4 interactions), the *dtype* keyword, and
+   is true for third neighbors (1--4 interactions), the *dtype* keyword, and
    the "dihedral yes" option used with the
    :doc:`special_bonds <special_bonds>` command.
 
@@ -203,20 +205,20 @@ define a :doc:`bond_style <bond_style>` and use the
 :doc:`bond_coeff <bond_coeff>` command to specify coefficients for the
 *bondtype*\ .  Similarly, if new atom types are specified by the
 *iparam* or *jparam* keywords, they must be within the range of atom
-types allowed by the simulation and pairwise coefficients must be
+types allowed by the simulation and pair-wise coefficients must be
 specified for the new types.
 
-Computationally, each timestep this fix operates, it loops over
+Computationally, each time step this fix is invoked, it loops over
 neighbor lists and computes distances between pairs of atoms in the
 list.  It also communicates between neighboring processors to
 coordinate which bonds are created.  Moreover, if any bonds are
 created, neighbor lists must be immediately updated on the same
-timestep.  This is to insure that any pairwise interactions that
+time step.  This is to ensure that any pair-wise interactions that
 should be turned "off" due to a bond creation, because they are now
 excluded by the presence of the bond and the settings of the
 :doc:`special_bonds <special_bonds>` command, will be immediately
-recognized.  All of these operations increase the cost of a timestep.
+recognized.  All of these operations increase the cost of a time step.
-Thus you should be cautious about invoking this fix too frequently.
+Thus, you should be cautious about invoking this fix too frequently.
 
 You can dump out snapshots of the current bond topology via the :doc:`dump local <dump>` command.
 
@@ -225,8 +227,8 @@ You can dump out snapshots of the current bond topology via the :doc:`dump local
    Creating a bond typically alters the energy of a system.  You
    should be careful not to choose bond creation criteria that induce a
    dramatic change in energy.  For example, if you define a very stiff
-   harmonic bond and create it when 2 atoms are separated by a distance
+   harmonic bond and create it when two atoms are separated by a distance
-   far from the equilibrium bond length, then the 2 atoms will oscillate
+   far from the equilibrium bond length, then the two atoms will oscillate
    dramatically when the bond is formed.  More generally, you may need to
    thermostat your system to compensate for energy changes resulting from
    created bonds (and angles, dihedrals, impropers).
@@ -245,10 +247,10 @@ length 2, which can be accessed by various :doc:`output commands
 <Howto_output>`.  The vector values calculated by this fix are
 "intensive".
 
-These are the 2 quantities:
+The two quantities in the global vector are
 
-* (1) # of bonds created on the most recent creation timestep
+  (1) number of bonds created on the most recent creation time step
-* (2) cumulative # of bonds created
+  (2) cumulative number of bonds created
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.

doc/src/fix_bond_react.rst

@@ -6,12 +6,12 @@ fix bond/react command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
-   fix ID group-ID bond/react common_keyword values ...
+   fix ID group-ID bond/react common_keyword values &
-     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
-     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
-     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values ...
+     react react-ID react-group-ID Nevery Rmin Rmax template-ID(pre-reacted) template-ID(post-reacted) map_file individual_keyword values &
      ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command.
@@ -22,11 +22,12 @@ Syntax
 
   .. parsed-literal::
 
-       *stabilization* values = *no* or *yes* *group-ID* *xmax*
+       *stabilization* values = stabilize group_prefix xmax
-         *no* = no reaction site stabilization (default)
+         stabilize = *yes* or *no*
            *yes* = perform reaction site stabilization
-           *group-ID* = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
+           *no* = no reaction site stabilization (default)
-           *xmax* = xmax value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
+         group_prefix = user-assigned prefix for the dynamic group of atoms not currently involved in a reaction
+         xmax = value that is used by an internally-created :doc:`nve/limit <fix_nve_limit>` integrator
        *reset_mol_ids* values = *yes* or *no*
          *yes* = update molecule IDs based on new global topology (default)
          *no* = do not update molecule IDs
@@ -51,18 +52,18 @@ Syntax
          *max_rxn* value = N
            N = maximum number of reactions allowed to occur
          *stabilize_steps* value = timesteps
-           timesteps = number of timesteps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
+           timesteps = number of time steps to apply the internally-created :doc:`nve/limit <fix_nve_limit>` fix to reacting atoms
-         *custom_charges* value = *no* or *fragmentID*
+         *custom_charges* value = *no* or fragment-ID
-           no = update all atomic charges (default)
+           *no* = update all atomic charges (default)
-           fragmentID = ID of molecule fragment whose charges are updated
+           fragment-ID = ID of molecule fragment whose charges are updated
          *molecule* value = *off* or *inter* or *intra*
-           off = allow both inter- and intramolecular reactions (default)
+           *off* = allow both inter- and intramolecular reactions (default)
-           inter = search for reactions between molecules with different IDs
+           *inter* = search for reactions between molecules with different IDs
-           intra = search for reactions within the same molecule
+           *intra* = search for reactions within the same molecule
-         *modify_create* keyword values
+         *modify_create* values = keyword arg
-           *fit* value = *all* or *fragmentID*
+           *fit* arg = *all* or fragment-ID
-             all = use all eligible atoms for create-atoms fit (default)
+             *all* = use all eligible atoms for create-atoms fit (default)
-             fragmentID = ID of molecule fragment used for create-atoms fit
+             fragment-ID = ID of molecule fragment used for create-atoms fit
            *overlap* value = R
              R = only insert atom/molecule if further than R from existing particles (distance units)
 
@@ -99,31 +100,32 @@ other molecules can be identified and deleted. Finally, atoms can be
 created and inserted at specific positions relative to the reaction
 site.
 
-Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
+Fix bond/react does not use quantum mechanical (e.g., :doc:`fix qmmm <fix_qmmm>`) or
-pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
+pairwise bond-order potential (e.g., :doc:`Tersoff <pair_tersoff>` or
+:doc:`AIREBO <pair_airebo>`) methods to
 determine bonding changes a priori. Rather, it uses a distance-based
 probabilistic criteria to effect predetermined topology changes in
 simulations using standard force fields.
 
 This fix was created to facilitate the dynamic creation of polymeric,
 amorphous or highly cross-linked systems. A suggested workflow for
-using this fix is: 1) identify a reaction to be simulated 2) build a
+using this fix is
-molecule template of the reaction site before the reaction has
+
-occurred 3) build a molecule template of the reaction site after the
+  (1) identify a reaction to be simulated
-reaction has occurred 4) create a map that relates the
+  (2) build a molecule template of the reaction site before the reaction has occurred
-template-atom-IDs of each atom between pre- and post-reaction molecule
+  (3) build a molecule template of the reaction site after the reaction has occurred
-templates 5) fill a simulation box with molecules and run a simulation
+  (4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates
-with fix bond/react.
+  (5) fill a simulation box with molecules and run a simulation with fix bond/react.
 
 Only one 'fix bond/react' command can be used at a time. Multiple
 reactions can be simultaneously applied by specifying multiple *react*
 arguments to a single 'fix bond/react' command. This syntax is
-necessary because the 'common keywords' are applied to all reactions.
+necessary because the "common" keywords are applied to all reactions.
 
 The *stabilization* keyword enables reaction site stabilization.
 Reaction site stabilization is performed by including reacting atoms
 in an internally-created fix :doc:`nve/limit <fix_nve_limit>` time
-integrator for a set number of timesteps given by the
+integrator for a set number of time steps given by the
 *stabilize_steps* keyword. While reacting atoms are being time
 integrated by the internal nve/limit, they are prevented from being
 involved in any new reactions. The *xmax* value keyword should
@@ -133,53 +135,54 @@ during the simulation.
 Fix bond/react creates and maintains two important dynamic groups of
 atoms when using the *stabilization* keyword. The first group contains
 all atoms currently involved in a reaction; this group is
-automatically thermostatted by an internally-created
+automatically time-integrated by an internally-created
 :doc:`nve/limit <fix_nve_limit>` integrator. The second group contains
 all atoms currently not involved in a reaction. This group should be
-used by a thermostat in order to time integrate the system. The name
+controlled by a thermostat in order to time integrate the system. The name
 of this group of non-reacting atoms is created by appending '_REACT'
 to the group-ID argument of the *stabilization* keyword, as shown in
 the second example above.
 
 .. note::
 
-   When using reaction stabilization, you should generally not have
+   When using reaction stabilization, you should generally **not** have
-   a separate thermostat which acts on the 'all' group.
+   a separate thermostat that acts on the "all" group.
 
 The group-ID set using the *stabilization* keyword can be an existing
 static group or a previously-unused group-ID. It cannot be specified
-as 'all'. If the group-ID is previously unused, the fix bond/react
+as "all". If the group-ID is previously unused, the fix bond/react
 command creates a :doc:`dynamic group <group>` that is initialized to
 include all atoms. If the group-ID is that of an existing static
 group, the group is used as the parent group of new,
 internally-created dynamic group. In both cases, this new dynamic
-group is named by appending '_REACT' to the group-ID, e.g.
+group is named by appending '_REACT' to the group-ID (e.g.,
-nvt_grp_REACT. By specifying an existing group, you may thermostat
+nvt_grp_REACT). By specifying an existing group, you may thermostat
 constant-topology parts of your system separately. The dynamic group
-contains only atoms not involved in a reaction at a given timestep,
+contains only atoms not involved in a reaction at a given time step,
 and therefore should be used by a subsequent system-wide time
-integrator such as nvt, npt, or nve, as shown in the second example
+integrator such as :doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, or
-above (full examples can be found at examples/PACKAGES/reaction). The time
+:doc:`fix nve <fix_nve>`, as shown in the second example
+above (full examples can be found in examples/PACKAGES/reaction). The time
 integration command should be placed after the fix bond/react command
 due to the internal dynamic grouping performed by fix bond/react.
 
 .. note::
 
    If the group-ID is an existing static group, react-group-IDs
-   should also be specified as this static group, or a subset.
+   should also be specified as this static group or a subset.
 
 The *reset_mol_ids* keyword invokes the :doc:`reset_mol_ids <reset_mol_ids>`
 command after a reaction occurs, to ensure that molecule IDs are
 consistent with the new bond topology. The group-ID used for
 :doc:`reset_mol_ids <reset_mol_ids>` is the group-ID for this fix.
-Resetting molecule IDs is necessarily a global operation, and so can
+Resetting molecule IDs is necessarily a global operation, so it can
 be slow for very large systems.
 
 The following comments pertain to each *react* argument (in other
-words, can be customized for each reaction, or reaction step):
+words, they can be customized for each reaction, or reaction step):
 
 A check for possible new reaction sites is performed every *Nevery*
-timesteps. *Nevery* can be specified with an equal-style
+time steps. *Nevery* can be specified with an equal-style
 :doc:`variable <variable>`, whose value is rounded up to the nearest
 integer.
 
@@ -194,11 +197,11 @@ reaction site is eligible to be modified to match the post-reaction
 template.
 
 An initiator atom pair will be identified if several conditions are
-met. First, a pair of atoms I,J within the specified react-group-ID of
+met. First, a pair of atoms :math:`i` and :math:`j` within the specified
-type itype and jtype must be separated by a distance between *Rmin*
+react-group-ID of type *itype* and *jtype* must be separated by a distance
-and *Rmax*\ . *Rmin* and *Rmax* can be specified with equal-style
+between *Rmin* and *Rmax*\ . *Rmin* and *Rmax* can be specified with
-:doc:`variables <variable>`. For example, these reaction cutoffs can
+equal-style :doc:`variables <variable>`. For example, these reaction cutoffs
-be a function of the reaction conversion using the following commands:
+can be functions of the reaction conversion using the following commands:
 
 .. code-block:: LAMMPS
 
@@ -207,23 +210,28 @@ be a function of the reaction conversion using the following commands:
    variable rmax equal 3+f_myrxn[1]/100 # arbitrary function of reaction count
 
 The following criteria are used if multiple candidate initiator atom
-pairs are identified within the cutoff distance: 1) If the initiator
+pairs are identified within the cutoff distance:
-atoms in the pre-reaction template are not 1-2 neighbors (i.e. not
+
-directly bonded) the closest potential partner is chosen. 2)
+  (1) If the initiator atoms in the pre-reaction template are not 1--2
-Otherwise, if the initiator atoms in the pre-reaction template are 1-2
+      neighbors (i.e., not directly bonded) the closest potential partner is
-neighbors (i.e. directly bonded) the farthest potential partner is
+      chosen.
-chosen. 3) Then, if both an atom I and atom J have each other as their
+  (2) Otherwise, if the initiator atoms in the pre-reaction template are 1--2
-initiator partners, these two atoms are identified as the initiator
+      neighbors (i.e. directly bonded) the farthest potential partner is
-atom pair of the reaction site. Note that it can be helpful to select
+      chosen.
+  (3) Then, if both an atom :math:`i` and atom :math:`j` have each other as
+      initiator partners, these two atoms are identified as the initiator atom
+      pair of the reaction site.
+
+Note that it can be helpful to select
 unique atom types for the initiator atoms: if an initiator atom pair
-is identified, as described in the previous steps, but does not
+is identified, as described in the previous steps, but it does not
 correspond to the same pair specified in the pre-reaction template, an
 otherwise eligible reaction could be prevented from occurring. Once
 this unique initiator atom pair is identified for each reaction, there
 could be two or more reactions that involve the same atom on the same
-timestep. If this is the case, only one such reaction is permitted to
+time step. If this is the case, only one such reaction is permitted to
 occur. This reaction is chosen randomly from all potential reactions
-involving the overlapping atom. This capability allows e.g. for
+involving the overlapping atom. This capability allows, for example,
 different reaction pathways to proceed from identical reaction sites
 with user-specified probabilities.
 
@@ -247,19 +255,19 @@ pre-reaction template atoms should be linked to an initiator atom, via
 at least one path that does not involve edge atoms. When the
 pre-reaction template contains edge atoms, not all atoms, bonds,
 charges, etc. specified in the reaction templates will be updated.
-Specifically, topology that involves only atoms that are 'too near' to
+Specifically, topology that involves only atoms that are "too near" to
-template edges will not be updated. The definition of 'too near the
+template edges will not be updated. The definition of "too near the
-edge' depends on which interactions are defined in the simulation. If
+edge" depends on which interactions are defined in the simulation. If
 the simulation has defined dihedrals, atoms within two bonds of edge
-atoms are considered 'too near the edge.' If the simulation defines
+atoms are considered "too near the edge." If the simulation defines
 angles, but not dihedrals, atoms within one bond of edge atoms are
-considered 'too near the edge.' If just bonds are defined, only edge
+considered "too near the edge." If just bonds are defined, only edge
-atoms are considered 'too near the edge.'
+atoms are considered "too near the edge."
 
 .. note::
 
-   Small molecules, i.e. ones that have all their atoms contained
+   Small molecules (i.e., ones that have all their atoms contained
-   within the reaction templates, never have edge atoms.
+   within the reaction templates) never have edge atoms.
 
 Note that some care must be taken when a building a molecule template
 for a given simulation. All atom types in the pre-reacted template
@@ -282,7 +290,7 @@ provided on the :doc:`molecule <molecule>` command page.
 .. note::
 
    When a reaction occurs, it is possible that the resulting
-   topology/atom (e.g. special bonds, dihedrals, etc.) exceeds that of
+   topology/atom (e.g., special bonds, dihedrals) exceeds that of
    the existing system and reaction templates. As when inserting
    molecules, enough space for this increased topology/atom must be
    reserved by using the relevant "extra" keywords to the
@@ -292,14 +300,14 @@ The map file is a text document with the following format:
 
 A map file has a header and a body. The header of map file the
 contains one mandatory keyword and five optional keywords. The
-mandatory keyword is 'equivalences':
+mandatory keyword is *equivalences*\ :
 
 .. parsed-literal::
 
    N *equivalences* = # of atoms N in the reaction molecule templates
 
-The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
+The optional keywords are *edgeIDs*\ , *deleteIDs*\ , *chiralIDs*\ , and
-'constraints':
+*constraints*\ :
 
 .. parsed-literal::
 
@@ -311,25 +319,25 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
 
 The body of the map file contains two mandatory sections and five
 optional sections. The first mandatory section begins with the keyword
-'InitiatorIDs' and lists the two atom IDs of the initiator atom pair
+"InitiatorIDs" and lists the two atom IDs of the initiator atom pair
 in the pre-reacted molecule template. The second mandatory section
-begins with the keyword 'Equivalences' and lists a one-to-one
+begins with the keyword "Equivalences" and lists a one-to-one
 correspondence between atom IDs of the pre- and post-reacted
 templates. The first column is an atom ID of the pre-reacted molecule
 template, and the second column is the corresponding atom ID of the
 post-reacted molecule template. The first optional section begins with
-the keyword 'EdgeIDs' and lists the atom IDs of edge atoms in the
+the keyword "EdgeIDs" and lists the atom IDs of edge atoms in the
 pre-reacted molecule template. The second optional section begins with
-the keyword 'DeleteIDs' and lists the atom IDs of pre-reaction
+the keyword "DeleteIDs" and lists the atom IDs of pre-reaction
 template atoms to delete. The third optional section begins with the
-keyword 'CreateIDs' and lists the atom IDs of the post-reaction
+keyword "CreateIDs" and lists the atom IDs of the post-reaction
 template atoms to create. The fourth optional section begins with the
-keyword 'ChiralIDs' lists the atom IDs of chiral atoms whose
+keyword "ChiralIDs" lists the atom IDs of chiral atoms whose
 handedness should be enforced. The fifth optional section begins with
-the keyword 'Constraints' and lists additional criteria that must be
+the keyword "Constraints" and lists additional criteria that must be
 satisfied in order for the reaction to occur. Currently, there are
-six types of constraints available, as discussed below: 'distance',
+six types of constraints available, as discussed below: "distance",
-'angle', 'dihedral', 'arrhenius', 'rmsd', and 'custom'.
+"angle", "dihedral", "arrhenius", "rmsd", and "custom".
 
 A sample map file is given below:
 
@@ -384,18 +392,24 @@ two sub-keywords, *fit* and *overlap*. One or more of the sub-keywords
 may be used after the *modify_create* keyword. The *fit* sub-keyword
 can be used to specify which post-reaction atoms are used for the
 optimal translation and rotation of the post-reaction template. The
-*fragmentID* value of the *fit* sub-keyword must be the name of a
+fragment-ID value of the *fit* sub-keyword must be the name of a
 molecule fragment defined in the post-reaction :doc:`molecule
 <molecule>` template, and only atoms in this fragment are used for the
 fit. Atoms are created only if no current atom in the simulation is
-within a distance R of any created atom, including the effect of
+within a distance :math:`R` of any created atom, including the effect of
-periodic boundary conditions if applicable. R is defined by the
+periodic boundary conditions if applicable. :math:`R` is defined by the
-*overlap* sub-keyword. Note that the default value for R is 0.0, which
+*overlap* sub-keyword. Note that the default value for :math:`R` is 0.0, which
 will allow atoms to strongly overlap if you are inserting where other
 atoms are present. The velocity of each created atom is initialized in
 a random direction with a magnitude calculated from the instantaneous
 temperature of the reaction site.
 
+.. note::
+
+   The 'Coords' section must be included in the post-reaction template
+   when creating atoms because these coordinates are used to determine
+   where new atoms are inserted.
+
 The handedness of atoms that are chiral centers can be enforced by
 listing their IDs in the ChiralIDs section. A chiral atom must be
 bonded to four atoms with mutually different atom types. This feature
@@ -406,40 +420,40 @@ and the relative position of the fourth bonded atom determines the
 chiral center's handedness.
 
 Any number of additional constraints may be specified in the
-Constraints section of the map file. The constraint of type 'distance'
+Constraints section of the map file. The constraint of type "distance"
 has syntax as follows:
 
 .. parsed-literal::
 
    distance *ID1* *ID2* *rmin* *rmax*
 
-where 'distance' is the required keyword, *ID1* and *ID2* are
+where "distance" is the required keyword, *ID1* and *ID2* are
 pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
 two atoms must be separated by a distance between *rmin* and *rmax*
 for the reaction to occur.
 
-The constraint of type 'angle' has the following syntax:
+The constraint of type "angle" has the following syntax:
 
 .. parsed-literal::
 
    angle *ID1* *ID2* *ID3* *amin* *amax*
 
-where 'angle' is the required keyword, *ID1*, *ID2* and *ID3* are
+where "angle" is the required keyword, *ID1*, *ID2* and *ID3* are
 pre-reaction atom IDs (or molecule-fragment IDs, see below), and these
 three atoms must form an angle between *amin* and *amax* for the
 reaction to occur (where *ID2* is the central atom). Angles must be
 specified in degrees. This constraint can be used to enforce a certain
 orientation between reacting molecules.
 
-The constraint of type 'dihedral' has the following syntax:
+The constraint of type "dihedral" has the following syntax:
 
 .. parsed-literal::
 
    dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2*
 
-where 'dihedral' is the required keyword, and *ID1*, *ID2*, *ID3*
+where "dihedral" is the required keyword, and *ID1*, *ID2*, *ID3*
 and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see
-below). Dihedral angles are calculated in the interval (-180,180].
+below). Dihedral angles are calculated in the interval :math:`(-180^\circ,180^\circ]`.
 Refer to the :doc:`dihedral style <dihedral_style>` documentation for
 further details on convention. If *amin* is less than *amax*, these
 four atoms must form a dihedral angle greater than *amin* **and** less
@@ -447,7 +461,7 @@ than *amax* for the reaction to occur. If *amin* is greater than
 *amax*, these four atoms must form a dihedral angle greater than
 *amin* **or** less than *amax* for the reaction to occur. Angles must
 be specified in degrees. Optionally, a second range of permissible
-angles *amin2*-*amax2* can be specified.
+angles *amin2* to *amax2* can be specified.
 
 For the 'distance', 'angle', and 'dihedral' constraints (explained
 above), atom IDs can be replaced by pre-reaction molecule-fragment
@@ -457,11 +471,11 @@ fragment. The molecule fragment must have been defined in the
 :doc:`molecule <molecule>` command for the pre-reaction template.
 
 The constraint of type 'arrhenius' imposes an additional reaction
-probability according to the temperature-dependent Arrhenius equation:
+probability according to the modified Arrhenius equation,
 
 .. math::
 
-   k = AT^{n}e^{\frac{-E_{a}}{k_{B}T}}
+   k = AT^{n}e^{-E_{a}/k_{B}T}.
 
 The Arrhenius constraint has the following syntax:
 
@@ -469,11 +483,11 @@ The Arrhenius constraint has the following syntax:
 
    arrhenius *A* *n* *E_a* *seed*
 
-where 'arrhenius' is the required keyword, *A* is the pre-exponential
+where "arrhenius" is the required keyword, *A* is the pre-exponential
 factor, *n* is the exponent of the temperature dependence, :math:`E_a`
 is the activation energy (:doc:`units <units>` of energy), and *seed* is a
 random number seed. The temperature is defined as the instantaneous
-temperature averaged over all atoms in the reaction site, and is
+temperature averaged over all atoms in the reaction site and is
 calculated in the same manner as for example
 :doc:`compute temp/chunk <compute_temp_chunk>`. Currently, there are no
 options for additional temperature averaging or velocity-biased
@@ -487,7 +501,7 @@ The constraint of type 'rmsd' has the following syntax:
 
    rmsd *RMSDmax* *molfragment*
 
-where 'rmsd' is the required keyword, and *RMSDmax* is the maximum
+where "rmsd" is the required keyword, and *RMSDmax* is the maximum
 root-mean-square deviation between atom positions of the pre-reaction
 template and the local reaction site (distance units), after optimal
 translation and rotation of the pre-reaction template. Optionally, the
@@ -500,26 +514,26 @@ example, the molecule fragment could consist of only the backbone
 atoms of a polymer chain. This constraint can be used to enforce a
 specific relative position and orientation between reacting molecules.
 
-The constraint of type 'custom' has the following syntax:
+The constraint of type "custom" has the following syntax:
 
 .. parsed-literal::
 
    custom *varstring*
 
-where 'custom' is the required keyword, and *varstring* is a
+where "custom" is the required keyword, and *varstring* is a
 variable expression. The expression must be a valid equal-style
 variable formula that can be read by the :doc:`variable <variable>` command,
 after any special reaction functions are evaluated. If the resulting
 expression is zero, the reaction is prevented from occurring;
 otherwise, it is permitted to occur. There are two special reaction
-functions available, 'rxnsum' and 'rxnave'. These functions operate
+functions available, "rxnsum" and "rxnave". These functions operate
 over the atoms in a given reaction site, and have one mandatory
 argument and one optional argument. The mandatory argument is the
 identifier for an atom-style variable. The second, optional argument
 is the name of a molecule fragment in the pre-reaction template, and
 can be used to operate over a subset of atoms in the reaction site.
-The 'rxnsum' function sums the atom-style variable over the reaction
+The "rxnsum" function sums the atom-style variable over the reaction
-site, while the 'rxnave' returns the average value. For example, a
+site, while the "rxnave" returns the average value. For example, a
 constraint on the total potential energy of atoms involved in the
 reaction can be imposed as follows:
 
@@ -535,8 +549,8 @@ reaction can be imposed as follows:
 The above example prevents the reaction from occurring unless the
 total potential energy of the reaction site is above 100. The variable
 expression can be interpreted as the probability of the reaction
-occurring by using an inequality and the 'random(x,y,z)' function
+occurring by using an inequality and the :doc:`random(x,y,z) <variable>`
-available as an equal-style variable input, similar to the 'arrhenius'
+function available for equal-style variables, similar to the 'arrhenius'
 constraint above.
 
 By default, all constraints must be satisfied for the reaction to
@@ -561,40 +575,42 @@ within LAMMPS that store bond topology are updated to reflect the
 post-reacted molecule template. All force fields with fixed bonds,
 angles, dihedrals or impropers are supported.
 
-A few capabilities to note: 1) You may specify as many *react*
+A few capabilities to note:
-arguments as desired. For example, you could break down a complicated
+
-reaction mechanism into several reaction steps, each defined by its
+  (1) You may specify as many *react* arguments as desired. For example, you
-own *react* argument. 2) While typically a bond is formed or removed
+      could break down a complicated reaction mechanism into several reaction
-between the initiator atoms specified in the pre-reacted molecule
+      steps, each defined by its own *react* argument.
-template, this is not required. 3) By reversing the order of the pre-
+  (2) While typically a bond is formed or removed between the initiator atoms
-and post- reacted molecule templates in another *react* argument, you
+      specified in the pre-reacted molecule template, this is not required.
-can allow for the possibility of one or more reverse reactions.
+  (3) By reversing the order of the pre- and post-reacted molecule templates in
+      another *react* argument, you can allow for the possibility of one or
+      more reverse reactions.
 
 The optional keywords deal with the probability of a given reaction
 occurring as well as the stable equilibration of each reaction site as
-it occurs:
+it occurs.
 
 The *prob* keyword can affect whether or not an eligible reaction
 actually occurs. The fraction setting must be a value between 0.0 and
 1.0, and can be specified with an equal-style :doc:`variable <variable>`.
 A uniform random number between 0.0 and 1.0 is generated and the
 eligible reaction only occurs if the random number is less than the
-fraction. Up to N reactions are permitted to occur, as optionally
+fraction. Up to :math:`N` reactions are permitted to occur, as optionally
 specified by the *max_rxn* keyword.
 
 The *stabilize_steps* keyword allows for the specification of how many
-timesteps a reaction site is stabilized before being returned to the
+time steps a reaction site is stabilized before being returned to the
 overall system thermostat. In order to produce the most physical
-behavior, this 'reaction site equilibration time' should be tuned to
+behavior, this "reaction site equilibration time" should be tuned to
 be as small as possible while retaining stability for a given system
 or reaction step. After a limited number of case studies, this number
-has been set to a default of 60 timesteps. Ideally, it should be
+has been set to a default of 60 time steps. Ideally, it should be
 individually tuned for each fix reaction step. Note that in some
 situations, decreasing rather than increasing this parameter will
 result in an increase in stability.
 
 The *custom_charges* keyword can be used to specify which atoms'
-atomic charges are updated. When the value is set to 'no', all atomic
+atomic charges are updated. When the value is set to *no*\ , all atomic
 charges are updated to those specified by the post-reaction template
 (default). Otherwise, the value should be the name of a molecule
 fragment defined in the pre-reaction molecule template. In this case,
@@ -602,10 +618,10 @@ only the atomic charges of atoms in the molecule fragment are updated.
 
 The *molecule* keyword can be used to force the reaction to be
 intermolecular, intramolecular or either. When the value is set to
-'off', molecule IDs are not considered when searching for reactions
+*off*\ , molecule IDs are not considered when searching for reactions
-(default). When the value is set to 'inter', the initiator atoms must
+(default). When the value is set to *inter*\ , the initiator atoms must
 have different molecule IDs in order to be considered for the
-reaction. When the value is set to 'intra', only initiator atoms with
+reaction. When the value is set to *intra*\ , only initiator atoms with
 the same molecule ID are considered for the reaction.
 
 A few other considerations:
@@ -627,15 +643,15 @@ all currently-reacting atoms:
    This command must be added after the fix bond/react command, and
    will apply to all reactions.
 
-Computationally, each timestep this fix operates, it loops over
+Computationally, each time step this fix is invoked, it loops over
 neighbor lists (for bond-forming reactions) and computes distances
 between pairs of atoms in the list. It also communicates between
 neighboring processors to coordinate which bonds are created and/or
-removed. All of these operations increase the cost of a timestep. Thus
+removed. All of these operations increase the cost of a time step. Thus,
 you should be cautious about invoking this fix too frequently.
 
-You can dump out snapshots of the current bond topology via the dump
+You can dump out snapshots of the current bond topology via the
-local command.
+:doc:`dump local <dump>` command.
 
 ----------
 
@@ -649,20 +665,20 @@ allow for smooth restarts. None of the :doc:`fix_modify <fix_modify>`
 options are relevant to this fix.
 
 This fix computes one statistic for each *react* argument that it
-stores in a global vector, of length 'number of react arguments', that
+stores in a global vector, of length (number of react arguments), that
 can be accessed by various :doc:`output commands <Howto_output>`. The
 vector values calculated by this fix are "intensive".
 
-These is 1 quantity for each react argument:
+There is one quantity in the global vector for each *react* argument:
 
-* (1) cumulative # of reactions occurred
+  (1) cumulative number of reactions that occurred
 
 No parameter of this fix can be used with the *start/stop* keywords
 of the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
 
-When fix bond/react is 'unfixed', all internally-created groups are
+When fix bond/react is ":doc:`unfixed <unfix>`", all internally-created
-deleted. Therefore, fix bond/react can only be unfixed after unfixing
+groups are deleted. Therefore, fix bond/react can only be unfixed after
-all other fixes that use any group created by fix bond/react.
+unfixing all other fixes that use any group created by fix bond/react.
 
 Restrictions
 """"""""""""
@@ -683,7 +699,7 @@ Default
 """""""
 
 The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
-reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
+reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = *fit all*
 
 ----------
 

doc/src/fix_brownian.rst

@@ -14,7 +14,7 @@ fix brownian/asphere command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    fix ID group-ID style_name temp seed keyword args
 
@@ -43,7 +43,7 @@ Syntax
         *gt* = magnitude of the (isotropic) translational friction tensor
      *rotation_temp* values = *T* for *brownian/sphere* and *brownian/asphere*
         *T* = rotation temperature, which can be different then *temp* when out of equilibrium
-        *planar_rotation* values = None (constrains rotational diffusion to be in xy plane if in 3D)
+     *planar_rotation* values = none (constrains rotational diffusion to be in xy plane if in 3D)
 
 Examples
 """"""""
@@ -71,9 +71,10 @@ positions is
 
 .. math::
 
-   d\mathbf{r} = \mathbf{\gamma}_t^{-1}\mathbf{F}dt+\sqrt{2k_BT}\mathbf{\gamma}_t^{-1/2}d\mathbf{W}_t,
+   d\mathbf{r} = \boldsymbol{\gamma}_t^{-1}\mathbf{F}dt
+   + \sqrt{2k_B T}\boldsymbol{\gamma}_t^{-1/2}d\mathbf{W}_t,
 
-in the lab-frame (i.e. :math:`\mathbf{\gamma}_t` is not diagonal, but
+in the lab-frame (i.e., :math:`\boldsymbol{\gamma}_t` is not diagonal, but
 only depends on orientation and so the noise is still additive).
 
 The rotational motion for the spherical and ellipsoidal particles is not
@@ -92,15 +93,15 @@ updated. This style therefore requires the hybrid atom style
 
 .. math::
 
-   \mathbf{\mu}(t+dt) = \frac{\mathbf{\mu}(t) + \mathbf{\omega} \times \mathbf{\mu}dt
+   \boldsymbol{\mu}(t+dt) = \frac{\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}dt
-   }{|\mathbf{\mu}(t) + \mathbf{\omega} \times \mathbf{\mu}|}
+   }{|\boldsymbol{\mu}(t) + \boldsymbol{\omega} \times \boldsymbol{\mu}|}
 
 which correctly reproduces a Boltzmann distribution of orientations and
 rotational diffusion moments (see :ref:`(Ilie) <Ilie1>`) when
 
 .. math::
 
-   \mathbf{\omega} = \frac{\mathbf{T}}{\gamma_r} + \sqrt{\frac{2 k_B T_{rot}}{\gamma_r}\frac{d\mathbf{W}}{dt}},
+   \boldsymbol{\omega} = \frac{\mathbf{T}}{\gamma_r} + \sqrt{\frac{2 k_B T_{rot}}{\gamma_r}\frac{d\mathbf{W}}{dt}},
 
 with :math:`d\mathbf{W}` being a random number with zero mean and variance :math:`dt`
 and :math:`T_{rot}` is *rotation_temp*.
@@ -114,19 +115,20 @@ the quaternion
 
 .. math::
 
-   \mathbf{q}(t+dt) = \frac{\mathbf{q}(t) + d\mathbf{q}}{|\mathbf{q}(t) + d\mathbf{q}|}
+   \mathbf{q}(t+dt) = \frac{\mathbf{q}(t) + d\mathbf{q}}{\lVert\mathbf{q}(t) + d\mathbf{q}\rVert}
 
 which correctly reproduces a Boltzmann distribution of orientations and rotational
-diffusion moments (see :ref:`(Ilie) <Ilie1>`) when the quaternion step given by
+diffusion moments [see :ref:`(Ilie) <Ilie1>`] when the quaternion step is given by
 
 .. math::
 
-   d\mathbf{q} = \mathbf{\Psi}\mathbf{\omega}dt
+   d\mathbf{q} = \boldsymbol{\Psi}\boldsymbol{\omega}dt
 
-where :math:`\mathbf{Psi}` has rows :math:`(-q_1,-q_2,-q_3)`, :math:`(q_0,-q_3,q_2)`,
+where :math:`\boldsymbol{\Psi}` has rows :math:`(-q_1,-q_2,-q_3)`,
-:math:`(q_3,q_0,-q_1)`, and :math:`(-q_2,q_1,q_0)`. :math:`\mathbf{\omega}` is
+:math:`(q_0,-q_3,q_2)`, :math:`(q_3,q_0,-q_1)`, and :math:`(-q_2,q_1,q_0)`.
-evaluated in the body frame of reference where the friction tensor is diagonal.
+:math:`\boldsymbol{\omega}` is evaluated in the body frame of reference where the
-See :ref:`(Delong) <Delong1>` for more details of a similar algorithm.
+friction tensor is diagonal.  See :ref:`(Delong) <Delong1>` for more details of
+a similar algorithm.
 
 
 ---------
@@ -136,11 +138,11 @@ See :ref:`(Delong) <Delong1>` for more details of a similar algorithm.
    This integrator does not by default assume a relationship between the
    rotational and translational friction tensors, though such a
    relationship should exist in the case of no-slip boundary conditions
-   between the particles and the surrounding (implicit) solvent. E.g. in
+   between the particles and the surrounding (implicit) solvent. For example,
-   the case of spherical particles, the condition
+   in the case of spherical particles, the condition
    :math:`\gamma_t=3\gamma_r/\sigma^2` must be explicitly accounted for
    by setting *gamma_t* to 3x and *gamma_r* to x (where :math:`\sigma`
-   is the spherical diameter). A similar (though more complex)
+   is the sphere's diameter). A similar (though more complex)
    relationship holds for ellipsoids and rod-like particles. The
    translational diffusion and rotational diffusion are given by
    *temp/gamma_t* and *rotation_temp/gamma_r*.
@@ -150,7 +152,7 @@ See :ref:`(Delong) <Delong1>` for more details of a similar algorithm.
 .. note::
 
    Temperature computation using the :doc:`compute temp <compute_temp>`
-   will not correctly compute temperature of these overdamped dynamics
+   will not correctly compute the temperature of these overdamped dynamics
    since we are explicitly neglecting inertial effects.  Furthermore,
    this time integrator does not add the stochastic terms or viscous
    terms to the force and/or torques.  Rather, they are just added in to
@@ -165,7 +167,7 @@ is generated from a uniform distribution (see
 of noise generation as used in :doc:`fix_langevin <fix_langevin>`.
 
 If the *rng* keyword is used with the *gaussian* value, then the noise
-is generated from a gaussian distribution. Typically this added
+is generated from a Gaussian distribution. Typically this added
 complexity is unnecessary, and one should be fine using the *uniform*
 value for reasons argued in :ref:`(Dunweg) <Dunweg7>`.
 
@@ -184,8 +186,8 @@ The *gamma_r_eigen*, and *gamma_t_eigen* keywords are the eigenvalues of
 the rotational and viscous damping tensors (having the same units as
 their isotropic counterparts). Required for (and only compatible with)
 *brownian/asphere*. For a 2D system, the first two values of
-*gamma_r_eigen* must be inf (only rotation in xy plane), and the third
+*gamma_r_eigen* must be *inf* (only rotation in *x*\ --\ *y* plane), and the third
-value of *gamma_t_eigen* must be inf (only diffusion in xy plane).
+value of *gamma_t_eigen* must be *inf* (only diffusion in the *x*\ --\ *y* plane).
 
 If the *dipole* keyword is used, then the dipole moments of the particles
 are updated as described above. Only compatible with *brownian/asphere*
@@ -196,13 +198,13 @@ will be occur at this prescribed temperature instead of *temp*. Only
 compatible with *brownian/sphere* and *brownian/asphere*.
 
 If the *planar_rotation* keyword is used, then rotation is constrained
-to the xy plane in a 3D simulation. Only compatible with
+to the *x*\ -- *y* plane in a 3D simulation. Only compatible with
 *brownian/sphere* and *brownian/asphere* in 3D.
 
 ----------
 
 .. note::
-   For style *brownian/asphere*, the components *gamma_t_eigen* =(x,x,x) and
+   For style *brownian/asphere*, the components *gamma_t_eigen* = (x,x,x) and
    *gamma_r_eigen* = (y,y,y), the dynamics will replicate those of the
    *brownian/sphere* style with *gamma_t* = x and *gamma_r* = y.
 
@@ -215,7 +217,6 @@ No information about this fix is written to :doc:`binary restart files
 <restart>`.  No global or per-atom quantities are stored by this fix for
 access by various :doc:`output commands <Howto_output>`.
 
-
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.  This fix is not invoked during
 :doc:`energy minimization <minimize>`.

doc/src/fix_colvars.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * colvars = style name of this fix command
 * configfile = the configuration file for the colvars module
-* keyword = *input* or *output* or *seed* or *tstat*
+* keyword = *input* or *output* or *seed* or *unwrap* or *tstat*
 
   .. parsed-literal::
 

doc/src/fix_deposit.rst

@@ -17,7 +17,7 @@ Syntax
 * M = insert a single atom or molecule every M steps
 * seed = random # seed (positive integer)
 * one or more keyword/value pairs may be appended to args
-* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *mol* or *rigid* or *shake* or *units*
+* keyword = *region* or *id* or *global* or *local* or *near* or *gaussian* or *attempt* or *rate* or *vx* or *vy* or *vz* or *target* or *mol* or *molfrac* or *rigid* or *shake* or *orient* or *units*
 
   .. parsed-literal::
 

doc/src/fix_imd.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * imd = style name of this fix command
 * port = port number on which the fix listens for an IMD client
-* keyword = *unwrap* or *fscale* or *trate*
+* keyword = *unwrap* or *fscale* or *trate* or *nowait*
 
   .. parsed-literal::
 

doc/src/fix_langevin.rst

@@ -20,7 +20,7 @@ Syntax
 * damp = damping parameter (time units)
 * seed = random number seed to use for white noise (positive integer)
 * zero or more keyword/value pairs may be appended
-* keyword = *angmom* or *omega* or *scale* or *tally* or *zero*
+* keyword = *angmom* or *gjf* or *omega* or *scale* or *tally* or *zero*
 
   .. parsed-literal::
 

doc/src/fix_lb_fluid.rst

@@ -16,7 +16,7 @@ Syntax
 * viscosity = the fluid viscosity (units of mass/(time\*length)).
 * density = the fluid density.
 * zero or more keyword/value pairs may be appended
-* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19*  or *dumpxdmf* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw*
+* keyword = *dx* or *dm* or *noise* or *stencil* or *read_restart* or *write_restart* or *zwall_velocity* or *pressurebcx* or *bodyforce* or *D3Q19* or *dumpxdmf* or *linearInit* or *dof* or *scaleGamma* or *a0* or *npits* or *wp* or *sw*
 
   .. parsed-literal::
 
@@ -36,6 +36,7 @@ Syntax
            N = output the force and torque every N timesteps
            file = output file name
            timeI = 1 (use simulation time to index xdmf file), 0 (use output frame number to index xdmf file)
+       *linearInit* values = none = initialize density and velocity using linear interpolation (default is uniform density, no velocities)
        *dof* values = dof = specify the number of degrees of freedom for temperature calculation
        *scaleGamma* values = type gammaFactor
            type = atom type (1-N)

doc/src/fix_npt_cauchy.rst

@@ -13,7 +13,7 @@ Syntax
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * style_name = *npt/cauchy*
 * one or more keyword/value pairs may be appended
-* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *fixedpoint*
+* keyword = *temp* or *iso* or *aniso* or *tri* or *x* or *y* or *z* or *xy* or *yz* or *xz* or *couple* or *tchain* or *pchain* or *mtk* or *tloop* or *ploop* or *nreset* or *drag* or *dilate* or *scalexy* or *scaleyz* or *scalexz* or *flip* or *alpha* or *continue* or *fixedpoint*
 
   .. parsed-literal::
 

doc/src/fix_pour.rst

@@ -16,7 +16,7 @@ Syntax
 * type = atom type to assign to inserted particles (offset for molecule insertion)
 * seed = random # seed (positive integer)
 * one or more keyword/value pairs may be appended to args
-* keyword = *region* or *diam* or *vol* or *rate* or *dens* or *vel* or *mol* or *rigid* or *shake* or *ignore*
+* keyword = *region* or *diam* or *id* or *vol* or *rate* or *dens* or *vel* or *mol* or *molfrac* or *rigid* or *shake* or *ignore*
 
   .. parsed-literal::
 

doc/src/fix_rigid.rst

@@ -80,7 +80,7 @@ Syntax
          groupID1, groupID2, ... = list of N group IDs
 
 * zero or more keyword/value pairs may be appended
-* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile*
+* keyword = *langevin* or *reinit* or *temp* or *iso* or *aniso* or *x* or *y* or *z* or *couple* or *tparam* or *pchain* or *dilate* or *force* or *torque* or *infile* or *gravity*
 
   .. parsed-literal::
 
@@ -115,6 +115,11 @@ Syntax
          xflag,yflag,zflag = off/on if component of center-of-mass torque is active
        *infile* filename
          filename = file with per-body values of mass, center-of-mass, moments of inertia
+       *gravity* values = gravity-ID
+         gravity-ID = ID of fix gravity command to add gravitational forces
+
+..
+    FIXME These don't seem to be included in the source code
        *mol* value = template-ID
          template-ID = ID of molecule template specified in a separate :doc:`molecule <molecule>` command
 

doc/src/fix_viscosity.rst

@@ -17,7 +17,7 @@ Syntax
 * pdim = *x* or *y* or *z* = direction of momentum transfer
 * Nbin = # of layers in pdim direction (must be even number)
 * zero or more keyword/value pairs may be appended
-* keyword = *swap* or *target*
+* keyword = *swap* or *vtarget*
 
   .. parsed-literal::
 

doc/src/fix_wall.rst

@@ -70,7 +70,7 @@ Syntax
          cutoff = distance from wall at which wall-particle interaction is cut off (distance units)
 
 * zero or more keyword/value pairs may be appended
-* keyword = *units* or *fld*
+* keyword = *units* or *fld* or *pbc*
 
   .. parsed-literal::
 

doc/src/fix_wall_piston.rst

@@ -14,7 +14,7 @@ Syntax
 * wall/piston = style name of this fix command
 * face = *zlo*
 * zero or more keyword/value pairs may be appended
-* keyword = *pos* or *vel* or *ramp* or *units*
+* keyword = *pos* or *vel* or *ramp* or *temp* or *units*
 
   .. parsed-literal::
 
@@ -32,6 +32,10 @@ Syntax
          *lattice* = the wall position is defined in lattice units
          *box* = the wall position is defined in simulation box units
 
+..
+    FIXME: There are several "undocumented" key words for this fix: *rough*,
+    *rampNL1*, *rampNL2*, *rampNL3*, *rampNL4*, and *rampNL5*.
+
 Examples
 """"""""
 

doc/src/kspace_modify.rst

@@ -11,7 +11,7 @@ Syntax
    kspace_modify keyword value ...
 
 * one or more keyword/value pairs may be listed
-* keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol*
+* keyword = *collective* or *compute* or *cutoff/adjust* or *diff* or *disp/auto* or *fftbench* or *force/disp/kspace* or *force/disp/real* or *force* or *gewald/disp* or *gewald* or *kmax/ewald* or *mesh* or *minorder* or *mix/disp* or *order/disp* or *order* or *overlap* or *scafacos* or *slab* or *splittol* or *wire*
 
   .. parsed-literal::
 

doc/src/mdi.rst

@@ -6,7 +6,7 @@ mdi command
 Syntax
 """"""
 
-.. parsed-literal::
+.. code-block:: LAMMPS
 
    mdi option args
 
@@ -19,7 +19,7 @@ Syntax
          *elements* args = N_1 N_2 ... N_ntypes
            N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
      *plugin* args = name keyword value keyword value ...
-       name = name of plugin library, e.g. lammps means a liblammps.so library will be loaded
+       name = name of plugin library (e.g., *lammps* means a liblammps.so library will be loaded)
        keyword/value pairs in any order, some are required, some are optional
        keywords = *mdi* or *infile* or *extra* or *command*
          *mdi* value = args passed to MDI for driver to operate with plugins (required)
@@ -173,8 +173,8 @@ commands, which are described further below.
    atom type values are consistent in both codes, then the >TYPES
    command can be used.  If not, the optional *elements* keyword can
    be used to specify what element each LAMMPS atom type corresponds
-   to.  This is specified by the atomic number of the element, e.g. 13
+   to.  This is specified by the atomic number of the element (e.g., 13
-   for Al.  An atomic number must be specified for each of the ntypes
+   for Al).  An atomic number must be specified for each of the ntypes
    LAMMPS atom types.  Ntypes is typically specified via the
    create_box command or in the data file read by the read_data
    command.  In this has been done, the MDI driver can send an
@@ -325,15 +325,15 @@ able to initiate and terminate the connection to the engine code.
 
 The only current MDI driver command in LAMMPS is the :doc:`fix mdi/qm
 <fix_mdi_qm>` command.  If it is only used once in an input script
-then it can initiate and terminate the connection.  But if it is being
+then it can initiate and terminate the connection, but if it is being
-issued multiple times, e.g. in a loop that issues a :doc:`clear
+issued multiple times (e.g., in a loop that issues a :doc:`clear
-<clear>` command, then it cannot initiate or terminate the connection
+<clear>` command), then it cannot initiate or terminate the connection
 multiple times.  Instead, the *mdi connect* and *mdi exit* commands
 should be used outside the loop to initiate or terminate the connection.
 
 See the examples/mdi/in.series.driver script for an example of how
 this is done.  The LOOP in that script is reading a series of data
-file configurations and passing them to an MDI engine (e.g. quantum
+file configurations and passing them to an MDI engine (e.g., quantum
 code) for energy and force evaluation.  A *clear* command inside the
 loop wipes out the current system so a new one can be defined.  This
 operation also destroys all fixes.  So the :doc:`fix mdi/qm
@@ -356,7 +356,7 @@ LAMMPS and MDI units, which the other codes will also perform in their
 preferred units.
 
 LAMMPS can also be used as an MDI engine in other unit choices it
-supports, e.g. *lj*, but then no unit conversion is performed.
+supports (e.g., *lj*), but then no unit conversion is performed.
 
 Related commands
 """"""""""""""""

doc/src/neigh_modify.rst

@@ -16,12 +16,12 @@ Syntax
 
      keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
        *delay* value = N
-         N = delay building until this many steps since last build
+         N = delay building neighbor lists until this many steps since last build
        *every* value = M
-         M = build neighbor list every this many steps
+         M = consider building neighbor lists every this many steps
        *check* value = *yes* or *no*
-         *yes* = only build if some atom has moved half the skin distance or more
+         *yes* = only build if at least one atom has moved half the skin distance or more
-         *no* = always build on 1st step that *every* and *delay* are satisfied
+         *no* = always build on 1st step where *every* and *delay* are conditions are satisfied
        *once* value = *yes* or *no*
          *yes* = only build neighbor list once at start of run and never rebuild
          *no* = rebuild neighbor list according to other settings
@@ -71,30 +71,53 @@ Description
 """""""""""
 
 This command sets parameters that affect the building and use of
-pairwise neighbor lists.  Depending on what pair interactions and
+pairwise neighbor lists.  Depending on what pair interactions and other
-other commands are defined, a simulation may require one or more
+commands are defined, a simulation may require one or more neighbor
-neighbor lists.
+lists.
 
-The *every*, *delay*, *check*, and *once* options affect how often
+The *every*, *delay*, *check*, and *once* options affect how often lists
-lists are built as a simulation runs.  The *delay* setting means never
+are built as a simulation runs.  The *delay* setting means never build
-build new lists until at least N steps after the previous build.  The
+new lists until at least N steps after the previous build.  The *every*
-*every* setting means build lists every M steps (after the delay has
+setting means attempt to build lists every M steps (after the delay has
 passed).  If the *check* setting is *no*, the lists are built on the
 first step that satisfies the *delay* and *every* settings.  If the
 *check* setting is *yes*, then the *every* and *delay* settings
 determine when a build may possibly be performed, but an actual build
-only occurs if some atom has moved more than half the skin distance
+only occurs if at least one atom has moved more than half the neighbor
-(specified in the :doc:`neighbor <neighbor>` command) since the last
+skin distance (specified in the :doc:`neighbor <neighbor>` command)
-build.
+since the last neighbor list build.
 
-If the *once* setting is yes, then the neighbor list is only built
+.. admonition:: Impact of neighbor list settings
-once at the beginning of each run, and never rebuilt, except on steps
+   :class: note
-when a restart file is written, or steps when a fix forces a rebuild
+
-to occur (e.g. fixes that create or delete atoms, such as :doc:`fix deposit <fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).
+   The choice of neighbor list settings can have a significant impact on
-This setting should only be made if you are certain atoms will not
+   the (parallel) performance of LAMMPS and the correctness of the
-move far enough that the neighbor list should be rebuilt, e.g. running
+   simulation results.  Since building the neighbor lists is time
-a simulation of a cold crystal.  Note that it is not that expensive to
+   consuming, doing it less frequently can speed up a calculation.  If
-check if neighbor lists should be rebuilt.
+   the lists are rebuilt too infrequently, however, interacting pairs
+   may be missing and thus the resulting pairwise interactions
+   incorrect.  The optimal settings depend on many factors like the
+   properties of the simulated system (density, geometry, topology,
+   temperature, pressure), the force field parameters and settings, the
+   size of the timestep, neighbor list skin distance and more.  The
+   default settings are chosen to be very conservative to guarantee
+   correctness of the simulation.  They depend on the *check* flag
+   heuristics to reduce the number of neighbor list rebuilds at a minor
+   expense for executing the check.  Determining the correctness of a
+   specific choice of neighbor list settings is complicated by the fact
+   that a neighbor list rebuild changes the order in which pairwise
+   interactions are computed and thus
+   - due to the limitations of floating-point math - the trajectory.
+
+If the *once* setting is yes, then the neighbor list is only built once
+at the beginning of each run, and never rebuilt, except on steps when a
+restart file is written, or steps when a fix forces a rebuild to occur
+(e.g. fixes that create or delete atoms, such as :doc:`fix deposit
+<fix_deposit>` or :doc:`fix evaporate <fix_evaporate>`).  This setting
+should only be made if you are certain atoms will not move far enough
+that the neighbor list should be rebuilt, e.g. running a simulation of a
+cold crystal.  Note that it is not that expensive to check if neighbor
+lists should be rebuilt.
 
 When the rRESPA integrator is used (see the :doc:`run_style <run_style>`
 command), the *every* and *delay* parameters refer to the longest
@@ -234,11 +257,11 @@ depend on their atom type.
 Restrictions
 """"""""""""
 
-If the "delay" setting is non-zero, then it must be a multiple of the
+If the *delay* setting is non-zero, then it must be a multiple of the
-"every" setting.
+*every* setting.
 
-The molecule/intra and molecule/inter exclude options can only be used
+The *molecule/intra* and *molecule/inter* exclusion options can only
-with atom styles that define molecule IDs.
+be used with atom styles that define molecule IDs.
 
 The value of the *page* setting must be at least 10x larger than the
 *one* setting.  This insures neighbor pages are not mostly empty
@@ -252,6 +275,6 @@ Related commands
 Default
 """""""
 
-The option defaults are delay = 10, every = 1, check = yes, once = no,
+The option defaults are delay = 0, every = 1, check = yes, once = no,
 cluster = no, include = all (same as no include option defined),
 exclude = none, page = 100000, one = 2000, and binsize = 0.0.

doc/src/pair_amoeba.rst

@@ -156,7 +156,7 @@ settings.
 
 ----------
 
-.. versionadded:: TBD
+.. versionadded:: 3Nov2022
 
 The *amoeba* and *hippo* pair styles support extraction of two per-atom
 quantities by the :doc:`fix pair <fix_pair>` command.  This allows the

doc/src/pair_dipole.rst

@@ -58,22 +58,26 @@ Examples
 
 .. code-block:: LAMMPS
 
-   pair_style lj/cut/dipole/cut 10.0
+   pair_style lj/cut/dipole/cut 2.5 5.0
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 2.5 4.0
 
    pair_style lj/sf/dipole/sf 9.0
    pair_coeff * * 1.0 1.0
    pair_coeff 2 3 1.0 1.0 2.5 4.0 scale 0.5
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 2.5 4.0
 
-   pair_style lj/cut/dipole/long 10.0
+   pair_style lj/cut/dipole/long 2.5 3.5
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0 3.0
 
-   pair_style lj/long/dipole/long long long 3.5 10.0
+   pair_style lj/long/dipole/long long long 3.5
    pair_coeff * * 1.0 1.0
-   pair_coeff 2 3 1.0 1.0 2.5 4.0
+   pair_coeff 2 3 0.8 1.0
+
+   pair_style lj/long/dipole/long cut long 2.5 3.5
+   pair_coeff * * 1.0 1.0
+   pair_coeff 2 3 0.8 1.0 3.0
 
 Description
 """""""""""
@@ -254,23 +258,28 @@ long-range LJ interactions, the :doc:`kspace_style ewald/disp
 
 ----------
 
-The following coefficients must be defined for each pair of atoms
+The following coefficients must be defined for each pair of atoms types
-types via the :doc:`pair_coeff <pair_coeff>` command as in the examples
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
-above, or in the data file or restart files read by the
+or in the data file or restart files read by the :doc:`read_data
-:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
-commands, or by mixing as described below:
+mixing as described below:
 
 * :math:`\epsilon` (energy units)
 * :math:`\sigma` (distance units)
 * cutoff1 (distance units)
 * cutoff2 (distance units)
 
-The latter 2 coefficients are optional.  If not specified, the global
+The latter 2 coefficients are optional.  If not specified, the global LJ
-LJ and Coulombic cutoffs specified in the pair_style command are used.
+and Coulombic cutoffs specified in the pair_style command are used.  If
-If only one cutoff is specified, it is used as the cutoff for both LJ
+only one cutoff is specified, it is used as the cutoff for both LJ and
-and Coulombic interactions for this type pair.  If both coefficients
+Coulombic interactions for this type pair.  If both coefficients are
-are specified, they are used as the LJ and Coulombic cutoffs for this
+specified, they are used as the LJ and Coulombic cutoffs for this type
-type pair.
+pair.  When using a long-rang Coulomb solver, only a global Coulomb
+cutoff may be used and only the LJ cutoff may be changed with the
+:doc:`pair_coeff <pair_coeff>` command.  When using the
+*lj/long/dipole/long* pair style with *long* *long* setting, only a
+single global cutoff may be provided and no cutoff for the
+:doc:`pair_coeff <pair_coeff>` command.
 
 ----------
 

doc/src/pair_eam.rst

@@ -440,7 +440,7 @@ identical to the FS EAM files (see above).
 
 ----------
 
-.. versionadded:: TBD
+.. versionadded:: 3Nov2022
 
 The *eam*, *eam/alloy*, *eam/fs*, and *eam/he* pair styles support
 extraction of two per-atom quantities by the :doc:`fix pair <fix_pair>`

doc/src/pair_granular.rst

@@ -97,7 +97,7 @@ on particle *i* due to contact with particle *j* is given by:
 
 Where :math:`\delta_{ij} = R_i + R_j - \|\mathbf{r}_{ij}\|` is the particle
 overlap, :math:`R_i, R_j` are the particle radii, :math:`\mathbf{r}_{ij} = \mathbf{r}_i - \mathbf{r}_j` is the vector separating the two
-particle centers (note the i-j ordering so that :math:`F_{ne}` is
+particle centers (note the i-j ordering so that :math:`\mathbf{F}_{ne}` is
 positive for repulsion), and :math:`\mathbf{n} = \frac{\mathbf{r}_{ij}}{\|\mathbf{r}_{ij}\|}`.  Therefore,
 for *hooke*, the units of the spring constant :math:`k_n` are
 *force*\ /\ *distance*, or equivalently *mass*\ /*time\^2*.

doc/src/pair_list.rst

@@ -57,7 +57,7 @@ The format of the list file is as follows:
        ID2 = atom ID of second atom
        style = style of interaction
        coeffs = list of coeffs
-       cutoff = cutoff for interaction (optional, except for style *quartic*)
+       cutoff = cutoff for interaction (optional)
 
 The cutoff parameter is optional for all but the *quartic* interactions.
 If it is not specified, the global cutoff is used.
@@ -71,7 +71,7 @@ Here is an example file:
    15 259 lj126     1.0 1.0      50.0
    15 603 morse    10.0 1.2 2.0  10.0 # and another comment
    18 470 harmonic 50.0 1.2       5.0
-   19 332 quartic   5.0 -1.2 1.2  5.0
+   19 332 quartic  10.0 5.0 -1.2 1.2
 
 The style *lj126* computes pairwise interactions with the formula
 
@@ -100,7 +100,7 @@ The style *harmonic* computes pairwise interactions with the formula
 
 .. math::
 
-   E = K (r - r_0)^2
+   E = K (r - r_0)^2 \qquad r < r_c
 
 and the coefficients:
 
@@ -113,16 +113,14 @@ The style *quartic* computes pairwise interactions with the formula
 
 .. math::
 
-   E = K (r - r_c)^2 (r - r_c -b_1) (r - r_c - b_2) \qquad r < r_c
+   E = K (r - r_0)^2 (r - r_0 -b_1) (r - r_0 - b_2) \qquad r < r_c
 
 and the coefficients:
 
 * :math:`K` (energy units)
+* :math:`r_0` (distance units)
 * :math:`b_1` (distance units)
 * :math:`b_2` (distance units)
-* :math:`r_c` (distance units)
-
-Note that the per list entry cutoff :math:`r_c` is **required** for *quartic* interactions.
 
 ----------
 

doc/src/pair_mliap.rst

@@ -1,8 +1,11 @@
 .. index:: pair_style mliap
+.. index:: pair_style mliap/kk
 
 pair_style mliap command
 ========================
 
+Accelerator Variants: *mliap/kk*
+
 Syntax
 """"""
 
@@ -177,7 +180,7 @@ to specify the path for these *model* and *descriptor* files.
    larger systems since their size depends on the total number of
    neighbors per MPI process.
 
-.. versionadded:: TBD
+.. versionadded:: 3Nov2022
 
 The *unified* keyword is followed by an argument specifying the
 filename containing the serialized unified Python object and the "ghostneigh" toggle
@@ -207,6 +210,12 @@ cutoff manually, such as in the following example.
   on the active LAMMPS object before the pair style is defined. This call locates
   and loads the mliap-specific python module that is built into LAMMPS.
 
+----------
+
+.. include:: accel_styles.rst
+
+----------
+
 Mixing, shift, table, tail correction, restart, rRESPA info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/pair_pace.rst

@@ -112,8 +112,7 @@ requests to compute `gamma`, as shown in example below:
     compute max_pace_gamma all reduce max f_pace_gamma
     variable dump_skip equal "c_max_pace_gamma < 5"
 
-
+    dump pace_dump all custom 20 extrapolative_structures.dump id type x y z f_pace_gamma
-    dump pace_dump all custom 20 extrapolative_structures.dump id x y z f_pace_gamma
     dump_modify pace_dump skip v_dump_skip
 
     variable max_pace_gamma equal c_max_pace_gamma

doc/src/pair_style.rst

@@ -374,6 +374,7 @@ accelerated styles exist.
 * :doc:`vashishta <pair_vashishta>` - Vashishta 2-body and 3-body potential
 * :doc:`vashishta/table <pair_vashishta>` -
 * :doc:`wf/cut <pair_wf_cut>` - Wang-Frenkel Potential for short-ranged interactions
+* :doc:`ylz <pair_ylz>` - Yuan-Li-Zhang Potential for anisotropic interactions
 * :doc:`yukawa <pair_yukawa>` - Yukawa potential
 * :doc:`yukawa/colloid <pair_yukawa_colloid>` - screened Yukawa potential for finite-size particles
 * :doc:`zbl <pair_zbl>` - Ziegler-Biersack-Littmark potential

doc/src/pair_ylz.rst

@@ -0,0 +1,177 @@
+.. index:: pair_style ylz
+
+pair_style ylz command
+===========================
+
+Syntax
+""""""
+
+.. code-block:: LAMMPS
+
+   pair_style ylz cutoff
+
+
+* cutoff = global cutoff for interactions (distance units)
+
+Examples
+""""""""
+
+.. code-block:: LAMMPS
+
+   pair_style   ylz  2.6
+   pair_coeff   *  *  1.0  1.0  4  3  0.0  2.6
+
+
+Description
+"""""""""""
+
+.. versionadded:: 3Nov2022
+
+The *ylz* (Yuan-Li-Zhang) style computes an anisotropic interaction
+between pairs of coarse-grained particles considering the relative
+particle orientations. This potential was originally developed as a
+particle-based solvent-free model for biological membranes
+:ref:`(Yuan2010a) <Yuan>`.  Unlike :doc:`pair_style gayberne
+<pair_gayberne>`, whose orientation dependence is strictly derived from
+the closest distance between two ellipsoidal rigid bodies, the
+orientation-dependence of this pair style is mathematically defined such
+that the particles can self-assemble into one-particle-thick fluid
+membranes.  The potential of this pair style is described by:
+
+.. math::
+
+   U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} {u}_R(r)+\left [ 1-\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<{r}_{min} \\ {u}_A(r)\phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~  {r}_{min}<r<{r}_{c} \\ \end{matrix}\right.\\\\ \phi (\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=1+\left [  \mu (a(\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )-1) \right ] \\\\a(\mathbf{\hat{r}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=(\mathbf{n}_i\times\mathbf{\hat{r}}_{ij} )\cdot (\mathbf{n}_j\times\mathbf{\hat{r}}_{ij} )+{\beta}(\mathbf{n}_i-\mathbf{n}_j)\cdot \mathbf{\hat{r}}_{ij}-\beta^{2}\\\\  {u}_R(r)=\epsilon \left [ \left ( \frac{{r}_{min}}{r} \right )^{4}-2\left ( \frac{{r}_{min}}{r}\right )^{2} \right ] \\\\ {u}_A(r)=-\epsilon\;cos^{2\zeta }\left [ \frac{\pi}{2}\frac{\left ( {r}-{r}_{min} \right )}{\left ( {r}_{c}-{r}_{min} \right )} \right ]\\
+
+where :math:`\mathbf{r}_{i}` and :math:`\mathbf{r}_{j}` are the center
+position vectors of particles i and j, respectively,
+:math:`\mathbf{r}_{ij}=\mathbf{r}_{i}-\mathbf{r}_{j}` is the
+inter-particle distance vector, :math:`r=\left|\mathbf{r}_{ij} \right|`
+and :math:`{\hat{\mathbf{r}}}_{ij}=\mathbf{r}_{ij}/r`.  The unit vectors
+:math:`\mathbf{n}_{i}` and :math:`\mathbf{n}_{j}` represent the axes of
+symmetry of particles i and j, respectively, :math:`u_R` and :math:`u_A`
+are the repulsive and attractive potentials, :math:`\phi` is an angular
+function which depends on the relative orientation between pair
+particles, :math:`\mu` is the parameter related to the bending rigidity
+of the membrane, :math:`\beta` is the parameter related to the
+spontaneous curvature, and :math:`\epsilon` is the energy unit,
+respectively.   The :math:`\zeta` controls the slope of the attractive
+branch and hence the diffusivity of the particles in the in-plane
+direction of the membrane.  :math:`{r}_{c}` is the cutoff radius,
+:math:`r_{min}` is the distance which minimizes the potential energy
+:math:`u_{A}(r)` and :math:`r_{min}=2^{1/6}\sigma`, where :math:`\sigma`
+is the length unit.
+
+This pair style is suited for solvent-free coarse-grained simulations of
+biological systems involving lipid bilayer membranes, such as vesicle
+shape transformations :ref:`(Yuan2010b) <Yuan>`, nanoparticle
+endocytosis :ref:`(Huang) <Huang>`, modeling of red blood cell membranes
+:ref:`(Fu) <Fu>`, :ref:`(Appshaw) <Appshaw>`, and modeling of cell
+elasticity :ref:`(Becton) <Becton>`.
+
+Use of this pair style requires the NVE, NVT, or NPT fixes with the
+*asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in
+order to integrate particle rotation.  Additionally, :doc:`atom_style
+ellipsoid <atom_style>` should be used since it defines the rotational
+state of each particle.
+
+The following coefficients must be defined for each pair of atoms types
+via the :doc:`pair_coeff <pair_coeff>` command as in the examples above,
+or in the data file or restart files read by the :doc:`read_data
+<read_data>` or :doc:`read_restart <read_restart>` commands, or by
+mixing as described below:
+
+* :math:`\epsilon` = well depth (energy units)
+* :math:`\sigma` = minimum effective particle radii (distance units)
+* :math:`\zeta` = tune parameter for the slope of the attractive branch
+* :math:`\mu` = parameter related to bending rigidity
+* :math:`\beta` = parameter related to the spontaneous curvature
+* cutoff (distance units)
+
+The last coefficient is optional.  If not specified, the global
+cutoff specified in the pair_style command is used.
+
+----------
+
+Mixing, shift, table, tail correction, restart, rRESPA info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+For atom type pairs I,J and I != J, the epsilon and sigma coefficients
+and cutoff distance for this pair style can be mixed.  The default mix
+value is *geometric*\ .  See the "pair_modify" command for details.
+
+The :doc:`pair_modify <pair_modify>` table option is not relevant for
+this pair style.
+
+This pair style does not support the :doc:`pair_modify <pair_modify>`
+tail option for adding long-range tail corrections to energy and
+pressure.
+
+This pair style writes its information to :doc:`binary restart files
+<restart>`, so pair_style and pair_coeff commands do not need to be
+specified in an input script that reads a restart file.
+
+This pair style can only be used via the *pair* keyword of the
+:doc:`run_style respa <run_style>` command.  It does not support the
+*inner*, *middle*, *outer* keywords.
+
+----------
+
+Restrictions
+""""""""""""
+
+The *ylz* style is part of the ASPHERE package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+This pair style requires that atoms store torque and a quaternion to
+represent their orientation, as defined by the :doc:`atom_style
+<atom_style>`.  It also requires they store a per-atom :doc:`shape
+<set>`.  The particles cannot store a per-particle diameter.  To avoid
+being mistakenly considered as point particles, the shape parameters ought
+to be non-spherical, like [1 0.99 0.99].  Unlike the :doc:`resquared
+<pair_resquared>` pair style for which the shape directly determines the
+mathematical expressions of the potential, the shape parameters for this
+pair style is only involved in the computation of the moment of inertia
+and thus only influences the rotational dynamics of individual
+particles.
+
+This pair style requires that **all** atoms are ellipsoids as defined by
+the :doc:`atom_style ellipsoid <atom_style>` command.
+
+
+Related commands
+""""""""""""""""
+
+:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
+:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
+:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
+:doc:gayberne <pair_gayberne>`
+
+Default
+"""""""
+
+none
+
+----------
+
+.. _Yuan:
+
+**(Yuan2010a)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
+
+**(Yuan2010b)** Yuan, Huang, Zhang, Soft. Matter, 6, 4571(2010).
+
+.. _Huang:
+
+**(Huang)** Huang, Zhang, Yuan, Gao, Zhang, Nano Lett. 13, 4546(2013).
+
+.. _Fu:
+
+**(Fu)** Fu, Peng, Yuan, Kfoury, Young, Comput. Phys. Commun, 210, 193-203(2017).
+
+.. _Appshaw:
+
+**(Appshaw)** Appshaw, Seddon, Hanna, Soft. Matter,18, 1747(2022).
+
+.. _Becton:
+
+**(Becton)** Becton, Averett, Wang, Biomech. Model. Mechanobiology, 18, 425-433(2019).

doc/src/prd.rst

@@ -18,7 +18,7 @@ Syntax
 * compute-ID = ID of the compute used for event detection
 * random_seed = random # seed (positive integer)
 * zero or more keyword/value pairs may be appended
-* keyword = *min* or *temp* or *vel*
+* keyword = *min* or *temp* or *vel* or *time*
 
   .. parsed-literal::
 

doc/src/processors.rst

@@ -18,18 +18,17 @@ Syntax
 
        *grid* arg = gstyle params ...
          gstyle = *onelevel* or *twolevel* or *numa* or *custom*
-           onelevel params = none
+           *onelevel* params = none
-           twolevel params = Nc Cx Cy Cz
+           *twolevel* params = Nc Cx Cy Cz
              Nc = number of cores per node
              Cx,Cy,Cz = # of cores in each dimension of 3d sub-grid assigned to each node
-           numa params = none
+           *numa* params = none
-           custom params = infile
+           *custom* params = infile
              infile = file containing grid layout
        *map* arg = *cart* or *cart/reorder* or *xyz* or *xzy* or *yxz* or *yzx* or *zxy* or *zyx*
           cart = use MPI_Cart() methods to map processors to 3d grid with reorder = 0
           cart/reorder = use MPI_Cart() methods to map processors to 3d grid with reorder = 1
           xyz,xzy,yxz,yzx,zxy,zyx = map processors to 3d grid in IJK ordering
-       *numa* arg = none
        *part* args = Psend Precv cstyle
          Psend = partition # (1 to Np) which will send its processor layout
          Precv = partition # (1 to Np) which will recv the processor layout

doc/src/read_data.rst

@@ -71,8 +71,14 @@ Also see the explanation of the :doc:`-restart command-line switch
 
 This command can be used multiple times to add new atoms and their
 properties to an existing system by using the *add*, *offset*, and
-*shift* keywords.  See more details below, which includes the use case
+*shift* keywords.  However, it is important to understand that several
-for the *extra* keywords.
+system parameters, like the number of types of different kinds and per
+atom settings are **locked in** after the first *read_data* command,
+which means that no type ID (including its offset) may have a larger
+value when processing additional data files than what is set by the
+first data file and the corresponding *read_data* command options.  See
+more details on this situation below, which includes the use case for
+the *extra* keywords.
 
 The *group* keyword adds all the atoms in the data file to the
 specified group-ID.  The group will be created if it does not already

doc/src/run_style.rst

@@ -101,7 +101,7 @@ Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
 for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
 
 Typically the best way to do this is to let the first partition choose
-its onn optimal layout, then require the second partition's layout to
+its own optimal layout, then require the second partition's layout to
 match the integer multiple constraint.  See the
 :doc:`processors <processors>` command with its *part* keyword for a way
 to control this, e.g.

doc/src/tad.rst

@@ -18,7 +18,7 @@ Syntax
 * tmax = reciprocal of lowest expected pre-exponential factor (time units)
 * compute-ID = ID of the compute used for event detection
 * zero or more keyword/value pairs may be appended
-* keyword = *min* or *neb* or *min_style* or *neb_style* or *neb_log*
+* keyword = *min* or *neb* or *neb_style* or *neb_step* or *neb_log*
 
   .. parsed-literal::
 

doc/src/thermo_modify.rst

@@ -28,6 +28,7 @@ Syntax
        *format* values = *line* string, *int* string, *float* string, ID string, or *none*
          string = C-style format string
          ID = integer from 1 to N, or integer from -1 to -N, where N = # of quantities being output
+              *or* an integer range such as 2*6 (negative values are not allowed)
               *or* a thermo keyword or reference to compute, fix, property or variable.
        *temp* value = compute ID that calculates a temperature
        *press* value = compute ID that calculates a pressure
@@ -65,10 +66,10 @@ atom can be "lost" if it moves across a non-periodic simulation box
 :doc:`boundary <boundary>` or if it moves more than a box length outside
 the simulation domain (or more than a processor sub-domain length)
 before reneighboring occurs.  The latter case is typically due to bad
-dynamics, e.g. too large a timestep or huge forces and velocities.  If
+dynamics (e.g., too large a time step and/or huge forces and velocities).  If
 the value is *ignore*, LAMMPS does not check for lost atoms.  If the
 value is *error* or *warn*, LAMMPS checks and either issues an error or
-warning.  The code will exit with an error and continue with a warning.
+warning.  The simulation will exit with an error and continue with a warning.
 A warning will only be issued once, the first time an atom is lost.
 This can be a useful debugging option.
 
@@ -89,10 +90,10 @@ that should be investigated, but LAMMPS cannot determine for
 certain whether they are an indication of an error.
 
 Some warning messages are printed during a run (or immediately before)
-each time a specific MPI rank encounters the issue, e.g. bonds that are
+each time a specific MPI rank encounters the issue (e.g., bonds that are
-stretched too far or dihedrals in extreme configurations. These number
+stretched too far or dihedrals in extreme configurations). These number
 of these can quickly blow up the size of the log file and screen output.
-Thus a limit of 100 warning messages is applied by default.  The warning
+Thus, a limit of 100 warning messages is applied by default.  The warning
 count is applied to the entire input unless reset with a ``thermo_modify
 warn reset`` command.  If there are more warnings than the limit, LAMMPS
 will print one final warning that it will not print any additional
@@ -160,8 +161,8 @@ for a column or field of thermodynamic output.  The setting for *ID
 string* replaces the default text with the provided string.  *ID* can be
 a positive integer when it represents the column number counting from
 the left, a negative integer when it represents the column number from
-the right (i.e. -1 is the last column/keyword), or a thermo keyword (or
+the right (i.e., :math:`-1` is the last column/keyword), or a thermo keyword
-compute, fix, property, or variable reference) and then it replaces the
+(or compute, fix, property, or variable reference) and then it replaces the
 string for that specific thermo keyword.
 
 The *colname* keyword can be used multiple times. If multiple *colname*
@@ -171,19 +172,22 @@ to their default values.
 
 The *format* keyword can be used to change the default numeric format of
 any of quantities the :doc:`thermo_style <thermo_style>` command
-outputs.  All the specified format strings are C-style formats, e.g. as
+outputs.  All the specified format strings are C-style formats (i.e., as
-used by the C/C++ printf() command.  The *line* keyword takes a single
+used by the C/C++ printf() command).  The *line* keyword takes a single
 argument which is the format string for the entire line of thermo
-output, with N fields, which you must enclose in quotes if it is more
+output, with :math:`N` fields, which you must enclose in quotes if it is more
 than one field.  The *int* and *float* keywords take a single format
 argument and are applied to all integer or floating-point quantities
 output.  The setting for *ID string* also takes a single format argument
-which is used for the indexed value in each line.  The interpretation is
+that is used for the indexed value in each line.  The interpretation is
-the same as for *colname*, i.e. a positive integer is the n-th value
+the same as for *colname* (i.e., a positive integer is the n-th value
 corresponding to the n-th thermo keyword, a negative integer is counting
-backwards, and a string matches the entry with the thermo keyword.,
+backwards, and a string matches the entry with the thermo keyword).
-e.g. the fifth column is output in high precision for "format 5 %20.15g"
+For example, the fifth column is output in high precision for
-and the pair energy for "format epair %20.15g".
+"format 5 %20.15g", and the pair energy for "format epair %20.15g".
+The *ID* field can be a range, such as "3\*6", "*", "2*", or "\*3";
+in such cases, all fields in the range (inclusive) are set to the specified
+format string. Ranges containing negative numbers are not supported.
 
 The *format* keyword can be used multiple times.  The precedence is
 that for each value in a line of output, the *ID* format (if specified)
@@ -201,8 +205,8 @@ settings, reverting all values to their default format.
    to the corresponding 8-byte form when it is applied to those
    keywords.  However, when specifying the *line* option or *format ID
    string* option for *step* and *natoms*, you should specify a format
-   string appropriate for an 8-byte signed integer, e.g. one with "%ld"
+   string appropriate for an 8-byte signed integer (i.e., one with "%ld"
-   or "%lld" depending on the platform.
+   or "%lld", depending on the platform).
 
 The *temp* keyword is used to determine how thermodynamic temperature is
 calculated, which is used by all thermo quantities that require a

doc/src/variable.rst

@@ -213,6 +213,9 @@ from the list of active variables, and is thus available to be
 re-defined in a subsequent variable command.  The *delete* style does
 the same thing.
 
+Variables are **not** deleted by the :doc:`clear <clear>` command with
+the exception of atomfile-style variables.
+
 ----------
 
 The :doc:`Commands parse <Commands_parse>` page explains how
@@ -265,7 +268,7 @@ the first string is assigned to the variable.  Each time a
 string is assigned.  All processors assign the same string to the
 variable.
 
-*Index* style variables with a single string value can also be set by
+Index-style variables with a single string value can also be set by
 using the :doc:`command-line switch -var <Run_options>`.
 
 The *loop* style is identical to the *index* style except that the
@@ -285,7 +288,7 @@ be one string for each processor partition or "world".  LAMMPS can be
 run with multiple partitions via the :doc:`-partition command-line
 switch <Run_options>`.  This variable command assigns one string to
 each world.  All processors in the world are assigned the same string.
-The next command cannot be used with *equal* style variables, since
+The next command cannot be used with equal-style variables, since
 there is only one value per world.  This style of variable is useful
 when you wish to run different simulations on different partitions, or
 when performing a parallel tempering simulation (see the :doc:`temper
@@ -303,7 +306,7 @@ string.  This continues until all the variable strings are consumed.
 Thus, this command can be used to run 50 simulations on 8 processor
 partitions.  The simulations will be run one after the other on
 whatever partition becomes available, until they are all finished.
-*Universe* style variables are incremented using the files
+Universe-style variables are incremented using the files
 "tmp.lammps.variable" and "tmp.lammps.variable.lock" which you will
 see in your directory during such a LAMMPS run.
 
@@ -341,7 +344,9 @@ variable can be used to adapt the behavior of LAMMPS input scripts via
 environment variable settings, or to retrieve information that has
 been previously stored with the :doc:`shell putenv <shell>` command.
 Note that because environment variable settings are stored by the
-operating systems, they persist beyond a :doc:`clear <clear>` command.
+operating systems, they persist even if the corresponding *getenv*
+style variable is deleted, and also are set for sub-shells executed
+by the :doc:`shell <shell>` command.
 
 For the *file* style, a filename is provided which contains a list of
 strings to assign to the variable, one per line.  The strings can be
@@ -373,7 +378,9 @@ This means the variable can then be evaluated as many times as desired
 and will return those values.  There are two ways to cause the next
 set of per-atom values from the file to be read: use the
 :doc:`next <next>` command or the next() function in an atom-style
-variable, as discussed below.
+variable, as discussed below.  Unlike most variable styles
+atomfile-style variables are **deleted** during a :doc:`clear <clear>`
+command.
 
 The rules for formatting the file are as follows.  Each time a set of
 per-atom values is read, a non-blank line is searched for in the file.

doc/src/velocity.rst

@@ -33,7 +33,7 @@ Syntax
          *angular* = zero the angular momentum
 
 * zero or more keyword/value pairs may be appended
-* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *units*
+* keyword = *dist* or *sum* or *mom* or *rot* or *temp* or *bias* or *loop* or *rigid* or *units*
 
   .. parsed-literal::
 

doc/utils/converters/lammpsdoc/txt2html.py

@@ -3,7 +3,7 @@
 #
 # Python rewrite of txt2html
 # The original txt2html was written in C by Steve Plimpton
-# (http://www.cs.sandia.gov/cgi-bin/sjplimp/)
+# (https://sjplimp.github.io/)
 #
 # Copyright (C) 2015 Richard Berger
 #

doc/utils/sphinx-config/LAMMPSLexer.py

@@ -9,8 +9,8 @@ LAMMPS_COMMANDS = ("angle_coeff", "angle_style", "atom_modify", "atom_style",
 "displace_atoms", "dump_modify", "dynamical_matrix", "echo", "elif", "else",
 "fix_modify", "group2ndx", "hyper", "if", "improper_coeff",
 "improper_style", "include", "info", "jump", "kim",
-"kspace_modify", "kspace_style", "label", "lattice",
+"kspace_modify", "kspace_style", "label", "labelmap", "lattice", "log",
-"log", "mass", "message", "minimize", "min_modify", "min_style", "molecule",
+"mass", "mdi", "message", "minimize", "min_modify", "min_style", "molecule",
 "ndx2group", "neb", "neb/spin", "neighbor", "neigh_modify", "newton", "next",
 "package", "pair_coeff", "pair_modify", "pair_style", "pair_write",
 "partition", "prd", "print", "processors", "python", "quit", "read_data",

doc/utils/sphinx-config/conf.py.in

@@ -38,7 +38,7 @@ sys.path.append(os.path.join(LAMMPS_DOC_DIR, 'src', '_ext'))
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-#needs_sphinx = '1.0'
+needs_sphinx = '5.2.0'
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
@@ -53,10 +53,6 @@ extensions = [
     'tab_or_note',
     'breathe',
 ]
-# 2017-12-07: commented out, since this package is broken with Sphinx 16.x
-#             yet we can no longer use Sphinx 15.x, since that breaks with
-#             newer version of the multiprocessor module.
-#    'sphinxcontrib.images',
 
 images_config = {
   'default_image_width' : '25%',
@@ -287,7 +283,48 @@ latex_elements = {
 # Additional stuff for the LaTeX preamble.
 'preamble': r'''
 \setcounter{tocdepth}{2}
+\renewcommand{\sfdefault}{ptm}  % Use Times New Roman font for \textrm
+\renewcommand{\sfdefault}{phv}  % Use Helvetica font for \textsf
+% Set up math fonts to match text fonts
+\DeclareSymbolFont{operators}   {OT1}{ptm}{m}{n}
+\DeclareSymbolFont{bold}        {OT1}{ptm}{bx}{n}
+\DeclareSymbolFont{italic}      {OT1}{ptm}{m}{it}
+\DeclareSymbolFont{extraops}    {OT1}{ztmcm}{m}{n}
+\DeclareSymbolFont{letters}     {OML}{ztmcm}{m}{it}
+\DeclareSymbolFont{largesymbols}{OMX}{ztmcm}{m}{n}
+% symbols (and \mathcal) are taken from computer modern.
+% setup mappings
+\DeclareSymbolFontAlphabet{\mathrm}    {operators}
+\DeclareSymbolFontAlphabet{\mathnormal}{letters}
+\DeclareMathAlphabet{\mathnormal}{OT1}{ptm}{m}{n}
+\DeclareMathAlphabet{\mathrm}{OT1}{ptm}{m}{n}
+\DeclareMathAlphabet{\mathbf}{OT1}{ptm}{bx}{n}
+\DeclareMathAlphabet{\mathit}{OT1}{ptm}{m}{it}
+\DeclareMathAlphabet{\mathtt}{OT1}{pcr}{m}{n}
+\SetMathAlphabet\mathit{bold}{OT1}{ptm}{bx}{it}
+% declare missing operators
+\DeclareMathSymbol{\omicron}{0}{operators}{`\o}
+\DeclareMathSymbol{\Gamma}{\mathalpha}{extraops}{"00}
+\DeclareMathSymbol{\Delta}{\mathalpha}{extraops}{"01}
+\DeclareMathSymbol{\Theta}{\mathalpha}{extraops}{"02}
+\DeclareMathSymbol{\Lambda}{\mathalpha}{extraops}{"03}
+\DeclareMathSymbol{\Xi}{\mathalpha}{extraops}{"04}
+\DeclareMathSymbol{\Pi}{\mathalpha}{extraops}{"05}
+\DeclareMathSymbol{\Sigma}{\mathalpha}{extraops}{"06}
+\DeclareMathSymbol{\Upsilon}{\mathalpha}{extraops}{"07}
+\DeclareMathSymbol{\Phi}{\mathalpha}{extraops}{"08}
+\DeclareMathSymbol{\Psi}{\mathalpha}{extraops}{"09}
+\DeclareMathSymbol{\Omega}{\mathalpha}{extraops}{"0A}
+
 \renewcommand{\AA}{\mbox{\textrm{\r{A}}}}
+% Make ToC number fields wider to accommodate sections with >= 100 subsections
+%   or >= 10 subsections with >= 10 subsubsections
+\makeatletter
+\renewcommand*{\sphinxtableofcontentshook}{%
+  \renewcommand*\l@section{\@dottedtocline{1}{1.5em}{3.1em}}
+  \renewcommand*\l@subsection{\@dottedtocline{2}{4.6em}{4.5em}}
+}
+\makeatother
 '''
 }
 
@@ -372,9 +409,9 @@ at Sandia 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).
 
-The primary author of the code is Steve Plimpton, who can be emailed
+The LAMMPS developers can be contacted at developers@lammps.org.
-at sjplimp@sandia.gov.  The LAMMPS WWW Site at www.lammps.org has
+The LAMMPS WWW Site at www.lammps.org has more information about
-more information about the code and its uses.
+the code and its uses.
 """
 
 epub_author = 'The LAMMPS Developers'

doc/utils/sphinx-config/false_positives.txt

@@ -123,6 +123,7 @@ Antonelli
 api
 Apoorva
 Appl
+Appshaw
 apptainer
 Apu
 arallel
@@ -181,6 +182,7 @@ Avalos
 avalue
 aveforce
 Avendano
+Averett
 avi
 AVX
 awpmd
@@ -237,6 +239,7 @@ bcolor
 bdiam
 bdw
 Beckman
+Becton
 Belak
 Bellott
 bem
@@ -270,6 +273,7 @@ bilayers
 binsize
 binstyle
 binutils
+Biomech
 biomolecular
 biomolecule
 Biomolecules
@@ -925,6 +929,7 @@ Emmrich
 emol
 eN
 endian
+endocytosis
 energetics
 energyCorr
 eng
@@ -1156,6 +1161,7 @@ ftm
 ftol
 fuer
 fugacity
+Fu
 Fumi
 func
 funcs
@@ -1308,6 +1314,7 @@ Hamaker
 Hamel
 Hammerschmidt
 Hanley
+Hanna
 haptic
 Haque
 Hara
@@ -1659,6 +1666,7 @@ kepler
 keV
 Keyes
 keyfile
+Kfoury
 Khersonskii
 Khrapak
 Khvostov
@@ -1914,6 +1922,7 @@ lwsock
 lx
 ly
 Lybrand
+Lykotrafitis
 lyon
 Lysogorskiy
 Lyulin
@@ -2024,6 +2033,7 @@ MEAM
 meamf
 meanDist
 mech
+Mechanobiology
 Mecke
 mediumaquamarine
 mediumblue
@@ -2542,7 +2552,6 @@ oneAPI
 onelevel
 oneway
 onlysalt
-onn
 ons
 OO
 Oord
@@ -2740,6 +2749,7 @@ Polym
 polymorph
 polymorphism
 Ponder
+Ponte
 popen
 Popoola
 Popov
@@ -3145,6 +3155,7 @@ seagreen
 Secor
 sectoring
 sed
+Seddon
 segmental
 Seifert
 Seleson
@@ -3694,6 +3705,7 @@ vdw
 vdW
 vdwl
 vec
+Vecchio
 vectorial
 vectorization
 Vectorization
@@ -3903,6 +3915,7 @@ yhi
 yi
 ylat
 ylo
+ylz
 ymax
 ymin
 yml

examples/ASPHERE/README

@@ -29,8 +29,10 @@ stochastic rotation dynamics solvent, using the fix srd command.
 box = 2d rigid box particles in SRDs, self-diffusion and viscosity
 dimer = 2d rigid dimers in SRDs, self-diffusion and viscosity
 ellipsoid = 2d ellipsoids in SRDs, self-diffusion and viscosity
+flat_membrane = 2d flat membrane in NVE, self-diffusion and viscosity
 line = 2d line-faceted rigid particles, NEMD shearing for viscosity,
        implicit and in SRDs
 poly = 2d poly-disperse spheroids in SRDs, self-diffusion and viscosity
 star = 2d rigid star particles in SRDs, self-diffusion and viscosity
 tri = 3d triangle-faceted rigid particles in SRDs, NEMD shearing for viscosity
+vesicle = 3d vesicle in NVE, self-diffusionand viscosity

examples/ASPHERE/flat_membrane/in.flat_membrane

@@ -0,0 +1,55 @@
+# flat membrane demo
+variable     r0 equal  0.97
+variable     d1 equal  ${r0}
+variable     d2 equal  sqrt(3.0)*${r0}
+variable     d3 equal  3.0*${r0}
+variable     ro equal  2./${d1}/${d2}/${d3}
+
+variable     T  equal  0.23
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+lattice      custom ${ro} a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0 &
+             a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+
+
+region       box block   0 40  0 24  -20  20
+create_box   1 box
+region       membrane block  0 40  0 24 -0.5 0.5
+create_atoms 1 region membrane
+
+group        membrane  region membrane
+
+set type 1 mass  1.0
+
+set type 1 shape  1 0.99 0.99
+
+set          group all quat 0 -1 0  90
+
+#compute      memb  all temp/com
+#compute      rot all temp/asphere bias memb
+velocity     all create ${T} 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.01
+
+#dump         1 all atom 10 dump_onlymembrane.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+
+
+fix          2 all nve/asphere
+run          3000
+
+

examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1

@@ -0,0 +1,159 @@
+LAMMPS (15 Sep 2022)
+  using 1 OpenMP thread(s) per MPI task
+# flat membrane demo
+variable     r0 equal  0.97
+variable     d1 equal  ${r0}
+variable     d1 equal  0.97
+variable     d2 equal  sqrt(3.0)*${r0}
+variable     d2 equal  sqrt(3.0)*0.97
+variable     d3 equal  3.0*${r0}
+variable     d3 equal  3.0*0.97
+variable     ro equal  2./${d1}/${d2}/${d3}
+variable     ro equal  2./0.97/${d2}/${d3}
+variable     ro equal  2./0.97/1.68008928334181/${d3}
+variable     ro equal  2./0.97/1.68008928334181/2.91
+
+variable     T  equal  0.23
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+lattice      custom ${ro} a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 2.91  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+Lattice spacing in x,y,z = 0.97 1.6800893 2.91
+
+
+region       box block   0 40  0 24  -20  20
+create_box   1 box
+Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
+  1 by 1 by 1 MPI processor grid
+region       membrane block  0 40  0 24 -0.5 0.5
+create_atoms 1 region membrane
+Created 1920 atoms
+  using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
+  create_atoms CPU = 0.001 seconds
+
+group        membrane  region membrane
+1920 atoms in group membrane
+
+set type 1 mass  1.0
+Setting atom values ...
+  1920 settings made for mass
+
+set type 1 shape  1 1 1
+Setting atom values ...
+  1920 settings made for shape
+
+set          group all quat 0 -1 0  90
+Setting atom values ...
+  1920 settings made for quat
+
+#compute      memb  all temp/com
+#compute      rot all temp/asphere bias memb
+velocity     all create ${T} 87287 loop geom
+velocity     all create 0.23 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.01
+
+#dump         1 all atom 10 dump_onlymembrane.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+fix          1 all langevin 0.23 ${T}  ${LD}  48279
+fix          1 all langevin 0.23 0.23  ${LD}  48279
+fix          1 all langevin 0.23 0.23  1  48279
+
+
+fix          2 all nve/asphere
+run          3000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair ylz command:
+
+@Article{Yuan10,
+ author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
+ title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
+ journal = {Phys. Rev. E},
+ year =    2010,
+ volume =  82,
+ pages =   {011905}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 10 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 22 23 65
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair ylz, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
+   Step          Temp          Press           Pxx            Pyy      
+         0   0.23          -0.0073508785  -0.012283389   -0.012234574  
+       200   0.20903886    -0.0010605951  -0.0011885957  -0.00198842   
+       400   0.21898026    -0.00069250685 -0.0013217981  -0.00073225707
+       600   0.22689361    -0.00057919328 -0.00076880503 -0.0010242283 
+       800   0.22983221    -0.00032145682 -0.00051928834 -0.00059337525
+      1000   0.23819392    -0.00027969126 -0.00088082301 -5.2666567e-05
+      1200   0.22053795    -0.00029571329 -0.0004446455  -0.00035529929
+      1400   0.22285021    -0.0002690371  -0.00068896571 -3.6258442e-05
+      1600   0.22687044     2.8599875e-05 -0.00032651798  0.0004056081 
+      1800   0.23356905    -2.28742e-05   -0.00027073251  0.00025081131
+      2000   0.22499821     8.8230586e-06 -7.5750159e-05  0.0001988705 
+      2200   0.23162995    -9.026855e-05  -0.00025832535  5.4904927e-05
+      2400   0.22920223     0.00016700455  3.5283125e-05  0.00034955857
+      2600   0.2260299      5.3095557e-05  0.00025691786  0.00013353467
+      2800   0.2296401      0.00043234854  0.00058344966  0.00063645193
+      3000   0.22564577     2.6423111e-05  8.9918406e-05  0.00022146229
+Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
+
+Performance: 383058.431 tau/day, 443.355 timesteps/s
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 5.7968     | 5.7968     | 5.7968     |   0.0 | 85.67
+Neigh   | 0.086077   | 0.086077   | 0.086077   |   0.0 |  1.27
+Comm    | 0.034761   | 0.034761   | 0.034761   |   0.0 |  0.51
+Output  | 0.00038014 | 0.00038014 | 0.00038014 |   0.0 |  0.01
+Modify  | 0.8268     | 0.8268     | 0.8268     |   0.0 | 12.22
+Other   |            | 0.02181    |            |       |  0.32
+
+Nlocal:           1920 ave        1920 max        1920 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:            772 ave         772 max         772 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          46804 ave       46804 max       46804 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 46804
+Ave neighs/atom = 24.377083
+Neighbor list builds = 99
+Dangerous builds = 0
+
+
+Total wall time: 0:00:06

examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4

@@ -0,0 +1,159 @@
+LAMMPS (15 Sep 2022)
+  using 1 OpenMP thread(s) per MPI task
+# flat membrane demo
+variable     r0 equal  0.97
+variable     d1 equal  ${r0}
+variable     d1 equal  0.97
+variable     d2 equal  sqrt(3.0)*${r0}
+variable     d2 equal  sqrt(3.0)*0.97
+variable     d3 equal  3.0*${r0}
+variable     d3 equal  3.0*0.97
+variable     ro equal  2./${d1}/${d2}/${d3}
+variable     ro equal  2./0.97/${d2}/${d3}
+variable     ro equal  2./0.97/1.68008928334181/${d3}
+variable     ro equal  2./0.97/1.68008928334181/2.91
+
+variable     T  equal  0.23
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+lattice      custom ${ro} a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 ${d1}  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 ${d2}  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 ${d3}  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+lattice      custom 0.421728460751825 a1 0.97  0.0 0.0 a2 0.0 1.68008928334181  0.0              a3 0.0 0.0 2.91  basis 0.0 0.0 0.0 basis 0.5  0.5  0.0
+Lattice spacing in x,y,z = 0.97 1.6800893 2.91
+
+
+region       box block   0 40  0 24  -20  20
+create_box   1 box
+Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
+  1 by 1 by 4 MPI processor grid
+region       membrane block  0 40  0 24 -0.5 0.5
+create_atoms 1 region membrane
+Created 1920 atoms
+  using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
+  create_atoms CPU = 0.001 seconds
+
+group        membrane  region membrane
+1920 atoms in group membrane
+
+set type 1 mass  1.0
+Setting atom values ...
+  1920 settings made for mass
+
+set type 1 shape  1 1 1
+Setting atom values ...
+  1920 settings made for shape
+
+set          group all quat 0 -1 0  90
+Setting atom values ...
+  1920 settings made for quat
+
+#compute      memb  all temp/com
+#compute      rot all temp/asphere bias memb
+velocity     all create ${T} 87287 loop geom
+velocity     all create 0.23 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.01
+
+#dump         1 all atom 10 dump_onlymembrane.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+fix          1 all langevin 0.23 ${T}  ${LD}  48279
+fix          1 all langevin 0.23 0.23  ${LD}  48279
+fix          1 all langevin 0.23 0.23  1  48279
+
+
+fix          2 all nve/asphere
+run          3000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair ylz command:
+
+@Article{Yuan10,
+ author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
+ title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
+ journal = {Phys. Rev. E},
+ year =    2010,
+ volume =  82,
+ pages =   {011905}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 10 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 22 23 65
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair ylz, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
+   Step          Temp          Press           Pxx            Pyy      
+         0   0.23          -0.0073508785  -0.012283389   -0.012234574  
+       200   0.20647718    -0.0012368074  -0.0021167303  -0.0015343502 
+       400   0.21648371    -0.00085695085 -0.0015627331  -0.0011177093 
+       600   0.22929515    -0.00050218657 -0.0008332     -0.00062622609
+       800   0.22062664    -0.00049172378 -0.000611884   -0.00075089294
+      1000   0.22422425    -0.00039405068 -0.00037600355 -0.00070786572
+      1200   0.2298767     -0.00025939082 -0.00021616578 -0.00053125505
+      1400   0.2335927      5.8028332e-05  0.00017530192 -3.1675138e-05
+      1600   0.22884878    -0.0001733902  -0.0008056431   0.00014276754
+      1800   0.22813498     0.00019873459  0.00051040124  5.8860949e-05
+      2000   0.2273166     -3.3595127e-05  0.0001705632  -0.00026498213
+      2200   0.2251643     -2.4517311e-05 -4.0618888e-05  1.066658e-05 
+      2400   0.22460629    -4.5661259e-05 -0.00019144039 -1.6649099e-05
+      2600   0.23085675     0.00014029405  0.00017983536  0.00017895001
+      2800   0.22364591     4.2999164e-05 -0.00011000466  0.00024363243
+      3000   0.23421357     0.00023505702  0.00020752013  0.00053567111
+Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
+
+Performance: 553164.568 tau/day, 640.237 timesteps/s
+95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.00015072 | 1.6029     | 3.8573     | 131.7 | 34.21
+Neigh   | 0.00055747 | 0.025423   | 0.065858   |  17.0 |  0.54
+Comm    | 0.0052259  | 0.48173    | 1.624      |  96.5 | 10.28
+Output  | 0.0003894  | 0.023428   | 0.047223   |  15.0 |  0.50
+Modify  | 0.00037337 | 0.2141     | 0.44595    |  46.3 |  4.57
+Other   |            | 2.338      |            |       | 49.90
+
+Nlocal:            480 ave        1011 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 1 1
+Nghost:            860 ave        1771 max           0 min
+Histogram: 2 0 0 0 0 0 0 0 0 2
+Neighs:        11697.8 ave       30095 max           0 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 46791
+Ave neighs/atom = 24.370313
+Neighbor list builds = 99
+Dangerous builds = 0
+
+
+Total wall time: 0:00:04

examples/ASPHERE/vesicle/in.vesicle

@@ -0,0 +1,33 @@
+# Vesicle demo
+
+variable     T  equal  0.2
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+read_data    read_data.vesicle1026
+
+compute      ali  all temp/com
+compute      rott all temp/asphere bias ali
+
+velocity     all create ${T} 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.001
+
+#dump         1 all atom 10 onlymembrane2.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+fix          2 all nve/asphere
+
+run          3000
+

examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1

@@ -0,0 +1,122 @@
+LAMMPS (15 Sep 2022)
+  using 1 OpenMP thread(s) per MPI task
+# Vesicle demo
+
+variable     T  equal  0.2
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+read_data    read_data.vesicle1026
+Reading data file ...
+  orthogonal box = (-35 -35 -35) to (35 35 35)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2938 atoms
+  2938 ellipsoids
+  read_data CPU = 0.010 seconds
+
+compute      ali  all temp/com
+compute      rott all temp/asphere bias ali
+
+velocity     all create ${T} 87287 loop geom
+velocity     all create 0.2 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.001
+
+#dump         1 all atom 10 onlymembrane2.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+fix          1 all langevin 0.2 ${T}  ${LD}  48279
+fix          1 all langevin 0.2 0.2  ${LD}  48279
+fix          1 all langevin 0.2 0.2  1  48279
+fix          2 all nve/asphere
+
+run          3000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair ylz command:
+
+@Article{Yuan10,
+ author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
+ title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
+ journal = {Phys. Rev. E},
+ year =    2010,
+ volume =  82,
+ pages =   {011905}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 10 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 39 39 39
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair ylz, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes
+   Step          Temp          Press           Pxx            Pyy      
+         0   0.2           -0.0054891414  -0.0052713616  -0.0053641136 
+       200   0.12816247    -0.0051288861  -0.0048542514  -0.0049847561 
+       400   0.1377632     -0.0048071582  -0.0045651263  -0.0048444087 
+       600   0.14983781    -0.0045305725  -0.0043305994  -0.0046127777 
+       800   0.16205271    -0.0041176346  -0.0040534483  -0.0041351779 
+      1000   0.17462122    -0.0037000069  -0.0034938539  -0.0037915494 
+      1200   0.18335448    -0.0032674318  -0.0032790248  -0.0031967931 
+      1400   0.19195613    -0.0029332101  -0.0030823703  -0.0028287799 
+      1600   0.19261762    -0.0025263447  -0.0025152249  -0.0026205398 
+      1800   0.19758674    -0.0021087725  -0.001981333   -0.002309048  
+      2000   0.19748896    -0.0017662369  -0.0019316344  -0.0016696035 
+      2200   0.20196986    -0.0013363214  -0.0015581191  -0.0013384961 
+      2400   0.20109248    -0.0009190831  -0.0010331417  -0.0010664316 
+      2600   0.20228664    -0.00053590675 -0.00071808747 -0.00050218533
+      2800   0.20512955    -0.00030845899 -0.00016244901 -0.00047877516
+      3000   0.19855941    -7.9520073e-05 -0.00014969215 -5.4724226e-06
+Loop time of 9.6866 on 1 procs for 3000 steps with 2938 atoms
+
+Performance: 26758.610 tau/day, 309.706 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 8.3097     | 8.3097     | 8.3097     |   0.0 | 85.79
+Neigh   | 0.039037   | 0.039037   | 0.039037   |   0.0 |  0.40
+Comm    | 0.0021766  | 0.0021766  | 0.0021766  |   0.0 |  0.02
+Output  | 0.00048628 | 0.00048628 | 0.00048628 |   0.0 |  0.01
+Modify  | 1.3043     | 1.3043     | 1.3043     |   0.0 | 13.47
+Other   |            | 0.0309     |            |       |  0.32
+
+Nlocal:           2938 ave        2938 max        2938 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:              0 ave           0 max           0 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          73242 ave       73242 max       73242 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 73242
+Ave neighs/atom = 24.929204
+Neighbor list builds = 26
+Dangerous builds = 0
+
+Total wall time: 0:00:09

examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.4

@@ -0,0 +1,122 @@
+LAMMPS (15 Sep 2022)
+  using 1 OpenMP thread(s) per MPI task
+# Vesicle demo
+
+variable     T  equal  0.2
+variable     LD equal  1.0
+
+units        lj
+atom_style   ellipsoid
+
+boundary     p p p
+
+read_data    read_data.vesicle1026
+Reading data file ...
+  orthogonal box = (-35 -35 -35) to (35 35 35)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2938 atoms
+  2938 ellipsoids
+  read_data CPU = 0.137 seconds
+
+compute      ali  all temp/com
+compute      rott all temp/asphere bias ali
+
+velocity     all create ${T} 87287 loop geom
+velocity     all create 0.2 87287 loop geom
+
+pair_style   ylz  2.6
+pair_coeff   *  *   1.0  1.0  4  3  0.0  2.6
+neighbor     1.0 bin
+
+thermo_style custom step temp press pxx pyy
+thermo       200
+
+timestep     0.001
+
+#dump         1 all atom 10 onlymembrane2.lammpstrj
+
+fix          1 all langevin ${T} ${T}  ${LD}  48279
+fix          1 all langevin 0.2 ${T}  ${LD}  48279
+fix          1 all langevin 0.2 0.2  ${LD}  48279
+fix          1 all langevin 0.2 0.2  1  48279
+fix          2 all nve/asphere
+
+run          3000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair ylz command:
+
+@Article{Yuan10,
+ author =  {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
+ title =   {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
+ journal = {Phys. Rev. E},
+ year =    2010,
+ volume =  82,
+ pages =   {011905}
+}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 10 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 3.6
+  ghost atom cutoff = 3.6
+  binsize = 1.8, bins = 39 39 39
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair ylz, perpetual
+      attributes: half, newton on
+      pair build: half/bin/atomonly/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes
+   Step          Temp          Press           Pxx            Pyy      
+         0   0.2           -0.0054891414  -0.0052713616  -0.0053641136 
+       200   0.12893798    -0.0051492794  -0.0048734875  -0.0049624005 
+       400   0.13798694    -0.004875313   -0.0047071897  -0.0049305051 
+       600   0.14725193    -0.0046349542  -0.004719983   -0.0045791451 
+       800   0.16146954    -0.0042232199  -0.0040789193  -0.0043672895 
+      1000   0.17268468    -0.0037146703  -0.0036270393  -0.0039169034 
+      1200   0.18266242    -0.0032749755  -0.0032971704  -0.0033323855 
+      1400   0.18500165    -0.0028179031  -0.0030659821  -0.0027519633 
+      1600   0.19513132    -0.0023407512  -0.0025109801  -0.0023416835 
+      1800   0.19645259    -0.0019995412  -0.0019064341  -0.0021757747 
+      2000   0.19658104    -0.0015897919  -0.0015850523  -0.0016828478 
+      2200   0.1989936     -0.0011794062  -0.0011779716  -0.0012070706 
+      2400   0.20011525    -0.0009147432  -0.00094040885 -0.001073922  
+      2600   0.2013975     -0.00059253676 -0.00051920304 -0.00075138934
+      2800   0.19715513    -0.00020995605 -0.00024386426 -0.0005475745 
+      3000   0.1976782     -0.0001308553   5.693004e-05  -0.00034478469
+Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms
+
+Performance: 30603.800 tau/day, 354.211 timesteps/s
+77.9% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.1751     | 2.4162     | 2.6707     |  13.2 | 28.53
+Neigh   | 0.0090503  | 0.0098389  | 0.010503   |   0.6 |  0.12
+Comm    | 3.5807     | 4.1526     | 4.9283     |  24.3 | 49.03
+Output  | 0.00032165 | 0.0029648  | 0.010842   |   8.4 |  0.04
+Modify  | 0.34554    | 0.37442    | 0.39198    |   2.8 |  4.42
+Other   |            | 1.514      |            |       | 17.87
+
+Nlocal:          734.5 ave         739 max         730 min
+Histogram: 1 0 1 0 0 0 0 1 0 1
+Nghost:         420.25 ave         424 max         415 min
+Histogram: 1 0 0 0 0 1 0 1 0 1
+Neighs:        18304.5 ave       19839 max       16636 min
+Histogram: 1 0 0 0 1 0 1 0 0 1
+
+Total # of neighbors = 73218
+Ave neighs/atom = 24.921035
+Neighbor list builds = 25
+Dangerous builds = 0
+
+Total wall time: 0:00:08

examples/COUPLE/fortran/libfwrapper.c

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   www.cs.sandia.gov/~sjplimp/lammps.html
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran2/LAMMPS-wrapper.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran2/LAMMPS-wrapper.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran_dftb/LAMMPS-wrapper.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.cpp

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    https://www.lammps.org/
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/fortran_dftb/LAMMPS-wrapper2.h

@@ -1,7 +1,7 @@
 /* -----------------------------------------------------------------------
     LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-    www.cs.sandia.gov/~sjplimp/lammps.html
+    https://www.lammps.org/, Sandia National Laboratories
-    Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+    LAMMPS development team: developers@lammps.org
  
     Copyright (2003) Sandia Corporation.  Under the terms of Contract
     DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/multiple/multiple.cpp

@@ -1,7 +1,7 @@
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
-   https://www.lammps.org/
+   https://www.lammps.org/, Sandia National Laboratories
-   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
 
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains

examples/COUPLE/plugin/.gitignore

@@ -0,0 +1 @@
+/build

examples/COUPLE/plugin/CMakeLists.txt

@@ -0,0 +1,47 @@
+##########################################
+# CMake build system for coupling to the LAMMPS library
+# where the library is loaded dynamically at runtime.
+##########################################
+
+cmake_minimum_required(VERSION 3.10)
+
+# enforce out-of-source build
+if(${CMAKE_SOURCE_DIR} STREQUAL ${CMAKE_BINARY_DIR})
+  message(FATAL_ERROR "In-source builds are not allowed. You must create and use a build directory. "
+    "Please remove CMakeCache.txt and CMakeFiles first.")
+endif()
+
+project(liblammpsplugin VERSION 1.0 LANGUAGES C)
+
+# by default, install into $HOME/.local (not /usr/local),
+# so that no root access (and sudo) is needed
+if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
+   set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
+# and prints lots of pointless warnings about "unsafe" functions
+if(MSVC)
+  if(CMAKE_C_COMPILER_ID STREQUAL "MSVC")
+    if(LAMMPS_EXCEPTIONS)
+      add_compile_options(/EHsc)
+    endif()
+  endif()
+  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
+endif()
+
+find_package(MPI REQUIRED)
+# do not include the (obsolete) MPI C++ bindings which makes
+# for leaner object files and avoids namespace conflicts
+set(MPI_CXX_SKIP_MPICXX TRUE)
+
+##########################
+
+add_executable(simple-plugin simple.c liblammpsplugin.c)
+target_link_libraries(simple-plugin PRIVATE MPI::MPI_C)
+target_compile_definitions(simple-plugin PRIVATE LAMMPS_LIB_MPI)
+
+# link with -ldl or equivalent for plugin loading; except on Windows
+if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+   target_link_libraries(simple-plugin PRIVATE ${CMAKE_DL_LIBS})
+endif()