Merge branch 'master' of https://github.com/kipbarrett/lammps into pair_rann

.github/workflows/codeql-analysis.yml

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

.github/workflows/unittest-macos.yml

@@ -0,0 +1,34 @@
+# GitHub action to build LAMMPS on MacOS and run unit tests
+name: "Unittest for MacOS"
+
+on:
+  push:
+    branches: [master]
+
+jobs:
+  build:
+    name: MacOS Unit Test
+    if: ${{ github.repository == 'lammps/lammps' }}
+    runs-on: macos-latest
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+      with:
+        fetch-depth: 2
+
+    - name: Create Build Environment
+      run: cmake -E make_directory ${{github.workspace}}/build
+
+    - name: Building LAMMPS via CMake
+      shell: bash
+      working-directory: ${{github.workspace}}/build
+      run: |
+        cmake -C $GITHUB_WORKSPACE/cmake/presets/most.cmake $GITHUB_WORKSPACE/cmake \
+              -DENABLE_TESTING=ON -DBUILD_SHARED_LIBS=ON -DLAMMPS_EXCEPTIONS=ON
+        cmake --build . --parallel 2
+
+    - name: Run Tests
+      working-directory: ${{github.workspace}}/build
+      shell: bash
+      run: ctest -V

LICENSE

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

cmake/CMakeLists.txt

@@ -26,7 +26,14 @@ find_package(Git)
 
 # by default, install into $HOME/.local (not /usr/local), so that no root access (and sudo!!) is needed
 if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
-  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "default install path" FORCE )
+  set(CMAKE_INSTALL_PREFIX "$ENV{HOME}/.local" CACHE PATH "Default install path" FORCE)
+endif()
+
+# If enabled, no need to use LD_LIBRARY_PATH / DYLD_LIBRARY_PATH when installed
+option(LAMMPS_INSTALL_RPATH "Set runtime path for shared libraries linked to LAMMPS binaries" OFF)
+if (LAMMPS_INSTALL_RPATH)
+  set(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_FULL_LIBDIR})
+  set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
 # Cmake modules/macros are in a subdirectory to keep this file cleaner
@@ -107,13 +114,15 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
 set(STANDARD_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS DIPOLE
   GRANULAR KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE PERI POEMS
   QEQ REPLICA RIGID SHOCK SPIN SNAP SRD KIM PYTHON MSCG MPIIO VORONOI
-  USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK USER-COLVARS
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-MESODPD USER-CGSDK
-  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-LB
+  USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD
-  USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE
+  USER-LB USER-MANIFOLD USER-MEAMC USER-MESONT USER-MGPT USER-MISC USER-MOFFF
-  USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB USER-RANN USER-REACTION
+  USER-MOLFILE USER-NETCDF USER-PHONON USER-PLUMED USER-PTM USER-QTB
-  USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY
+  USER-RANN USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH
-  USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF USER-ADIOS)
+  USER-TALLY USER-UEF USER-VTK USER-QUIP USER-QMMM USER-YAFF)
-set(SUFFIX_PACKAGES CORESHELL USER-OMP KOKKOS OPT USER-INTEL GPU)
+
+set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT USER-INTEL USER-OMP)
+
 foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
   option(PKG_${PKG} "Build ${PKG} Package" OFF)
 endforeach()
@@ -154,8 +163,7 @@ if(BUILD_MPI)
     endif()
   endif()
 else()
-  enable_language(C)
+  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.cpp)
-  file(GLOB MPI_SOURCES ${LAMMPS_SOURCE_DIR}/STUBS/mpi.c)
   add_library(mpi_stubs STATIC ${MPI_SOURCES})
   set_target_properties(mpi_stubs PROPERTIES OUTPUT_NAME lammps_mpi_stubs${LAMMPS_MACHINE})
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
@@ -650,7 +658,7 @@ install(
 if(BUILD_SHARED_LIBS)
   if(CMAKE_VERSION VERSION_LESS 3.12)
     # adjust so we find Python 3 versions before Python 2 on old systems with old CMake
-    set(Python_ADDITIONAL_VERSIONS 3.8 3.7 3.6 3.5)
+    set(Python_ADDITIONAL_VERSIONS 3.9 3.8 3.7 3.6 3.5)
     find_package(PythonInterp) # Deprecated since version 3.12
     if(PYTHONINTERP_FOUND)
         set(Python_EXECUTABLE ${PYTHON_EXECUTABLE})
@@ -660,10 +668,10 @@ if(BUILD_SHARED_LIBS)
   endif()
   if (Python_EXECUTABLE)
     add_custom_target(
-      install-python
+      install-python ${CMAKE_COMMAND} -E remove_directory build
-      ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
+      COMMAND ${Python_EXECUTABLE} install.py -v ${LAMMPS_SOURCE_DIR}/version.h
       -p ${LAMMPS_PYTHON_DIR}/lammps
-      -l ${CMAKE_BINARY_DIR}/liblammps${CMAKE_SHARED_LIBRARY_SUFFIX}
+      -l ${CMAKE_BINARY_DIR}/liblammps${LAMMPS_MACHINE}${CMAKE_SHARED_LIBRARY_SUFFIX}
       WORKING_DIRECTORY  ${LAMMPS_PYTHON_DIR}
       COMMENT "Installing LAMMPS Python module")
   else()
@@ -776,9 +784,7 @@ if(PKG_GPU)
   message(STATUS "<<< GPU package settings >>>
 -- GPU API:          ${GPU_API}")
   if(GPU_API STREQUAL "CUDA")
-    message(STATUS "GPU architecture: ${GPU_ARCH}")
+    message(STATUS "GPU default architecture: ${GPU_ARCH}")
-  elseif(GPU_API STREQUAL "OPENCL")
-    message(STATUS "OpenCL tuning:    ${OCL_TUNE}")
   elseif(GPU_API STREQUAL "HIP")
     message(STATUS "HIP platform:     ${HIP_PLATFORM}")
     message(STATUS "HIP architecture: ${HIP_ARCH}")

cmake/Modules/Documentation.cmake

@@ -50,9 +50,9 @@ if(BUILD_DOC)
     OUTPUT ${DOC_BUILD_DIR}/requirements.txt
     DEPENDS docenv ${DOCENV_REQUIREMENTS_FILE}
     COMMAND ${CMAKE_COMMAND} -E copy ${DOCENV_REQUIREMENTS_FILE} ${DOC_BUILD_DIR}/requirements.txt
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade pip
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade pip
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install --upgrade ${LAMMPS_DOC_DIR}/utils/converters
-    COMMAND ${DOCENV_BINARY_DIR}/pip install --use-feature=2020-resolver -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
+    COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
   # download mathjax distribution and unpack to folder "mathjax"

cmake/Modules/GTest.cmake

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

cmake/Modules/OpenCLLoader.cmake

@@ -0,0 +1,48 @@
+message(STATUS "Downloading and building OpenCL loader library")
+
+include(ExternalProject)
+set(OPENCL_LOADER_URL "https://download.lammps.org/thirdparty/opencl-loader-2020.12.18.tar.gz" CACHE STRING "URL for OpenCL loader tarball")
+mark_as_advanced(OPENCL_LOADER_URL)
+ExternalProject_Add(opencl_loader
+                    URL ${OPENCL_LOADER_URL}
+                    URL_MD5         011cdcbd41030be94f3fced6d763a52a
+                    SOURCE_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-src"
+                    BINARY_DIR      "${CMAKE_BINARY_DIR}/opencl_loader-build"
+                    CMAKE_ARGS      ${CMAKE_REQUEST_PIC} ${CMAKE_EXTRA_OPENCL_LOADER_OPTS}
+                                    -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
+                                    -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>
+                                    -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
+                                    -DCMAKE_MAKE_PROGRAM=${CMAKE_MAKE_PROGRAM}
+                                    -DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}
+                    BUILD_BYPRODUCTS <BINARY_DIR>/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}
+                    LOG_DOWNLOAD ON
+                    LOG_CONFIGURE ON
+                    LOG_BUILD ON
+                    INSTALL_COMMAND ""
+                    TEST_COMMAND    "")
+
+ExternalProject_Get_Property(opencl_loader SOURCE_DIR)
+set(OPENCL_LOADER_INCLUDE_DIR ${SOURCE_DIR}/inc)
+
+# workaround for CMake 3.10 on ubuntu 18.04
+file(MAKE_DIRECTORY ${OPENCL_LOADER_INCLUDE_DIR})
+
+ExternalProject_Get_Property(opencl_loader BINARY_DIR)
+set(OPENCL_LOADER_LIBRARY_PATH "${BINARY_DIR}/libOpenCL${CMAKE_STATIC_LIBRARY_SUFFIX}")
+
+find_package(Threads QUIET)
+if(NOT WIN32)
+  set(OPENCL_LOADER_DEP_LIBS "Threads::Threads;${CMAKE_DL_LIBS}")
+else()
+  set(OPENCL_LOADER_DEP_LIBS "cfgmgr32;runtimeobject")
+endif()
+
+add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
+add_dependencies(OpenCL::OpenCL opencl_loader)
+
+set_target_properties(OpenCL::OpenCL PROPERTIES
+  IMPORTED_LOCATION ${OPENCL_LOADER_LIBRARY_PATH}
+  INTERFACE_INCLUDE_DIRECTORIES ${OPENCL_LOADER_INCLUDE_DIR}
+  INTERFACE_LINK_LIBRARIES "${OPENCL_LOADER_DEP_LIBS}")
+
+

cmake/Modules/Packages/GPU.cmake

@@ -1,7 +1,9 @@
 set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
 set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
                 ${GPU_SOURCES_DIR}/fix_gpu.h
-                ${GPU_SOURCES_DIR}/fix_gpu.cpp)
+                ${GPU_SOURCES_DIR}/fix_gpu.cpp
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.h
+                ${GPU_SOURCES_DIR}/fix_nh_gpu.cpp)
 target_compile_definitions(lammps PRIVATE -DLMP_GPU)
 
 set(GPU_API "opencl" CACHE STRING "API used by GPU package")
@@ -33,9 +35,12 @@ if(GPU_API STREQUAL "CUDA")
   if(NOT BIN2C)
     message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
   endif()
-  option(CUDPP_OPT "Enable CUDPP_OPT" ON)
+  option(CUDPP_OPT "Enable GPU binning via CUDAPP (should be off for modern GPUs)" OFF)
   option(CUDA_MPS_SUPPORT "Enable tweaks to support CUDA Multi-process service (MPS)" OFF)
   if(CUDA_MPS_SUPPORT)
+    if(CUDPP_OPT)
+      message(FATAL_ERROR "Must use -DCUDPP_OPT=OFF with -DGPU_CUDA_MPS_SUPPORT=ON")
+    endif()
     set(GPU_CUDA_MPS_FLAGS "-DCUDA_PROXY")
   endif()
 
@@ -98,6 +103,10 @@ if(GPU_API STREQUAL "CUDA")
   if(CUDA_VERSION VERSION_GREATER_EQUAL "11.0")
     string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_80,code=[sm_80,compute_80]")
   endif()
+  # Ampere (GPU Arch 8.6) is supported by CUDA 11.1 and later
+  if(CUDA_VERSION VERSION_GREATER_EQUAL "11.1")
+    string(APPEND GPU_CUDA_GENCODE " -gencode arch=compute_86,code=[sm_86,compute_86]")
+  endif()
   if(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
     message(WARNING "Unsupported CUDA version. Use at your own risk.")
   endif()
@@ -136,27 +145,13 @@ if(GPU_API STREQUAL "CUDA")
   target_include_directories(nvc_get_devices PRIVATE ${CUDA_INCLUDE_DIRS})
 
 elseif(GPU_API STREQUAL "OPENCL")
-  if(${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+  option(USE_STATIC_OPENCL_LOADER "Download and include a static OpenCL ICD loader" ON)
-    # download and unpack support binaries for compilation of windows binaries.
+  mark_as_advanced(USE_STATIC_OPENCL_LOADER)
-    set(LAMMPS_THIRDPARTY_URL "https://download.lammps.org/thirdparty")
+  if (USE_STATIC_OPENCL_LOADER)
-    file(DOWNLOAD "${LAMMPS_THIRDPARTY_URL}/opencl-win-devel.tar.gz" "${CMAKE_CURRENT_BINARY_DIR}/opencl-win-devel.tar.gz"
+    include(OpenCLLoader)
-            EXPECTED_MD5 2c00364888d5671195598b44c2e0d44d)
-    execute_process(COMMAND ${CMAKE_COMMAND} -E tar xzf opencl-win-devel.tar.gz WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
-    add_library(OpenCL::OpenCL UNKNOWN IMPORTED)
-    if(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win32/libOpenCL.dll")
-    elseif(${CMAKE_SYSTEM_PROCESSOR} STREQUAL "x86_64")
-      set_target_properties(OpenCL::OpenCL PROPERTIES IMPORTED_LOCATION "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/lib_win64/libOpenCL.dll")
-    endif()
-    set_target_properties(OpenCL::OpenCL PROPERTIES INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_BINARY_DIR}/OpenCL/include")
   else()
     find_package(OpenCL REQUIRED)
   endif()
-  set(OCL_TUNE "generic" CACHE STRING "OpenCL Device Tuning")
-  set(OCL_TUNE_VALUES intel fermi kepler cypress generic)
-  set_property(CACHE OCL_TUNE PROPERTY STRINGS ${OCL_TUNE_VALUES})
-  validate_option(OCL_TUNE OCL_TUNE_VALUES)
-  string(TOUPPER ${OCL_TUNE} OCL_TUNE)
 
   include(OpenCLUtils)
   set(OCL_COMMON_HEADERS ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_preprocessor.h ${LAMMPS_LIB_SOURCE_DIR}/gpu/lal_aux_fun1.h)
@@ -200,7 +195,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_library(gpu STATIC ${GPU_LIB_SOURCES})
   target_link_libraries(gpu PRIVATE OpenCL::OpenCL)
   target_include_directories(gpu PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/gpu)
-  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -D${OCL_TUNE}_OCL -DMPI_GERYON -DUCL_NO_EXIT)
+  target_compile_definitions(gpu PRIVATE -D_${GPU_PREC_SETTING} -DMPI_GERYON -DGERYON_NUMA_FISSION -DUCL_NO_EXIT)
   target_compile_definitions(gpu PRIVATE -DUSE_OPENCL)
 
   target_link_libraries(lammps PRIVATE gpu)
@@ -208,6 +203,7 @@ elseif(GPU_API STREQUAL "OPENCL")
   add_executable(ocl_get_devices ${LAMMPS_LIB_SOURCE_DIR}/gpu/geryon/ucl_get_devices.cpp)
   target_compile_definitions(ocl_get_devices PRIVATE -DUCL_OPENCL)
   target_link_libraries(ocl_get_devices PRIVATE OpenCL::OpenCL)
+  add_dependencies(ocl_get_devices OpenCL::OpenCL)
 elseif(GPU_API STREQUAL "HIP")
   if(NOT DEFINED HIP_PATH)
       if(NOT DEFINED ENV{HIP_PATH})
@@ -390,13 +386,10 @@ elseif(GPU_API STREQUAL "HIP")
   target_link_libraries(lammps PRIVATE gpu)
 endif()
 
-# GPU package
-FindStyleHeaders(${GPU_SOURCES_DIR} FIX_CLASS fix_ FIX)
-
 set_property(GLOBAL PROPERTY "GPU_SOURCES" "${GPU_SOURCES}")
-
+# detect styles which have a GPU version
-# detects styles which have GPU version
 RegisterStylesExt(${GPU_SOURCES_DIR} gpu GPU_SOURCES)
+RegisterFixStyle(${GPU_SOURCES_DIR}/fix_gpu.h)
 
 get_property(GPU_SOURCES GLOBAL PROPERTY GPU_SOURCES)
 

cmake/Modules/Packages/KIM.cmake

@@ -69,14 +69,14 @@ if(DOWNLOAD_KIM)
     BUILD_RPATH "${_rpath_prefix}/kim_build-prefix/lib"
     )
 else()
-  if(KIM-API_FOUND AND KIM_API_VERSION VERSION_GREATER_EQUAL 2.2.0)
+  if(KIM-API_FOUND AND KIM-API_VERSION VERSION_GREATER_EQUAL 2.2.0)
     # For kim-api >= 2.2.0
-    find_package(KIM-API ${KIM-API_MIN_VERSION} CONFIG REQUIRED)
+    find_package(KIM-API 2.2.0 CONFIG REQUIRED)
     target_link_libraries(lammps PRIVATE KIM-API::kim-api)
   else()
     # For kim-api 2.1.3 (consistent with previous version of this file)
     find_package(PkgConfig REQUIRED)
-    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=KIM-API_MIN_VERSION)
+    pkg_check_modules(KIM-API REQUIRED IMPORTED_TARGET libkim-api>=${KIM-API_MIN_VERSION})
     target_link_libraries(lammps PRIVATE PkgConfig::KIM-API)
   endif()
 endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,4 +1,7 @@
 ########################################################################
+# As of version 3.3.0 Kokkos requires C++14
+set(CMAKE_CXX_STANDARD 14)
+########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS
 if(Kokkos_ENABLE_CUDA)
   message(STATUS "KOKKOS: Enabling CUDA LAMBDA function support")
@@ -35,8 +38,8 @@ if(DOWNLOAD_KOKKOS)
   list(APPEND KOKKOS_LIB_BUILD_ARGS "-DCMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
   include(ExternalProject)
   ExternalProject_Add(kokkos_build
-    URL https://github.com/kokkos/kokkos/archive/3.2.01.tar.gz
+    URL https://github.com/kokkos/kokkos/archive/3.3.01.tar.gz
-    URL_MD5 ba72440e285ccde05b403694ea0c92e5
+    URL_MD5 08201d1c7cf5bc458ce0f5b44a629d5a
     CMAKE_ARGS ${KOKKOS_LIB_BUILD_ARGS}
     BUILD_BYPRODUCTS <INSTALL_DIR>/lib/libkokkoscore.a
   )
@@ -48,10 +51,12 @@ if(DOWNLOAD_KOKKOS)
     INTERFACE_INCLUDE_DIRECTORIES "${INSTALL_DIR}/include"
     INTERFACE_LINK_LIBRARIES ${CMAKE_DL_LIBS})
   target_link_libraries(lammps PRIVATE LAMMPS::KOKKOS)
+  target_link_libraries(lmp PRIVATE LAMMPS::KOKKOS)
   add_dependencies(LAMMPS::KOKKOS kokkos_build)
 elseif(EXTERNAL_KOKKOS)
-  find_package(Kokkos 3.2.01 REQUIRED CONFIG)
+  find_package(Kokkos 3.3.01 REQUIRED CONFIG)
   target_link_libraries(lammps PRIVATE Kokkos::kokkos)
+  target_link_libraries(lmp PRIVATE Kokkos::kokkos)
 else()
   set(LAMMPS_LIB_KOKKOS_SRC_DIR ${LAMMPS_LIB_SOURCE_DIR}/kokkos)
   set(LAMMPS_LIB_KOKKOS_BIN_DIR ${LAMMPS_LIB_BINARY_DIR}/kokkos)
@@ -63,6 +68,7 @@ else()
                           ${LAMMPS_LIB_KOKKOS_BIN_DIR})
   target_include_directories(lammps PRIVATE ${Kokkos_INCLUDE_DIRS})
   target_link_libraries(lammps PRIVATE kokkos)
+  target_link_libraries(lmp PRIVATE kokkos)
 endif()
 target_compile_definitions(lammps PRIVATE -DLMP_KOKKOS)
 

cmake/Modules/Packages/MESSAGE.cmake

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

cmake/Modules/Packages/MLIAP.cmake

@@ -1,7 +1,7 @@
 # if PYTHON package is included we may also include Python support in MLIAP
 set(MLIAP_ENABLE_PYTHON_DEFAULT OFF)
 if(PKG_PYTHON)
-  find_package(Cythonize)
+  find_package(Cythonize QUIET)
   if(Cythonize_FOUND)
     set(MLIAP_ENABLE_PYTHON_DEFAULT ON)
   endif()
@@ -14,6 +14,15 @@ if(MLIAP_ENABLE_PYTHON)
   if(NOT PKG_PYTHON)
     message(FATAL_ERROR "Must enable PYTHON package for including Python support in MLIAP")
   endif()
+  if(CMAKE_VERSION VERSION_LESS 3.12)
+    if(PYTHONLIBS_VERSION_STRING VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  else()
+    if(Python_VERSION VERSION_LESS 3.6)
+      message(FATAL_ERROR "Python support in MLIAP requires Python 3.6 or later")
+    endif()
+  endif()
 
   set(MLIAP_BINARY_DIR ${CMAKE_BINARY_DIR}/cython)
   set(MLIAP_CYTHON_SRC ${LAMMPS_SOURCE_DIR}/MLIAP/mliap_model_python_couple.pyx)

cmake/Modules/Packages/USER-INTEL.cmake

@@ -30,7 +30,12 @@ if(INTEL_LRT_MODE STREQUAL "THREADS")
   endif()
 endif()
 if(INTEL_LRT_MODE STREQUAL "C++11")
-  target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+  if(Threads_FOUND)
+    target_compile_definitions(lammps PRIVATE -DLMP_INTEL_USELRT -DLMP_INTEL_LRT11)
+    target_link_libraries(lammps PRIVATE Threads::Threads)
+  else()
+    message(FATAL_ERROR "Must have working threads library for Long-range thread support")
+  endif()
 endif()
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")

cmake/Modules/YAML.cmake

@@ -12,7 +12,7 @@ ExternalProject_Add(libyaml
                                       CXX=${CMAKE_CXX_COMPILER}
                                       CC=${CMAKE_C_COMPILER}
                                       --prefix=<INSTALL_DIR> --disable-shared
-                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a
+                    BUILD_BYPRODUCTS  <INSTALL_DIR>/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX}
                     TEST_COMMAND      "")
 
 ExternalProject_Get_Property(libyaml INSTALL_DIR)
@@ -23,7 +23,7 @@ set(YAML_LIBRARY_DIR ${INSTALL_DIR}/lib)
 file(MAKE_DIRECTORY ${YAML_INCLUDE_DIR})
 file(MAKE_DIRECTORY ${YAML_LIBRARY_DIR})
 
-set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/${CMAKE_FIND_LIBRARY_PREFIXES}yaml.a)
+set(YAML_LIBRARY_PATH ${INSTALL_DIR}/lib/libyaml${CMAKE_STATIC_LIBRARY_SUFFIX})
 
 add_library(Yaml::Yaml UNKNOWN IMPORTED)
 set_target_properties(Yaml::Yaml PROPERTIES

cmake/presets/oneapi.cmake

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

doc/Makefile

@@ -47,6 +47,8 @@ HAS_PDFLATEX = YES
 endif
 endif
 
+# override settings for PIP commands
+# PIP_OPTIONS = --cert /etc/pki/ca-trust/extracted/openssl/ca-bundle.trust.crt --proxy http://proxy.mydomain.org
 
 #SPHINXEXTRA = -j $(shell $(PYTHON) -c 'import multiprocessing;print(multiprocessing.cpu_count())') $(shell test -f $(BUILDDIR)/doxygen/xml/run.stamp && printf -- "-E")
 
@@ -94,7 +96,7 @@ $(SPHINXCONFIG)/conf.py: $(SPHINXCONFIG)/conf.py.in
 	    -e 's,@LAMMPS_PYTHON_DIR@,$(BUILDDIR)/../python,g' \
 	    -e 's,@LAMMPS_DOC_DIR@,$(BUILDDIR),g' $< > $@
 
-html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
+html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@$(MAKE) $(MFLAGS) -C graphviz all
 	@(\
@@ -118,7 +120,7 @@ html: xmlgen $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 	@rm -rf html/PDF/.[sg]*
 	@echo "Build finished. The HTML pages are in doc/html."
 
-spelling: xmlgen $(VENV) $(SPHINXCONFIG)/false_positives.txt
+spelling: xmlgen $(SPHINXCONFIG)/conf.py $(VENV) $(SPHINXCONFIG)/false_positives.txt
 	@if [ "$(HAS_BASH)" == "NO" ] ; then echo "bash was not found at $(OSHELL)! Please use: $(MAKE) SHELL=/path/to/bash" 1>&2; exit 1; fi
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= \
@@ -228,13 +230,13 @@ $(VENV):
 	@( \
 		$(VIRTUALENV) -p $(PYTHON) $(VENV); \
 		. $(VENV)/bin/activate; \
-		pip install --upgrade pip; \
+		pip $(PIP_OPTIONS) install --upgrade pip; \
-		pip install -r $(BUILDDIR)/utils/requirements.txt; \
+		pip $(PIP_OPTIONS) install -r $(BUILDDIR)/utils/requirements.txt; \
 		deactivate;\
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 https://github.com/mathjax/MathJax.git $@
+	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/doxygen/Doxyfile.in

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

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "24 December 2020" "2020-12-24"
+.TH LAMMPS "10 March 2021" "2021-03-10"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/src/Build_basics.rst

@@ -95,7 +95,7 @@ standard. A more detailed discussion of that is below.
 
       .. note::
 
-         The file ``src/STUBS/mpi.c`` provides a CPU timer function
+         The file ``src/STUBS/mpi.cpp`` provides a CPU timer function
          called ``MPI_Wtime()`` that calls ``gettimeofday()``.  If your
          operating system does not support ``gettimeofday()``, you will
          need to insert code to call another timer.  Note that the
@@ -234,6 +234,8 @@ LAMMPS.
          cmake ../cmake -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_Fortran_COMPILER=gfortran
          # Building with Intel Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort
+         # Building with Intel oneAPI Compilers:
+         cmake ../cmake -DCMAKE_C_COMPILER=icx -DCMAKE_CXX_COMPILER=icpx -DCMAKE_Fortran_COMPILER=ifx
          # Building with LLVM/Clang Compilers:
          cmake ../cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_Fortran_COMPILER=flang
          # Building with PGI/Nvidia Compilers:
@@ -243,8 +245,10 @@ LAMMPS.
       provided that can be loaded with
       `-C ../cmake/presets/clang.cmake`.  Similarly,
       `-C ../cmake/presets/intel.cmake` should switch the compiler
-      toolchain to the Intel compilers and `-C ../cmake/presets/pgi.cmake`
+      toolchain to the legacy Intel compilers, `-C ../cmake/presets/oneapi.cmake`
-      should switch the compiler to the PGI compilers.
+      will switch to the LLVM based oneAPI Intel compilers,
+      and `-C ../cmake/presets/pgi.cmake`
+      will switch the compiler to the PGI compilers.
 
       In addition you can set ``CMAKE_TUNE_FLAGS`` to specifically add
       compiler flags to tune for optimal performance on given hosts. By
@@ -526,6 +530,20 @@ you want to copy files to is protected.
          make                        # perform make after CMake command
          make install                # perform the installation into prefix
 
+      During the installation process CMake will by default remove any runtime
+      path settings for loading shared libraries.  Because of this you may
+      have to set or modify the ``LD_LIBRARY_PATH`` (or ``DYLD_LIBRARY_PATH``)
+      environment variable, if you are installing LAMMPS into a non-system
+      location and/or are linking to libraries in a non-system location that
+      depend on such runtime path settings.
+      As an alternative you may set the CMake variable ``LAMMPS_INSTALL_RPATH``
+      to ``on`` and then the runtime paths for any linked shared libraries
+      and the library installation folder for the LAMMPS library will be
+      embedded and thus the requirement to set environment variables is avoided.
+      The ``off`` setting is usually preferred for packaged binaries or when
+      setting up environment modules, the ``on`` setting is more convenient
+      for installing software into a non-system or personal folder.
+
    .. tab:: Traditional make
 
       There is no "install" option in the ``src/Makefile`` for LAMMPS.

doc/src/Build_extras.rst

@@ -120,8 +120,6 @@ CMake build
    -D GPU_API=value             # value = opencl (default) or cuda or hip
    -D GPU_PREC=value            # precision setting
                                 # value = double or mixed (default) or single
-   -D OCL_TUNE=value            # hardware choice for GPU_API=opencl
-                                # generic (default) or intel (Intel CPU) or fermi, kepler, cypress (NVIDIA)
    -D GPU_ARCH=value            # primary GPU hardware choice for GPU_API=cuda
                                 # value = sm_XX, see below
                                 # default is sm_50
@@ -130,11 +128,13 @@ CMake build
                                 # default is 'gfx906' for HIP_PLATFORM=hcc and 'sm_50' for HIP_PLATFORM=nvcc
    -D HIP_USE_DEVICE_SORT=value # enables GPU sorting
                                 # value = yes (default) or no
-   -D CUDPP_OPT=value           # optimization setting for GPU_API=cuda
+   -D CUDPP_OPT=value           # use GPU binning on with CUDA (should be off for modern GPUs)
-                                # enables CUDA Performance Primitives Optimizations
+                                # enables CUDA Performance Primitives, must be "no" for CUDA_MPS_SUPPORT=yes
-                                # value = yes (default) or no
+                                # value = yes or no (default)
    -D CUDA_MPS_SUPPORT=value    # enables some tweaks required to run with active nvidia-cuda-mps daemon
                                 # value = yes or no (default)
+   -D USE_STATIC_OPENCL_LOADER=value  # downloads/includes OpenCL ICD loader library, no local OpenCL headers/libs needed
+                                      # value = yes (default) or no
 
 :code:`GPU_ARCH` settings for different GPU hardware is as follows:
 
@@ -161,6 +161,12 @@ When building with CMake, you **must NOT** build the GPU library in ``lib/gpu``
 using the traditional build procedure. CMake will detect files generated by that
 process and will terminate with an error and a suggestion for how to remove them.
 
+If you are compiling for OpenCL, the default setting is to download, build, and
+link with a static OpenCL ICD loader library and standard OpenCL headers.  This
+way no local OpenCL development headers or library needs to be present and only
+OpenCL compatible drivers need to be installed to use OpenCL.  If this is not
+desired, you can set :code:`USE_STATIC_OPENCL_LOADER` to :code:`no`.
+
 If you are compiling with HIP, note that before running CMake you will have to
 set appropriate environment variables. Some variables such as
 :code:`HCC_AMDGPU_TARGET` or :code:`CUDA_PATH` are necessary for :code:`hipcc`
@@ -219,11 +225,20 @@ Makefile if desired:
 * ``CUDA_PRECISION`` = precision (double, mixed, single)
 * ``EXTRAMAKE`` = which Makefile.lammps.\* file to copy to Makefile.lammps
 
-The file Makefile.linux_multi is set up to include support for multiple
+The file Makefile.cuda is set up to include support for multiple
 GPU architectures as supported by the CUDA toolkit in use. This is done
 through using the "--gencode " flag, which can be used multiple times and
 thus support all GPU architectures supported by your CUDA compiler.
 
+To enable GPU binning via CUDA performance primitives set the Makefile variable
+``CUDPP_OPT = -DUSE_CUDPP -Icudpp_mini``.  This should **not** be used with
+most modern GPUs.
+
+To support the CUDA multiprocessor server you can set the define
+``-DCUDA_PROXY``.  Please note that in this case you must **not** use
+the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
+to empty.
+
 If the library build is successful, 3 files should be created:
 ``lib/gpu/libgpu.a``\ , ``lib/gpu/nvc_get_devices``\ , and
 ``lib/gpu/Makefile.lammps``\ .  The latter has settings that enable LAMMPS
@@ -250,18 +265,18 @@ To build with this package, the KIM library with API v2 must be downloaded
 and built on your system. It must include the KIM models that you want to
 use with LAMMPS.
 
-If you would like to use the :doc:`kim_query <kim_commands>`
+If you would like to use the :doc:`kim query <kim_commands>`
 command, you also need to have libcurl installed with the matching
 development headers and the curl-config tool.
 
-If you would like to use the :doc:`kim_property <kim_commands>`
+If you would like to use the :doc:`kim property <kim_commands>`
 command, you need to build LAMMPS with the PYTHON package installed
 and linked to Python 3.6 or later. See the :ref:`PYTHON package build info <python>`
 for more details on this. After successfully building LAMMPS with Python, you
-also need to install the kim-property Python package, which can be easily done using
+also need to install the ``kim-property`` Python package, which can be easily
-*pip* as ``pip install kim-property``, or from the *conda-forge* channel as
+done using *pip* as ``pip install kim-property``, or from the *conda-forge*
-``conda install kim-property`` if LAMMPS is built in Conda. More detailed
+channel as ``conda install kim-property`` if LAMMPS is built in Conda. More
-information is available at:
+detailed information is available at:
 `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 
 In addition to installing the KIM API, it is also necessary to install the
@@ -301,7 +316,7 @@ 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 dir, using a command like
+      this in one step from the lammps/src directory, using a command like
       these, which simply invoke the ``lib/kim/Install.py`` script with
       the specified args.
 
@@ -321,7 +336,7 @@ minutes to hours) to build.  Of course you only need to do that once.)
 
       .. code-block:: make
 
-         LMP_INC =       -DLMP_NO_SSL_CHECK
+         LMP_INC = -DLMP_NO_SSL_CHECK
 
 Debugging OpenKIM web queries in LAMMPS
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -369,10 +384,11 @@ Enabling the extra unit tests have some requirements,
   Conda. More detailed information is available at:
   `kim-property installation <https://github.com/openkim/kim-property#installing-kim-property>`_.
 * It is also necessary to install
-  ``EAM_Dynamo_Mendelev_2007_Zr__MO_848899341753_000``, and
+  ``EAM_Dynamo_MendelevAckland_2007v3_Zr__MO_004835508849_000``,
-  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005`` KIM models.
+  ``EAM_Dynamo_ErcolessiAdams_1994_Al__MO_123629422045_005``, and
+  ``LennardJones612_UniversalShifted__MO_959249795837_003`` KIM models.
   See `Obtaining KIM Models <http://openkim.org/doc/usage/obtaining-models>`_
-  to learn how to install a pre-build binary of the OpenKIM Repository of
+  to learn how to install a pre-built binary of the OpenKIM Repository of
   Models or see
   `Installing KIM Models <https://openkim.org/doc/usage/obtaining-models/#installing_models>`_
   to learn how to install the specific KIM models.
@@ -521,11 +537,14 @@ They must be specified in uppercase.
    *  - VEGA906
       - GPU
       - AMD GPU MI50/MI60 GFX906
+   *  - VEGA908
+      - GPU
+      - AMD GPU GFX908
    *  - INTEL_GEN
       - GPU
       - Intel GPUs Gen9+
 
-This list was last updated for version 3.2 of the Kokkos library.
+This list was last updated for version 3.3 of the Kokkos library.
 
 .. tabs::
 

doc/src/Build_link.rst

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

doc/src/Build_manual.rst

@@ -74,7 +74,11 @@ For the documentation build a python virtual environment is set up in
 the folder ``doc/docenv`` and various python packages are installed into
 that virtual environment via the ``pip`` tool.  For rendering embedded
 LaTeX code also the `MathJax <https://www.mathjax.org/>`_ JavaScript
-engine needs to be downloaded.
+engine needs to be downloaded.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable or uncomment and edit the ``PIP_OPTIONS`` setting
+at beginning of the makefile.
 
 The actual translation is then done via ``make`` commands in the doc
 folder.  The following ``make`` commands are available:
@@ -108,7 +112,10 @@ installation of the HTML manual pages into the "install" step when
 installing LAMMPS after the CMake build via ``cmake --build . --target
 install``.  The documentation build is included in the default build
 target, but can also be requested independently with
-``cmake --build . --target doc``.
+``cmake --build . --target doc``.  If you need to pass additional options
+to the pip commands to work (e.g. to use a web proxy or to point to
+additional SSL certificates) you can set them via the ``PIP_OPTIONS``
+environment variable.
 
 .. code-block:: bash
 

doc/src/Commands_all.rst

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

doc/src/Commands_fix.rst

@@ -114,7 +114,7 @@ OPT.
    * :doc:`nph/eff <fix_nh_eff>`
    * :doc:`nph/sphere (o) <fix_nph_sphere>`
    * :doc:`nphug <fix_nphug>`
-   * :doc:`npt (iko) <fix_nh>`
+   * :doc:`npt (giko) <fix_nh>`
    * :doc:`npt/asphere (o) <fix_npt_asphere>`
    * :doc:`npt/body <fix_npt_body>`
    * :doc:`npt/cauchy <fix_npt_cauchy>`
@@ -122,8 +122,8 @@ OPT.
    * :doc:`npt/sphere (o) <fix_npt_sphere>`
    * :doc:`npt/uef <fix_nh_uef>`
    * :doc:`numdiff <fix_numdiff>`
-   * :doc:`nve (iko) <fix_nve>`
+   * :doc:`nve (giko) <fix_nve>`
-   * :doc:`nve/asphere (i) <fix_nve_asphere>`
+   * :doc:`nve/asphere (gi) <fix_nve_asphere>`
    * :doc:`nve/asphere/noforce <fix_nve_asphere_noforce>`
    * :doc:`nve/awpmd <fix_nve_awpmd>`
    * :doc:`nve/body <fix_nve_body>`
@@ -138,7 +138,7 @@ OPT.
    * :doc:`nve/spin <fix_nve_spin>`
    * :doc:`nve/tri <fix_nve_tri>`
    * :doc:`nvk <fix_nvk>`
-   * :doc:`nvt (iko) <fix_nh>`
+   * :doc:`nvt (giko) <fix_nh>`
    * :doc:`nvt/asphere (o) <fix_nvt_asphere>`
    * :doc:`nvt/body <fix_nvt_body>`
    * :doc:`nvt/eff <fix_nh_eff>`

doc/src/Commands_pair.rst

@@ -122,7 +122,7 @@ OPT.
    * :doc:`lebedeva/z <pair_lebedeva_z>`
    * :doc:`lennard/mdf <pair_mdf>`
    * :doc:`line/lj <pair_line_lj>`
-   * :doc:`lj/charmm/coul/charmm (iko) <pair_charmm>`
+   * :doc:`lj/charmm/coul/charmm (giko) <pair_charmm>`
    * :doc:`lj/charmm/coul/charmm/implicit (ko) <pair_charmm>`
    * :doc:`lj/charmm/coul/long (gikot) <pair_charmm>`
    * :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
@@ -163,6 +163,7 @@ OPT.
    * :doc:`lj/long/dipole/long <pair_dipole>`
    * :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
    * :doc:`lj/mdf <pair_mdf>`
+   * :doc:`lj/relres (o) <pair_lj_relres>`
    * :doc:`lj/sdk (gko) <pair_sdk>`
    * :doc:`lj/sdk/coul/long (go) <pair_sdk>`
    * :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
@@ -264,6 +265,7 @@ OPT.
    * :doc:`ufm (got) <pair_ufm>`
    * :doc:`vashishta (gko) <pair_vashishta>`
    * :doc:`vashishta/table (o) <pair_vashishta>`
+   * :doc:`wf/cut <pair_wf_cut>`
    * :doc:`yukawa (gko) <pair_yukawa>`
    * :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
    * :doc:`zbl (gko) <pair_zbl>`

doc/src/Commands_parse.rst

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

doc/src/Developer_notes.rst

@@ -1,11 +1,133 @@
-Notes for Developers and Code Maintainers
+Notes for developers and code maintainers
 -----------------------------------------
 
-This section documents how a few large sections of code with LAMMPS
+This section documents how some of the code functionality within
-work at a conceptual level.  Comments on code in source files
+LAMMPS works at a conceptual level.  Comments on code in source files
 typically document what a variable stores, what a small section of
-code does, or what a function does or its input/outputs.  The topics
+code does, or what a function does and its input/outputs.  The topics
-on this page are intended to document code at a higher level.
+on this page are intended to document code functionality at a higher level.
+
+Fix contributions to instantaneous energy, virial, and cumulative energy
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+Fixes can calculate contributions to the instantaneous energy and/or
+virial of the system, both in a global and peratom sense.  Fixes that
+perform thermostatting or barostatting can calculate the cumulative
+energy they add to or subtract from the system, which is accessed by
+the *ecouple* and *econserve* thermodynamic keywords.  This subsection
+explains how both work and what flags to set in a new fix to enable
+this functionality.
+
+Let's start with thermostatting and barostatting fixes.  Examples are
+the :doc:`fix langevin <fix_langevin>` and :doc:`fix npt <fix_nh>`
+commands.  Here is what the fix needs to do:
+
+* Set the variable *ecouple_flag* = 1 in the constructor.  Also set
+  *scalar_flag* = 1, *extscalar* = 1, and *global_freq* to a timestep
+  increment which matches how often the fix is invoked.
+* Implement a compute_scalar() method that returns the cumulative
+  energy added or subtracted by the fix, e.g. by rescaling the
+  velocity of atoms.  The sign convention is that subtracted energy is
+  positive, added energy is negative.  This must be the total energy
+  added to the entire system, i.e. an "extensive" quantity, not a
+  per-atom energy.  Cumulative means the summed energy since the fix
+  was instantiated, even across multiple runs.  This is because the
+  energy is used by the *econserve* thermodynamic keyword to check
+  that the fix is conserving the total energy of the system,
+  i.e. potential energy + kinetic energy + coupling energy = a
+  constant.
+
+And here is how the code operates:
+
+* The Modify class makes a list of all fixes that set *ecouple_flag* = 1.
+* The :doc:`thermo_style custom <thermo_style>` command defines
+  *ecouple* and *econserve* keywords.
+* These keywords sum the energy contributions from all the
+  *ecouple_flag* = 1 fixes by invoking the energy_couple() method in
+  the Modify class, which calls the compute_scalar() method of each
+  fix in the list.
+
+------------------
+
+Next, here is how a fix contributes to the instantaneous energy and
+virial of the system.  First, it sets any or all of these flags to a
+value of 1 in their constructor:
+
+* *energy_global_flag* to contribute to global energy, example: :doc:`fix indent <fix_indent>`
+* *energy_peratom_flag* to contribute to peratom energy, :doc:`fix cmap <fix_cmap>`
+* *virial_global_flag* to contribute to global virial, example: :doc:`fix wall <fix_wall>`
+* *virial_peratom_flag* to contribute to peratom virial, example: :doc:`fix wall <fix_wall>`
+
+The fix must also do the following:
+
+* For global energy, implement a compute_scalar() method that returns
+  the energy added or subtracted on this timestep.  Here the sign
+  convention is that added energy is positive, subtracted energy is
+  negative.
+* For peratom energy, invoke the ev_init(eflag,vflag) function each
+  time the fix is invoked, which initializes per-atom energy storage.
+  The value of eflag may need to be stored from an earlier call to the
+  fix during the same timestep.  See how the :doc:`fix cmap
+  <fix_cmap>` command does this in src/MOLECULE/fix_cmap.cpp.  When an
+  energy for one or more atoms is calculated, invoke the ev_tally()
+  function to tally the contribution to each atom.  Both the ev_init()
+  and ev_tally() methods are in the parent Fix class.
+* For global and/or peratom virial, invoke the v_init(vflag) function
+  each time the fix is invoked, which initializes virial storage.
+  When forces on one or more atoms are calculated, invoke the
+  v_tally() function to tally the contribution.  Both the v_init() and
+  v_tally() methods are in the parent Fix class.  Note that there are
+  several variants of v_tally(); choose the one appropriate to your
+  fix.
+
+.. note::
+
+   The ev_init() and ev_tally() methods also account for global and
+   peratom virial contributions.  Thus you do not need to invoke the
+   v_init() and v_tally() methods, if the fix also calculates peratom
+   energies.
+
+The fix must also specify whether (by default) to include or exclude
+these contributions to the global/peratom energy/virial of the system.
+For the fix to include the contributions, set either of both of these
+variables in the constructor:
+
+* *thermo_energy* = 1, for global and peratom energy
+* *thermo_virial* = 1, for global and peratom virial
+
+Note that these variables are zeroed in fix.cpp.  Thus if you don't
+set the variables, the contributions will be excluded (by default)
+
+However, the user has ultimate control over whether to include or
+exclude the contributions of the fix via the :doc:`fix modify
+<fix_modify>` command:
+
+* fix modify *energy yes* to include global and peratom energy contributions
+* fix modify *virial yes* to include global and peratom virial contributions
+
+If the fix contributes to any of the global/peratom energy/virial
+values for the system, it should be explained on the fix doc page,
+along with the default values for the *energy yes/no* and *virial
+yes/no* settings of the :doc:`fix modify <fix_modify>` command.
+
+Finally, these 4 contributions are included in the output of 4
+computes:
+
+* global energy in :doc:`compute pe <compute_pe>`
+* peratom energy in :doc:`compute pe/atom <compute_pe_atom>`
+* global virial in :doc:`compute pressure <compute_pressure>`
+* peratom virial in :doc:`compute stress/atom <compute_stress_atom>`
+
+These computes invoke a method of the Modify class to include
+contributions from fixes that have the corresponding flags set,
+e.g. *energy_peratom_flag* and *thermo_energy* for :doc:`compute
+pe/atom <compute_pe_atom>`.
+
+Note that each compute has an optional keyword to either include or
+exclude all contributions from fixes.  Also note that :doc:`compute pe
+<compute_pe>` and :doc:`compute pressure <compute_pressure>` are what
+is used (by default) by :doc:`thermodynamic output <thermo_style>` to
+calculate values for its *pe* and *press* keywords.
 
 KSpace PPPM FFT grids
 ^^^^^^^^^^^^^^^^^^^^^

doc/src/Developer_org.rst

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

doc/src/Developer_utils.rst

@@ -71,12 +71,21 @@ and parsing files or arguments.
 
 ----------
 
+.. doxygenfunction:: strdup
+   :project: progguide
+
 .. doxygenfunction:: trim
    :project: progguide
 
 .. doxygenfunction:: trim_comment
    :project: progguide
 
+.. doxygenfunction:: has_utf8
+   :project: progguide
+
+.. doxygenfunction:: utf8_subst
+   :project: progguide
+
 .. doxygenfunction:: count_words(const char *text)
    :project: progguide
 
@@ -95,6 +104,9 @@ and parsing files or arguments.
 .. doxygenfunction:: strmatch
    :project: progguide
 
+.. doxygenfunction:: strfind
+   :project: progguide
+
 .. doxygenfunction:: is_integer
    :project: progguide
 
@@ -286,6 +298,50 @@ This code example should produce the following output:
 
 ----------
 
+
+Argument parsing classes
+---------------------------
+
+The purpose of argument parsing classes it to simplify and unify how
+arguments of commands in LAMMPS are parsed and to make abstractions of
+repetitive tasks.
+
+The :cpp:class:`LAMMPS_NS::ArgInfo` class provides an abstraction
+for parsing references to compute or fix styles or variables. These
+would start with a "c\_", "f\_", "v\_" followed by the ID or name of
+than instance and may be postfixed with one or two array indices
+"[<number>]" with numbers > 0.
+
+A typical code segment would look like this:
+
+.. code-block:: C++
+   :caption: Usage example for ArgInfo class
+
+   int nvalues = 0;
+   for (iarg = 0; iarg < nargnew; iarg++) {
+     ArgInfo argi(arg[iarg]);
+
+     which[nvalues] = argi.get_type();
+     argindex[nvalues] = argi.get_index1();
+     ids[nvalues] = argi.copy_name();
+
+     if ((which[nvalues] == ArgInfo::UNKNOWN)
+          || (which[nvalues] == ArgInfo::NONE)
+          || (argi.get_dim() > 1))
+       error->all(FLERR,"Illegal compute XXX command");
+
+     nvalues++;
+   }
+
+----------
+
+.. doxygenclass:: LAMMPS_NS::ArgInfo
+   :project: progguide
+   :members:
+
+
+----------
+
 File reader classes
 -------------------
 

doc/src/Howto_cmake.rst

@@ -296,6 +296,8 @@ Some common CMake variables
      - Description
    * - ``CMAKE_INSTALL_PREFIX``
      - root directory of install location for ``make install``  (default: ``$HOME/.local``)
+   * - ``LAMMPS_INSTALL_RPATH``
+     - set or remove runtime path setting from binaries for ``make install`` (default: ``off``)
    * - ``CMAKE_BUILD_TYPE``
      - controls compilation options:
        one of ``RelWithDebInfo`` (default), ``Release``, ``Debug``, ``MinSizeRel``
@@ -409,10 +411,10 @@ interface (``ccmake`` or ``cmake-gui``).
 .. note::
 
    Using a preset to select a compiler package (``clang.cmake``,
-   ``gcc.cmake``, or ``intel.cmake``) are an exception to the option
+   ``gcc.cmake``, ``intel.cmake``, ``oneapi.cmake``, or ``pgi.cmake``)
-   of updating the configuration incrementally, as they will trigger
+   are an exception to the mechanism of updating the configuration incrementally,
-   a reset of cached internal CMake settings and thus reset them to
+   as they will trigger a reset of cached internal CMake settings and thus
-   their default values.
+   reset settings to their default values.
 
 Compilation and build targets
 -----------------------------

doc/src/Install_tarball.rst

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

doc/src/Intro_citing.rst

@@ -38,17 +38,18 @@ In addition there are DOIs for individual stable releases. Currently there are:
 Home page
 ^^^^^^^^^
 
-The LAMMPS website at `https://lammps.sandia.gov/ <https://lammps.sandia.gov>`_ is the canonical
+The LAMMPS website at `https://lammps.sandia.gov/
-location for information about LAMMPS and more detailed lists of publications
+<https://lammps.sandia.gov>`_ is the canonical location for information
-using LAMMPS and contributing features.
+about LAMMPS and its features.
 
 Citing contributions
 ^^^^^^^^^^^^^^^^^^^^
 
-LAMMPS has many features and uses previously published methods and
+LAMMPS has many features and that use either previously published
-algorithms or novel features. It also includes potential parameter
+methods and algorithms or novel features.  It also includes potential
-filed for specific models.  You can look up relevant publications either
+parameter filed for specific models.  Where available, a reminder about
-in the LAMMPS output to the screen, the ``log.cite`` file (which is
+references for optional features used in a specific run is printed to
-populated with references to relevant papers through embedding them into
+the screen and log file.  Style and output location can be selected with
-the source code) and in the documentation of the :doc:`corresponding commands
+the :ref:`-cite command-line switch <cite>`.  Additional references are
+given in the documentation of the :doc:`corresponding commands
 <Commands_all>` or in the :doc:`Howto tutorials <Howto>`.

doc/src/Intro_features.rst

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

doc/src/Modify_contribute.rst

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

doc/src/Packages_details.rst

@@ -367,17 +367,19 @@ KIM package
 
 **Contents:**
 
-This package contains a set of commands that serve as a wrapper on the
+This package contains a command with a set of sub-commands that serve as a
+wrapper on the
 `Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
 repository of interatomic models (IMs) enabling compatible ones to be used in
 LAMMPS simulations.
 
-This includes :doc:`kim_init <kim_commands>`, and
+
-:doc:`kim_interactions <kim_commands>` commands to select, initialize and
+This includes :doc:`kim init <kim_commands>`, and
-instantiate the IM, a :doc:`kim_query <kim_commands>` command to perform web
+:doc:`kim interactions <kim_commands>` commands to select, initialize and
+instantiate the IM, a :doc:`kim query <kim_commands>` command to perform web
 queries for material property predictions of OpenKIM IMs, a
-:doc:`kim_param <kim_commands>` command to access KIM Model Parameters from
+:doc:`kim param <kim_commands>` command to access KIM Model Parameters from
-LAMMPS, and a :doc:`kim_property <kim_commands>` command to write material
+LAMMPS, and a :doc:`kim property <kim_commands>` command to write material
 properties computed in LAMMPS to standard KIM property instance format.
 
 Support for KIM IMs that conform to the
@@ -386,8 +388,8 @@ is provided by the :doc:`pair_style kim <pair_kim>` command.
 
 .. note::
 
-   The command *pair_style kim* is called by *kim_interactions* and
+   The command *pair_style kim* is called by *kim interactions* and is not
-   is not recommended to be directly used in input scripts.
+   recommended to be directly used in input scripts.
 
 To use this package you must have the KIM API library available on your
 system. The KIM API is available for download on the
@@ -404,7 +406,7 @@ and is funded by the `National Science Foundation <https://www.nsf.gov/>`_.
 API and the *pair_style kim* command. Yaser Afshar (U Minnesota),
 Axel Kohlmeyer (Temple U), Ellad Tadmor (U Minnesota), and
 Daniel Karls (U Minnesota) contributed to the
-:doc:`kim_commands <kim_commands>` interface in close collaboration with
+:doc:`kim command <kim_commands>` interface in close collaboration with
 Ryan Elliott.
 
 **Install:**
@@ -414,7 +416,7 @@ This package has :ref:`specific installation instructions <kim>` on the
 
 **Supporting info:**
 
-* :doc:`kim_commands <kim_commands>`
+* :doc:`kim command <kim_commands>`
 * :doc:`pair_style kim <pair_kim>`
 * src/KIM: filenames -> commands
 * src/KIM/README
@@ -668,8 +670,8 @@ A general interface for machine-learning interatomic potentials, including PyTor
 
 To use this package, also the :ref:`SNAP package <PKG-SNAP>` package needs
 to be installed.  To make the *mliappy* model available, also the
-:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version of
+:ref:`PYTHON package <PKG-PYTHON>` package needs to be installed, the version
-Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
+of Python must be 3.6 or later, and the `cython <https://cython.org/>`_ software
 must be installed.
 
 **Author:** Aidan Thompson (Sandia), Nicholas Lubbers (LANL).
@@ -1430,8 +1432,8 @@ oscillators as a model of polarization.  See the :doc:`Howto drude <Howto_drude>
 for an overview of how to use the package.  There are auxiliary tools
 for using this package in tools/drude.
 
-**Authors:** Alain Dequidt (U Blaise Pascal Clermont-Ferrand), Julien
+**Authors:** Alain Dequidt (U Clermont Auvergne), Julien
-Devemy (CNRS), and Agilio Padua (U Blaise Pascal).
+Devemy (CNRS), and Agilio Padua (ENS de Lyon).
 
 **Supporting info:**
 
@@ -1498,7 +1500,7 @@ methods for performing FEP simulations by using a :doc:`fix adapt/fep <fix_adapt
 which have a "soft" in their style name.  There are auxiliary tools
 for using this package in tools/fep; see its README file.
 
-**Author:** Agilio Padua (Universite Blaise Pascal Clermont-Ferrand)
+**Author:** Agilio Padua (ENS de Lyon)
 
 **Supporting info:**
 

doc/src/Python_atoms.rst

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

doc/src/Python_formats.rst

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

doc/src/Python_head.rst

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

doc/src/Python_install.rst

@@ -69,7 +69,7 @@ this.
          cd build
 
          # configure LAMMPS compilation
-         cmake -C cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
+         cmake -C ../cmake/presets/minimal.cmake -D BUILD_SHARED_LIBS=on \
                -D LAMMPS_EXCEPTIONS=on -D PKG_PYTHON=on ../cmake
 
          # compile LAMMPS
@@ -97,10 +97,12 @@ this.
 
       For a system-wide installation you need to set
       ``CMAKE_INSTALL_PREFIX`` to a system folder like ``/usr`` (or
-      ``/usr/local``).  The installation step (**not** the
+      ``/usr/local``); the default is ``${HOME}/.local``.  The
+      installation step for a system folder installation (**not** the
       configuration/compilation) needs to be done with superuser
       privilege, e.g. by using ``sudo cmake --install .``.  The
-      installation folders will then by changed to:
+      installation folders will then be changed to (assuming ``/usr`` as
+      prefix):
 
       +------------------------+---------------------------------------------------------+-------------------------------------------------------------+
       | File                   | Location                                                | Notes                                                       |

doc/src/Python_module.rst

@@ -26,6 +26,23 @@ There are multiple Python interface classes in the :py:mod:`lammps` module:
 
 .. _mpi4py_url: https://mpi4py.readthedocs.io
 
+.. admonition:: Version check
+   :class: note
+
+   The :py:mod:`lammps` module stores the version number of the LAMMPS
+   version it is installed from.  When initializing the
+   :py:class:`lammps <lammps.lammps>` class, this version is checked to
+   be the same as the result from :py:func:`lammps.version`, the version
+   of the LAMMPS shared library that the module interfaces to.  If the
+   they are not the same an AttributeError exception is raised since a
+   mismatch of versions (e.g.  due to incorrect use of the
+   ``LD_LIBRARY_PATH`` or ``PYTHONPATH`` environment variables can lead
+   to crashes or data corruption and otherwise incorrect behavior.
+
+.. automodule:: lammps
+   :members:
+   :noindex:
+
 ----------
 
 The ``lammps`` class API
@@ -44,7 +61,7 @@ functions. Below is a detailed documentation of the API.
 .. autoclass:: lammps.lammps
    :members:
 
-.. autoclass:: lammps.numpy::numpy_wrapper
+.. autoclass:: lammps.numpy_wrapper::numpy_wrapper
    :members:
 
 ----------
@@ -117,8 +134,8 @@ Style Constants
    to request from computes or fixes. See :cpp:enum:`_LMP_STYLE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_type_constants:
 
@@ -132,8 +149,8 @@ Type Constants
    to request  from computes  or fixes.  See :cpp:enum:`_LMP_TYPE_CONST`
    for the equivalent constants in the C library interface. Used in
    :py:func:`lammps.extract_compute`, :py:func:`lammps.extract_fix`, and their NumPy variants
-   :py:func:`lammps.numpy.extract_compute() <lammps.numpy.numpy_wrapper.extract_compute>` and
+   :py:func:`lammps.numpy.extract_compute() <lammps.numpy_wrapper.numpy_wrapper.extract_compute>` and
-   :py:func:`lammps.numpy.extract_fix() <lammps.numpy.numpy_wrapper.extract_fix>`.
+   :py:func:`lammps.numpy.extract_fix() <lammps.numpy_wrapper.numpy_wrapper.extract_fix>`.
 
 .. _py_vartype_constants:
 
@@ -153,6 +170,6 @@ Classes representing internal objects
    :members:
    :no-undoc-members:
 
-.. autoclass:: lammps.numpy::NumPyNeighList
+.. autoclass:: lammps.numpy_wrapper::NumPyNeighList
    :members:
    :no-undoc-members:

doc/src/Python_neighbor.rst

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

doc/src/Python_objects.rst

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

doc/src/Run_options.rst

@@ -11,6 +11,7 @@ letter abbreviation can be used:
 * :ref:`-k or -kokkos <run-kokkos>`
 * :ref:`-l or -log <log>`
 * :ref:`-m or -mpicolor <mpicolor>`
+* :ref:`-c or -cite <cite>`
 * :ref:`-nc or -nocite <nocite>`
 * :ref:`-pk or -package <package>`
 * :ref:`-p or -partition <partition>`
@@ -220,14 +221,31 @@ links with from the lib/message directory.  See the
 
 ----------
 
+.. _cite:
+
+**-cite style or file name**
+
+Select how and where to output a reminder about citing contributions
+to the LAMMPS code that were used during the run. Available styles are
+"both", "none", "screen", or "log".  Any flag will be considered a file
+name to write the detailed citation info to.  Default is the "log" style
+where there is a short summary in the screen output and detailed citations
+in BibTeX format in the logfile.  The option "both" selects the detailed
+output for both, "none", the short output for both, and "screen" will
+write the detailed info to the screen and the short version to the log
+file.  If a dedicated citation info file is requested, the screen and
+log file output will be in the short format (same as with "none").
+
+See the :doc:`citation page <Intro_citing>` for more details on
+how to correctly reference and cite LAMMPS.
+
+----------
+
 .. _nocite:
 
 **-nocite**
 
-Disable writing the log.cite file which is normally written to list
+Disable generating a citation reminder (see above) at all.
-references for specific cite-able features used during a LAMMPS run.
-See the `citation page <https://lammps.sandia.gov/cite.html>`_ for more
-details.
 
 ----------
 

doc/src/Speed_gpu.rst

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

doc/src/Speed_kokkos.rst

@@ -26,6 +26,15 @@ task). These are Serial (MPI-only for CPUs and Intel Phi), OpenMP
 GPUs) and HIP (for AMD GPUs). You choose the mode at build time to
 produce an executable compatible with a specific hardware.
 
+.. admonition:: C++14 support
+      :class: note
+
+   Kokkos requires using a compiler that supports the c++14 standard. For
+   some compilers, it may be necessary to add a flag to enable c++14 support.
+   For example, the GNU compiler uses the -std=c++14 flag. For a list of
+   compilers that have been tested with the Kokkos library, see the Kokkos
+   `README <https://github.com/kokkos/kokkos/blob/master/README.md>`_.
+
 .. admonition:: NVIDIA CUDA support
    :class: note
 

doc/src/Speed_packages.rst

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

doc/src/Tools.rst

@@ -93,6 +93,7 @@ Miscellaneous tools
    * :ref:`i-pi <ipi>`
    * :ref:`kate <kate>`
    * :ref:`LAMMPS shell <lammps_shell>`
+   * :ref:`LAMMPS magic patterns for file(1) <magic>`
    * :ref:`singularity <singularity_tool>`
    * :ref:`SWIG interface <swig>`
    * :ref:`vim <vim>`
@@ -267,7 +268,7 @@ data file in the required format.
 See the header of the polarizer.py file for details.
 
 The tool is authored by Agilio Padua and Alain Dequidt: agilio.padua
-at univ-bpclermont.fr, alain.dequidt at univ-bpclermont.fr
+at ens-lyon.fr, alain.dequidt at uca.fr
 
 ----------
 
@@ -341,8 +342,7 @@ The tools/fep directory contains Python scripts useful for
 post-processing results from performing free-energy perturbation
 simulations using the USER-FEP package.
 
-The scripts were contributed by Agilio Padua (Universite Blaise
+The scripts were contributed by Agilio Padua (ENS de Lyon), agilio.padua at ens-lyon.fr.
-Pascal Clermont-Ferrand), agilio.padua at univ-bpclermont.fr.
 
 See README file in the tools/fep directory.
 
@@ -642,6 +642,39 @@ This tool was written by Ara Kooser at Sandia (askoose at sandia.gov).
 
 ----------
 
+.. _magic:
+
+Magic patterns for the "file" command
+-------------------------------------
+
+.. versionadded:: 10Mar2021
+
+The file ``magic`` contains patterns that are used by the
+`file program <https://en.wikipedia.org/wiki/File_(command)>`_
+available on most Unix-like operating systems which enables it
+to detect various LAMMPS files and print some useful information
+about them.  To enable these patterns, append or copy the contents
+of the file to either the file ``.magic`` in your home directory
+or (as administrator) to ``/etc/magic`` (for a system-wide
+installation).  Afterwards the ``file`` command should be able to
+detect most LAMMPS restarts, dump, data and log files. Examples:
+
+.. code-block:: bash
+
+   $ file *.*
+   dihedral-quadratic.restart:   LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
+   mol-pair-wf_cut.restart:      LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
+   atom.bin:                     LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
+   custom.bin:                   LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
+   bn1.lammpstrj:                LAMMPS text mode dump, First time step: 5000
+   data.fourmol:                 LAMMPS data file written by LAMMPS
+   pnc.data:                     LAMMPS data file written by msi2lmp
+   data.spce:                    LAMMPS data file written by TopoTools
+   B.data:                       LAMMPS data file written by OVITO
+   log.lammps:                   LAMMPS log file written by version 10 Feb 2021
+
+----------
+
 .. _matlab:
 
 matlab tool

doc/src/compute_displace_atom.rst

@@ -46,11 +46,12 @@ the compute command was issued.  The value of the displacement will be
 .. note::
 
    Initial coordinates are stored in "unwrapped" form, by using the
-   image flags associated with each atom.  See the :doc:`dump custom <dump>` command for a discussion of "unwrapped" coordinates.
+   image flags associated with each atom.  See the :doc:`dump custom
-   See the Atoms section of the :doc:`read_data <read_data>` command for a
+   <dump>` command for a discussion of "unwrapped" coordinates.  See
-   discussion of image flags and how they are set for each atom.  You can
+   the Atoms section of the :doc:`read_data <read_data>` command for a
-   reset the image flags (e.g. to 0) before invoking this compute by
+   discussion of image flags and how they are set for each atom.  You
-   using the :doc:`set image <set>` command.
+   can reset the image flags (e.g. to 0) before invoking this compute
+   by using the :doc:`set image <set>` command.
 
 .. note::
 

doc/src/compute_fep.rst

@@ -163,7 +163,7 @@ the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/compute_pressure.rst

@@ -122,8 +122,11 @@ Output info
 This compute calculates a global scalar (the pressure) and a global
 vector of length 6 (pressure tensor), which can be accessed by indices
 1-6.  These values can be used by any command that uses global scalar
-or vector values from a compute as input.  See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS output
+or vector values from a compute as input.  See the :doc:`Howto output
-options.
+<Howto_output>` doc page for an overview of LAMMPS output options.
+
+The ordering of values in the symmetric pressure tensor is as follows:
+pxx, pyy, pzz, pxy, pxz, pyz.
 
 The scalar and vector values calculated by this compute are
 "intensive".  The scalar and vector values will be in pressure

doc/src/compute_reduce_chunk.rst

@@ -30,7 +30,7 @@ Examples
 
 .. code-block:: LAMMPS
 
-   compute 1 all reduce/chunk/atom mychunk min c_cluster
+   compute 1 all reduce/chunk mychunk min c_cluster
 
 Description
 """""""""""

doc/src/compute_stress_atom.rst

@@ -216,6 +216,11 @@ an identical manner to compute *stress/atom*.  See the :doc:`Howto
 output <Howto_output>` doc page for an overview of LAMMPS output
 options.
 
+The ordering of the 6 columns for *stress/atom* is as follows: xx, yy,
+zz, xy, xz, yz.  The ordering of the 9 columns for
+*centroid/stress/atom* is as follows: xx, yy, zz, xy, xz, yz, yx, zx,
+zy.
+
 The per-atom array values will be in pressure\*volume :doc:`units
 <units>` as discussed above.
 

doc/src/compute_temp_chunk.rst

@@ -153,7 +153,7 @@ temp/chunk calculation to a file is to use the :doc:`fix ave/time <fix_ave_time>
 
    compute cc1 all chunk/atom molecule
    compute myChunk all temp/chunk cc1 temp
-   fix 1 all ave/time 100 1 100 c_myChunk file tmp.out mode vector
+   fix 1 all ave/time 100 1 100 c_myChunk[1] file tmp.out mode vector
 
 ----------
 

doc/src/create_bonds.rst

@@ -125,6 +125,16 @@ cannot appear in the neighbor list, to avoid creation of duplicate
 bonds.  The neighbor list for all atom type pairs must also extend to
 a distance that encompasses the *rmax* for new bonds to create.
 
+.. note::
+
+   If you want to create bonds between pairs of 1-3 or 1-4 atoms in
+   the current bond topology, then you need to use :doc:`special_bonds
+   lj 0 1 1 <special_bonds>` to insure those pairs appear in the
+   neighbor list.  They will not appear with the default special_bonds
+   settings which are zero for 1-2, 1-3, and 1-4 atoms.  1-3 or 1-4
+   atoms are those which are 2 hops or 3 hops apart in the bond
+   topology.
+
 An additional requirement for this style is that your system must be
 ready to perform a simulation.  This means, for example, that all
 :doc:`pair_style <pair_style>` coefficients be set via the

doc/src/create_box.rst

@@ -13,7 +13,7 @@ Syntax
 * N = # of atom types to use in this simulation
 * region-ID = ID of region to use as simulation domain
 * zero or more keyword/value pairs may be appended
-* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom*
+* keyword = *bond/types* or *angle/types* or *dihedral/types* or *improper/types* or *extra/bond/per/atom* or *extra/angle/per/atom* or *extra/dihedral/per/atom* or *extra/improper/per/atom* or *extra/special/per/atom*
 
   .. parsed-literal::
 

doc/src/fix_adapt.rst

@@ -128,9 +128,9 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`born/coul/long, born/coul/msm <pair_born>`                             | coulombic_cutoff                                 | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                                              | type pairs  |
+| :doc:`buck, buck/coul/cut  <pair_buck>`                                      | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | coulombic_cutoff                                 | type global |
+| :doc:`buck/coul/long, buck/coul/msm <pair_buck>`                             | a,c,coulombic_cutoff                             | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+

doc/src/fix_adapt_fep.rst

@@ -120,7 +120,7 @@ styles and their energy formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`born <pair_born>`                                                      | a,b,c                   | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
-| :doc:`buck <pair_buck>`                                                      | a,c                     | type pairs |
+| :doc:`buck, buck/coul/cut, buck/coul/long, buck/coul/msm  <pair_buck>`       | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                     | type pairs |
 +------------------------------------------------------------------------------+-------------------------+------------+

doc/src/fix_addforce.rst

@@ -118,32 +118,38 @@ converge properly.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added force to the
+this fix to add the potential energy inferred by the added force to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+the global potential energy of the system as part of
-needed so that the :doc:`minimize <minimize>` command can include the
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-forces added by this fix in a consistent manner.  I.e. there is a
+this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
-decrease in potential energy when atoms move in the direction of the
+energy is a fictitious quantity but is needed so that the
-added force.
+:doc:`minimize <minimize>` command can include the forces added by
+this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the added forces on atoms to the
+this fix to add the contribution due to the added forces on atoms to
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+both the global pressure and per-atom stress of the system via the
-The default is *virial no*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost
+<run_style>` integrator the fix is adding its forces. Default is the
-level.
+outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the potential energy discussed above.  The vector is the
+<Howto_output>`.  The scalar is the potential energy discussed above.
-total force on the group of atoms before the forces on individual
+The vector is the total force on the group of atoms before the forces
-atoms are changed by the fix.  The scalar and vector values calculated
+on individual atoms are changed by the fix.  The scalar and vector
-by this fix are "extensive".
+values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_addtorque.rst

@@ -55,13 +55,15 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added forces to the
+this fix to add the potential "energy" inferred by the added torques
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+to the global potential energy of the system as part of
-needed so that the :doc:`minimize <minimize>` command can include the
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
-forces added by this fix in a consistent manner.  I.e. there is a
+this fix is :doc:`fix_modify energy no <fix_modify>`.  Note that this
-decrease in potential energy when atoms move in the direction of the
+is a fictitious quantity but is needed so that the :doc:`minimize
-added forces.
+<minimize>` command can include the forces added by this fix in a
+consistent manner.  I.e. there is a decrease in potential energy when
+atoms move in the direction of the added forces.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by
 this fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
@@ -78,16 +80,28 @@ No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
 The forces due to this fix are imposed during an energy minimization,
-invoked by the :doc:`minimize <minimize>` command.  You should not
+invoked by the :doc:`minimize <minimize>` command.
-specify force components with a variable that has time-dependence for
+
-use with a minimizer, since the minimizer increments the timestep as
+.. note::
-the iteration count during the minimization.
+
+   If you want the fictitious potential energy associated with the
+   added forces to be included in the total potential energy of the
+   system (the quantity being minimized), you MUST enable the
+   :doc:`fix_modify <fix_modify>` *energy* option for this fix.
+
+.. note::
+
+   You should not specify force components with a variable that has
+   time-dependence for use with a minimizer, since the minimizer
+   increments the timestep as the iteration count during the
+   minimization.
 
 Restrictions
 """"""""""""
 
 This fix is part of the USER-MISC package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

doc/src/fix_atc.rst

@@ -122,10 +122,22 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 No information about this fix is written to :doc:`binary restart files
-<restart>`.  The :doc:`fix_modify <fix_modify>` options relevant to this
+<restart>`.
-fix are listed below.  No global scalar or vector or per-atom quantities
+
-are stored by this fix for access by various :doc:`output commands
+The :doc:`fix_modify <fix_modify>` *energy* option is not supported by
-<Howto_output>`.  No parameter of this fix can be used with the
+this fix, but this fix does add the kinetic energy imparted to atoms
+by the momentum coupling mode of the AtC package to the global
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.
+
+Additional :doc:`fix_modify <fix_modify>` options relevant to this
+fix are listed below.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the energy
+discussed in the previous paragraph.  The scalar value is "extensive".
+
+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>`.
 
@@ -145,10 +157,10 @@ one, e.g. nve, nvt, etc. In addition, currently:
 Related commands
 """"""""""""""""
 
-After specifying this fix in your input script, several other
+After specifying this fix in your input script, several
-:doc:`fix_modify <fix_modify>` commands are used to setup the problem,
+:doc:`fix_modify AtC <fix_modify>` commands are used to setup the
-e.g. define the finite element mesh and prescribe initial and boundary
+problem, e.g. define the finite element mesh and prescribe initial and
-conditions.
+boundary conditions.  Each of these options has its own doc page.
 
 *fix_modify* commands for setup:
 
@@ -240,7 +252,8 @@ miscellaneous *fix_modify* commands:
 * :doc:`fix_modify AtC remove_species <atc_remove_species>`
 * :doc:`fix_modify AtC remove_molecule <atc_remove_molecule>`
 
-Note: a set of example input files with the attendant material files are included in the ``examples/USER/atc`` folders.
+Note: a set of example input files with the attendant material files
+are included in the ``examples/USER/atc`` folders.
 
 Default
 """""""
@@ -252,30 +265,52 @@ For detailed exposition of the theory and algorithms please see:
 
 .. _Wagner:
 
-**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An atomistic-to-continuum coupling method for heat transfer in solids." Special Issue of Computer Methods and Applied Mechanics (2008) 197:3351.
+**(Wagner)** Wagner, GJ; Jones, RE; Templeton, JA; Parks, MA, "An
+ atomistic-to-continuum coupling method for heat transfer in solids."
+ Special Issue of Computer Methods and Applied Mechanics (2008)
+ 197:3351.
 
 .. _Zimmeman2004:
 
-**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE; Klein, PA; Bammann, DJ, "Calculation of stress in atomistic simulation." Special Issue of Modelling and Simulation in Materials Science and Engineering (2004), 12:S319.
+**(Zimmerman2004)** Zimmerman, JA; Webb, EB; Hoyt, JJ;. Jones, RE;
+ Klein, PA; Bammann, DJ, "Calculation of stress in atomistic
+ simulation." Special Issue of Modelling and Simulation in Materials
+ Science and Engineering (2004), 12:S319.
 
 .. _Zimmerman2010:
 
-**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A material frame approach for evaluating continuum variables in atomistic simulations." Journal of Computational Physics (2010), 229:2364.
+**(Zimmerman2010)** Zimmerman, JA; Jones, RE; Templeton, JA, "A
+ material frame approach for evaluating continuum variables in
+ atomistic simulations." Journal of Computational Physics (2010),
+ 229:2364.
 
 .. _Templeton2010:
 
-**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application of a field-based method to spatially varying thermal transport problems in molecular dynamics." Modelling and Simulation in Materials Science and Engineering (2010), 18:085007.
+**(Templeton2010)** Templeton, JA; Jones, RE; Wagner, GJ, "Application
+ of a field-based method to spatially varying thermal transport
+ problems in molecular dynamics." Modelling and Simulation in
+ Materials Science and Engineering (2010), 18:085007.
 
 .. _Jones:
 
-**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine, JA, "Electron transport enhanced molecular dynamics for metals and semi-metals." International Journal for Numerical Methods in Engineering (2010), 83:940.
+**(Jones)** Jones, RE; Templeton, JA; Wagner, GJ; Olmsted, D; Modine,
+ JA, "Electron transport enhanced molecular dynamics for metals and
+ semi-metals." International Journal for Numerical Methods in
+ Engineering (2010), 83:940.
 
 .. _Templeton2011:
 
-**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA; Wong, BM, "A long-range electric field solver for molecular dynamics based on atomistic-to-continuum modeling." Journal of Chemical Theory and Computation (2011), 7:1736.
+**(Templeton2011)** Templeton, JA; Jones, RE; Lee, JW; Zimmerman, JA;
+ Wong, BM, "A long-range electric field solver for molecular dynamics
+ based on atomistic-to-continuum modeling." Journal of Chemical Theory
+ and Computation (2011), 7:1736.
 
 .. _Mandadapu:
 
-**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization as a field variable from molecular dynamics simulations." Journal of Chemical Physics (2013), 139:054115.
+**(Mandadapu)** Mandadapu, KK; Templeton, JA; Lee, JW, "Polarization
+ as a field variable from molecular dynamics simulations." Journal of
+ Chemical Physics (2013), 139:054115.
 
-Please refer to the standard finite element (FE) texts, e.g. T.J.R Hughes " The finite element method ", Dover 2003, for the basics of FE simulation.
+Please refer to the standard finite element (FE) texts, e.g. T.J.R
+Hughes " The finite element method ", Dover 2003, for the basics of FE
+simulation.

doc/src/fix_bocs.rst

@@ -75,6 +75,39 @@ 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
 coefficients should all be in atmospheres \* cubic angstroms.
 
+----------
+
+Restart, fix_modify, output, run start/stop, minimize info
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+
+This fix writes the cumulative global energy change to :doc:`binary
+restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+command for info on how to re-specify a fix in an input script that
+reads a restart file, so that the fix continues in an uninterrupted
+fashion.
+
+The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
+fix.  You can use it to assign a temperature :doc:`compute <compute>`
+you have defined to this fix which will be used in its thermostatting
+procedure, as described above.  For consistency, the group used by
+this fix and by the compute should be the same.
+
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
+This fix can ramp its target temperature over multiple runs, using the
+*start* and *stop* keywords of the :doc:`run <run>` command.  See the
+:doc:`run <run>` command for details of how to do this.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
 Restrictions
 """"""""""""
 

doc/src/fix_bond_react.rst

@@ -41,7 +41,7 @@ Syntax
 * template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
 * map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
 * zero or more individual keyword/value pairs may be appended to each react argument
-* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
+* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *molecule* or *modify_create*
 
   .. parsed-literal::
 
@@ -59,6 +59,12 @@ Syntax
            off = allow both inter- and intramolecular reactions (default)
            inter = search for reactions between molecules with different IDs
            intra = search for reactions within the same molecule
+         *modify_create* keyword values
+           *fit* value = *all* or *fragmentID*
+             all = use all eligible atoms for create-atoms fit (default)
+             fragmentID = 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)
 
 Examples
 """"""""
@@ -89,7 +95,9 @@ documentation. Topology changes are defined in pre- and post-reaction
 molecule templates and can include creation and deletion of bonds,
 angles, dihedrals, impropers, bond types, angle types, dihedral types,
 atom types, or atomic charges. In addition, reaction by-products or
-other molecules can be identified and deleted.
+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
 pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
@@ -262,14 +270,14 @@ command page.
 
 The post-reacted molecule template contains a sample of the reaction
 site and its surrounding topology after the reaction has occurred. It
-must contain the same number of atoms as the pre-reacted template. A
+must contain the same number of atoms as the pre-reacted template
-one-to-one correspondence between the atom IDs in the pre- and
+(unless there are created atoms). A one-to-one correspondence between
-post-reacted templates is specified in the map file as described
+the atom IDs in the pre- and post-reacted templates is specified in
-below. Note that during a reaction, an atom, bond, etc. type may
+the map file as described below. Note that during a reaction, an atom,
-change to one that was previously not present in the simulation. These
+bond, etc. type may change to one that was previously not present in
-new types must also be defined during the setup of a given simulation.
+the simulation. These new types must also be defined during the setup
-A discussion of correctly handling this is also provided on the
+of a given simulation. A discussion of correctly handling this is also
-:doc:`molecule <molecule>` command page.
+provided on the :doc:`molecule <molecule>` command page.
 
 .. note::
 
@@ -283,7 +291,7 @@ A discussion of correctly handling this is also provided on the
 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 four optional keywords. The
+contains one mandatory keyword and five optional keywords. The
 mandatory keyword is 'equivalences':
 
 .. parsed-literal::
@@ -296,11 +304,12 @@ The optional keywords are 'edgeIDs', 'deleteIDs', 'chiralIDs' and
 .. parsed-literal::
 
    N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template
-   N *deleteIDs* = # of atoms N that are specified for deletion
+   N *deleteIDs* = # of atoms N that are deleted
-   N *chiralIDs* = # of specified chiral centers N
+   N *createIDs* = # of atoms N that are created
-   N *constraints* = # of specified reaction constraints N
+   N *chiralIDs* = # of chiral centers N
+   N *constraints* = # of reaction constraints N
 
-The body of the map file contains two mandatory sections and four
+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
 in the pre-reacted molecule template. The second mandatory section
@@ -313,8 +322,10 @@ 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
 template atoms to delete. The third optional section begins with the
+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
-handedness should be enforced. The fourth optional section begins with
+handedness should be enforced. The fifth optional section begins with
 the keyword 'Constraints' and lists additional criteria that must be
 satisfied in order for the reaction to occur. Currently, there are
 five types of constraints available, as discussed below: 'distance',
@@ -353,6 +364,38 @@ A sample map file is given below:
 
 ----------
 
+A user-specified set of atoms can be deleted by listing their
+pre-reaction template IDs in the DeleteIDs section. A deleted atom
+must still be included in the post-reaction molecule template, in
+which it cannot be bonded to an atom that is not deleted. In addition
+to deleting unwanted reaction by-products, this feature can be used to
+remove specific topologies, such as small rings, that may be otherwise
+indistinguishable.
+
+Atoms can be created by listing their post-reaction template IDs in
+the CreateIDs section. A created atom should not be included in the
+pre-reaction template. The inserted positions of created atoms are
+determined by the coordinates of the post-reaction template, after
+optimal translation and rotation of the post-reaction template to the
+reaction site (using a fit with atoms that are neither created nor
+deleted). The *modify_create* keyword can be used to modify the
+default behavior when creating atoms. The *modify_create* keyword has
+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
+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
+periodic boundary conditions if applicable. R is defined by the
+*overlap* sub-keyword. Note that the default value for 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.
+
 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
@@ -528,15 +571,6 @@ the same molecule ID are considered for the reaction.
 
 A few other considerations:
 
-Many reactions result in one or more atoms that are considered
-unwanted by-products. Therefore, bond/react provides the option to
-delete a user-specified set of atoms. These pre-reaction atoms are
-identified in the map file. A deleted atom must still be included in
-the post-reaction molecule template, in which it cannot be bonded to
-an atom that is not deleted. In addition to deleting unwanted reaction
-by-products, this feature can be used to remove specific topologies,
-such as small rings, that may be otherwise indistinguishable.
-
 Optionally, you can enforce additional behaviors on reacting atoms.
 For example, it may be beneficial to force reacting atoms to remain at
 a certain temperature. For this, you can use the internally-created
@@ -610,14 +644,14 @@ Default
 """""""
 
 The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60,
-reset_mol_ids = yes, custom_charges = no, molecule = off
+reset_mol_ids = yes, custom_charges = no, molecule = off, modify_create = no
 
 ----------
 
 .. _Gissinger:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
+**(Gissinger2017)** Gissinger, Jensen and Wise, Polymer, 128, 211-217 (2017).
 
 .. _Gissinger2020:
 
-**(Gissinger)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).
+**(Gissinger2020)** Gissinger, Jensen and Wise, Macromolecules, 53, 22, 9953-9961 (2020).

doc/src/fix_client_md.rst

@@ -47,14 +47,15 @@ for running *ab initio* MD with quantum forces.
 The group associated with this fix is ignored.
 
 The protocol and :doc:`units <units>` for message format and content
-that LAMMPS exchanges with the server code is defined on the :doc:`server md <server_md>` doc page.
+that LAMMPS exchanges with the server code is defined on the
+:doc:`server md <server_md>` doc page.
 
 Note that when using LAMMPS as an MD client, your LAMMPS input script
 should not normally contain force field commands, like a
 :doc:`pair_style <pair_style>`, :doc:`bond_style <bond_style>`, or
-:doc:`kspace_style <kspace_style>` command.  However it is possible for
+:doc:`kspace_style <kspace_style>` command.  However it is possible
-a server code to only compute a portion of the full force-field, while
+for a server code to only compute a portion of the full force-field,
-LAMMPS computes the remaining part.  Your LAMMPS script can also
+while LAMMPS computes the remaining part.  Your LAMMPS script can also
 specify boundary conditions or force constraints in the usual way,
 which will be added to the per-atom forces returned by the server
 code.
@@ -69,16 +70,21 @@ LAMMPS and another code in tandem to perform a coupled simulation.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy computed by the server application to
+this fix to add the potential energy set by the server application to
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy yes <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the server application's contribution to the system's
+this fix to add the contribution computed by the server application to
-virial as part of :doc:`thermodynamic output <thermo_style>`.  The
+the global pressure of the system via the :doc:`compute pressure
-default is *virial yes*
+<compute_pressure>` command.  This can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -86,13 +92,16 @@ energy discussed above.  The scalar value calculated by this fix is
 "extensive".
 
 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>`.
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 This fix is part of the MESSAGE package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 A script that uses this command must also use the
 :doc:`message <message>` command to setup and shut down the messaging

doc/src/fix_cmap.rst

@@ -29,11 +29,12 @@ Description
 This command enables CMAP cross-terms to be added to simulations which
 use the CHARMM force field.  These are relevant for any CHARMM model
 of a peptide or protein sequences that is 3 or more amino-acid
-residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>` for details,
+residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>`
-including the analytic energy expressions for CMAP interactions.  The
+for details, including the analytic energy expressions for CMAP
-CMAP cross-terms add additional potential energy contributions to pairs
+interactions.  The CMAP cross-terms add additional potential energy
-of overlapping phi-psi dihedrals of amino-acids, which are important
+contributions to pairs of overlapping phi-psi dihedrals of
-to properly represent their conformational behavior.
+amino-acids, which are important to properly represent their
+conformational behavior.
 
 The examples/cmap directory has a sample input script and data file
 for a small peptide, that illustrates use of the fix cmap command.
@@ -93,19 +94,27 @@ the note below about how to include the CMAP energy when performing an
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the list of CMAP cross-terms to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>` command
+This fix writes the list of CMAP cross-terms to :doc:`binary restart
+files <restart>`.  See the :doc:`read_restart <read_restart>` command
 for info on how to re-specify a fix in an input script that reads a
 restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" of the CMAP interactions system's
+this fix to add the potential energy of the CMAP interactions to both
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy and peratom potential energies of the
+system as part of :doc:`thermodynamic output <thermo_style>` or
+output by the :doc:`compute pe/atom <compute_pe_atom>` command.  The
+default setting for this fix is :doc:`fix_modify energy yes
+<fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interaction between atoms to
+this fix to add the contribution due to the CMAP interactions to both
-the system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+the global pressure and per-atom stress of the system via the
-The default is *virial yes*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -121,8 +130,8 @@ invoked by the :doc:`minimize <minimize>` command.
 .. note::
 
    If you want the potential energy associated with the CMAP terms
-   forces to be included in the total potential energy of the system (the
+   forces to be included in the total potential energy of the system
-   quantity being minimized), you MUST enable the
+   (the quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions

doc/src/fix_colvars.rst

@@ -35,12 +35,12 @@ Examples
 Description
 """""""""""
 
-This fix interfaces LAMMPS to the collective variables "Colvars"
+This fix interfaces LAMMPS to the collective variables (Colvars)
-library, which allows to calculate potentials of mean force
+library, which allows to calculate potentials of mean force (PMFs) for
-(PMFs) for any set of colvars, using different sampling methods:
+any set of colvars, using different sampling methods: currently
-currently implemented are the Adaptive Biasing Force (ABF) method,
+implemented are the Adaptive Biasing Force (ABF) method, metadynamics,
-metadynamics, Steered Molecular Dynamics (SMD) and Umbrella Sampling
+Steered Molecular Dynamics (SMD) and Umbrella Sampling (US) via a
-(US) via a flexible harmonic restraint bias.
+flexible harmonic restraint bias.
 
 This documentation describes only the fix colvars command itself and
 LAMMPS specific parts of the code.  The full documentation of the
@@ -98,9 +98,11 @@ This fix writes the current status of the colvars module into
 mode status file that is written by the colvars module itself and the
 kind of information in both files is identical.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy change from the biasing force added by the fix
+this fix to add the energy change from the biasing force added by
-to the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+Colvars to the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
 The *fix_modify configfile <config file>* option allows to add settings
 from an additional config file to the colvars module. This option can
@@ -113,15 +115,16 @@ in a pair of double quotes ("), or can span multiple lines when bracketed
 by a pair of triple double quotes (""", like python embedded documentation).
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the Colvars
-energy change due to this fix.  The scalar value calculated by this
+energy mentioned above.  The scalar value calculated by this fix is
-fix is "extensive".
+"extensive".
 
 Restrictions
 """"""""""""
 
 This fix is part of the USER-COLVARS package.  It is only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 There can only be one colvars fix active at a time. Since the interface
 communicates only the minimum amount of information and colvars module

doc/src/fix_efield.rst

@@ -100,9 +100,9 @@ minimize the orientation of dipoles in an applied electric field.
 
 The *energy* keyword specifies the name of an atom-style
 :doc:`variable <variable>` which is used to compute the energy of each
-atom as function of its position.  Like variables used for *ex*\ , *ey*\ ,
+atom as function of its position.  Like variables used for *ex*\ ,
-*ez*\ , the energy variable is specified as v_name, where name is the
+*ey*\ , *ez*\ , the energy variable is specified as v_name, where name
-variable name.
+is the variable name.
 
 Note that when the *energy* keyword is used during an energy
 minimization, you must insure that the formula defined for the
@@ -117,31 +117,38 @@ minimization will not converge properly.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" inferred by the added force due to
+this fix to add the potential energy inferred by the added force due
-the electric field to the system's potential energy as part of
+to the electric field to the global potential energy of the system as
-:doc:`thermodynamic output <thermo_style>`.  This is a fictitious
+part of :doc:`thermodynamic output <thermo_style>`.  The default
-quantity but is needed so that the :doc:`minimize <minimize>` command
+setting for this fix is :doc:`fix_modify energy no <fix_modify>`.
-can include the forces added by this fix in a consistent manner.
+Note that this energy is a fictitious quantity but is needed so that
-I.e. there is a decrease in potential energy when atoms move in the
+the :doc:`minimize <minimize>` command can include the forces added by
-direction of the added force due to the electric field.
+this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force
+due to the electric field.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the added forces on atoms to the
+this fix to add the contribution due to the added forces on atoms to
-system's virial as part of :doc:`thermodynamic output <thermo_style>`.
+both the global pressure and per-atom stress of the system via the
-The default is *virial no*
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix adding its forces. Default is the outermost level.
+<run_style>` integrator the fix adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the potential energy discussed above.  The vector is the
+<Howto_output>`.  The scalar is the potential energy discussed above.
-total force added to the group of atoms.  The scalar and vector values
+The vector is the total force added to the group of atoms.  The scalar
-calculated by this fix are "extensive".
+and vector values calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.

doc/src/fix_external.rst

@@ -84,7 +84,8 @@ code `Quest <quest_>`_.
 
 If mode is *pf/array* then the fix simply stores force values in an
 array.  The fix adds these forces to each atom in the group, once
-every *Napply* steps, similar to the way the :doc:`fix addforce <fix_addforce>` command works.
+every *Napply* steps, similar to the way the :doc:`fix addforce
+<fix_addforce>` command works.
 
 The name of the public force array provided by the FixExternal
 class is
@@ -150,19 +151,27 @@ of properties that the caller code may want to communicate  to LAMMPS
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential "energy" set by the external driver to the
+this fix to add the potential energy set by the external driver to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  This is a fictitious quantity but is
+both the global potential energy and peratom potential energies of the
-needed so that the :doc:`minimize <minimize>` command can include the
+system as part of :doc:`thermodynamic output <thermo_style>` or output
-forces added by this fix in a consistent manner.  I.e. there is a
+by the :doc:`compute pe/atom <compute_pe_atom>` command.  The default
-decrease in potential energy when atoms move in the direction of the
+setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
-added force.
+Note that this energy may be a fictitious quantity but it is needed so
+that the :doc:`minimize <minimize>` command can include the forces
+added by this fix in a consistent manner.  I.e. there is a decrease in
+potential energy when atoms move in the direction of the added force.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the contribution due to the interactions computed by the
+this fix to add the contribution computed by the external program to
-external program to the system's virial as part of :doc:`thermodynamic output <thermo_style>`. The default is *virial yes*
+both the global pressure and per-atom stress of the system via the
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -178,7 +187,7 @@ invoked by the :doc:`minimize <minimize>` command.
 
    If you want the fictitious potential energy associated with the
    added forces to be included in the total potential energy of the
-   system (the quantity being minimized), you MUST enable the
+   system (the quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions

doc/src/fix_ffl.rst

@@ -76,28 +76,31 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 The instantaneous values of the extended variables are written to
-:doc:`binary restart files <restart>`.  Because the state of the random
+:doc:`binary restart files <restart>`.  Because the state of the
-number generator is not saved in restart files, this means you cannot
+random number generator is not saved in restart files, this means you
-do "exact" restarts with this fix, where the simulation continues on
+cannot do "exact" restarts with this fix, where the simulation
-the same as if no restart had taken place. However, in a statistical
+continues on the same as if no restart had taken place. However, in a
-sense, a restarted simulation should produce the same behavior.
+statistical sense, a restarted simulation should produce the same
-Note however that you should use a different seed each time you
+behavior.  Note however that you should use a different seed each time
-restart, otherwise the same sequence of random numbers will be used
+you restart, otherwise the same sequence of random numbers will be
-each time, which might lead to stochastic synchronization and
+used each time, which might lead to stochastic synchronization and
 subtle artifacts in the sampling.
 
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the
 :doc:`run <run>` command for details of how to do this.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+This fix is not invoked during :doc:`energy minimization <minimize>`.
-fix to add the energy change induced by Langevin thermostatting to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
-
-This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
-energy change due to this fix.  The scalar value calculated by this
-fix is "extensive".
 
 Restrictions
 """"""""""""

doc/src/fix_flow_gauss.rst

@@ -55,17 +55,22 @@ momentum.
 GD applies an external fluctuating gravitational field that acts as a
 driving force to keep the system away from equilibrium. To maintain
 steady state, a profile-unbiased thermostat must be implemented to
-dissipate the heat that is added by the driving force. :doc:`Compute temp/profile <compute_temp_profile>` can be used to implement a
+dissipate the heat that is added by the driving force. :doc:`Compute
+temp/profile <compute_temp_profile>` can be used to implement a
 profile-unbiased thermostat.
 
 A common use of this fix is to compute a pressure drop across a pipe,
 pore, or membrane. The pressure profile can be computed in LAMMPS with
-:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc <fix_atc>`. Note that the simple :doc:`compute stress/atom <compute_stress_atom>` method is only accurate away
+:doc:`compute stress/atom <compute_stress_atom>` and :doc:`fix
-from inhomogeneities in the fluid, such as fixed wall atoms. Further,
+ave/chunk <fix_ave_chunk>`, or with the hardy method in :doc:`fix atc
-the computed pressure profile must be corrected for the acceleration
+<fix_atc>`. Note that the simple :doc:`compute stress/atom
+<compute_stress_atom>` method is only accurate away from
+inhomogeneities in the fluid, such as fixed wall atoms. Further, the
+computed pressure profile must be corrected for the acceleration
 applied by GD before computing a pressure drop or comparing it to
-other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The pressure
+other methods, such as the pump method :ref:`(Zhu) <Zhu>`. The
-correction is discussed and described in :ref:`(Strong) <Strong>`.
+pressure correction is discussed and described in :ref:`(Strong)
+<Strong>`.
 
 For a complete example including the considerations discussed
 above, see the examples/USER/flow_gauss directory.
@@ -102,14 +107,15 @@ computed by the fix will return zero.
    of wall atoms fixed, such as :doc:`fix spring/self <fix_spring_self>`.
 
 If this fix is used in a simulation with the :doc:`rRESPA <run_style>`
-integrator, the applied acceleration must be computed and applied at the same
+integrator, the applied acceleration must be computed and applied at
-rRESPA level as the interactions between the flowing fluid and the obstacle.
+the same rRESPA level as the interactions between the flowing fluid
-The rRESPA level at which the acceleration is applied can be changed using
+and the obstacle.  The rRESPA level at which the acceleration is
-the :doc:`fix_modify <fix_modify>` *respa* option discussed below. If the
+applied can be changed using the :doc:`fix_modify <fix_modify>`
-flowing fluid and the obstacle interact through multiple interactions that are
+*respa* option discussed below. If the flowing fluid and the obstacle
-computed at different rRESPA levels, then there must be a separate flow/gauss
+interact through multiple interactions that are computed at different
-fix for each level. For example, if the flowing fluid and obstacle interact
+rRESPA levels, then there must be a separate flow/gauss fix for each
-through pairwise and long-range Coulomb interactions, which are computed at
+level. For example, if the flowing fluid and obstacle interact through
+pairwise and long-range Coulomb interactions, which are computed at
 rRESPA levels 3 and 4, respectively, then there must be two separate
 flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
 *fix_modify respa 4*.
@@ -119,38 +125,49 @@ flow/gauss fixes, one that specifies *fix_modify respa 3* and one with
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix is part of the USER-MISC package.  It is only enabled if
+No information about this fix is written to :doc:`binary restart files
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+<restart>`.
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-
+this fix to add the potential energy added by the fix to the global
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+potential energy of the system as part of :doc:`thermodynamic output
-fix to subtract the work done from the
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows the user to set at which level of the :doc:`rRESPA <run_style>`
+fix. This allows the user to set at which level of the :doc:`rRESPA
-integrator the fix computes and adds the external acceleration. Default is the
+<run_style>` integrator the fix computes and adds the external
-outermost level.
+acceleration. Default is the outermost level.
 
 This fix computes a global scalar and a global 3-vector of forces,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the negative of the work done on the system, see above
+<Howto_output>`.  The scalar is the negative of the work done on the
-discussion.  The vector is the total force that this fix applied to
+system, see the discussion above.  It is only calculated if the
-the group of atoms on the current timestep.  The scalar and vector
+*energy* keyword is enabled or :doc:`fix_modify energy yes
-values calculated by this fix are "extensive".
+<fix_modify>` is set.
+
+The vector is the total force that this fix applied to the group of
+atoms on the current timestep.  The scalar and vector values
+calculated by this fix are "extensive".
 
 No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
+This fix is not invoked during :doc:`energy minimization <minimize>`.
+
 Restrictions
 """"""""""""
- none
+
+This fix is part of the USER-MISC package.  It is only enabled if
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""
 
-:doc:`fix addforce <fix_addforce>`, :doc:`compute temp/profile <compute_temp_profile>`, :doc:`velocity <velocity>`
+:doc:`fix addforce <fix_addforce>`,
+:doc:`compute temp/profile <compute_temp_profile>`,
+:doc:`velocity <velocity>`
 
 Default
 """""""

doc/src/fix_gcmc.rst

@@ -398,12 +398,13 @@ adds all inserted atoms of the specified type to the
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+This fix writes the state of the fix to :doc:`binary restart files
-number generator seed, the next timestep for MC exchanges,  the number
+<restart>`.  This includes information about the random number
-of MC step attempts and successes etc.  See
+generator seed, the next timestep for MC exchanges, the number of MC
-the :doc:`read_restart <read_restart>` command for info on how to
+step attempts and successes etc.  See the :doc:`read_restart
-re-specify a fix in an input script that reads a restart file, so that
+<read_restart>` command for info on how to re-specify a fix in an
-the operation of the fix continues in an uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 .. note::
 
@@ -411,8 +412,8 @@ the operation of the fix continues in an uninterrupted fashion.
    after reading the restart with :doc:`reset_timestep <reset_timestep>`.
    The fix will try to detect it and stop with an error.
 
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this
+None of the :doc:`fix_modify <fix_modify>` options are relevant to
-fix.
+this fix.
 
 This fix computes a global vector of length 8, which can be accessed
 by various :doc:`output commands <Howto_output>`.  The vector values are
@@ -430,7 +431,8 @@ the following global cumulative quantities:
 The vector values calculated by this fix are "extensive".
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_gle.rst

@@ -103,28 +103,31 @@ Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 The instantaneous values of the extended variables are written to
-:doc:`binary restart files <restart>`.  Because the state of the random
+:doc:`binary restart files <restart>`.  Because the state of the
-number generator is not saved in restart files, this means you cannot
+random number generator is not saved in restart files, this means you
-do "exact" restarts with this fix, where the simulation continues on
+cannot do "exact" restarts with this fix, where the simulation
-the same as if no restart had taken place. However, in a statistical
+continues on the same as if no restart had taken place. However, in a
-sense, a restarted simulation should produce the same behavior.
+statistical sense, a restarted simulation should produce the same
-Note however that you should use a different seed each time you
+behavior.  Note however that you should use a different seed each time
-restart, otherwise the same sequence of random numbers will be used
+you restart, otherwise the same sequence of random numbers will be
-each time, which might lead to stochastic synchronization and
+used each time, which might lead to stochastic synchronization and
 subtle artifacts in the sampling.
 
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the
 :doc:`run <run>` command for details of how to do this.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+This fix is not invoked during :doc:`energy minimization <minimize>`.
-fix to add the energy change induced by Langevin thermostatting to the
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
-
-This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
-energy change due to this fix.  The scalar value calculated by this
-fix is "extensive".
 
 Restrictions
 """"""""""""

doc/src/fix_gravity.rst

@@ -103,23 +103,27 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the gravitational potential energy of the system to the
+this fix to add the gravitational potential energy of the system to
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+the global potential energy of the system as part of
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  This scalar is the gravitational
+:doc:`output commands <Howto_output>`.  This scalar is the
-potential energy of the particles in the defined field, namely mass \*
+gravitational potential energy of the particles in the defined field,
-(g dot x) for each particles, where x and mass are the particles
+namely mass \* (g dot x) for each particles, where x and mass are the
-position and mass, and g is the gravitational field.  The scalar value
+particles position and mass, and g is the gravitational field.  The
-calculated by this fix is "extensive".
+scalar value calculated by this fix is "extensive".
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_hyper_global.rst

@@ -200,16 +200,20 @@ algorithm.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of the bias potential to the system's
+this fix to add the energy of the bias potential to the global
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
-This fix computes a global scalar and global vector of length 12, which
+This fix computes a global scalar and global vector of length 12,
-can be accessed by various :doc:`output commands <Howto_output>`.  The
+which can be accessed by various :doc:`output commands
-scalar is the magnitude of the bias potential (energy units) applied on
+<Howto_output>`.  The scalar is the magnitude of the bias potential
-the current timestep.  The vector stores the following quantities:
+(energy units) applied on the current timestep.  The vector stores the
+following quantities:
 
 * 1 = boost factor on this step (unitless)
 * 2 = max strain :math:`E_{ij}` of any bond on this step (absolute value, unitless)
@@ -253,7 +257,8 @@ The scalar and vector values calculated by this fix are all
 "intensive".
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_hyper_local.rst

@@ -370,15 +370,17 @@ Restart, fix_modify, output, run start/stop, minimize info
 
 No information about this fix is written to :doc:`binary restart files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of the bias potential to the system's potential
+this fix to add the energy of the bias potential to the global
-energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy no <fix_modify>`.
 
 This fix computes a global scalar and global vector of length 28,
-which can be accessed by various :doc:`output commands <Howto_output>`.
+which can be accessed by various :doc:`output commands
-The scalar is the magnitude of the bias potential (energy units)
+<Howto_output>`.  The scalar is the magnitude of the bias potential
-applied on the current timestep, summed over all biased bonds.  The
+(energy units) applied on the current timestep, summed over all biased
-vector stores the following quantities:
+bonds.  The vector stores the following quantities:
 
 * 1 = average boost for all bonds on this step (unitless)
 * 2 = # of biased bonds on this step
@@ -510,8 +512,8 @@ Value 27 computes the average boost for biased bonds only on this step.
 Value 28 is the count of bonds with an absolute value of strain >= q
 on this step.
 
-The scalar and vector values calculated by this fix are all
+The scalar value is an "extensive" quantity since it grows with the
-"intensive".
+system size; the vector values are all "intensive".
 
 This fix also computes a local vector of length the number of bonds
 currently in the system.  The value for each bond is its :math:`C_{ij}`
@@ -524,7 +526,8 @@ close to 1.0, which indicates a good choice of :math:`V^{max}`.
 The local values calculated by this fix are unitless.
 
 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>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""

doc/src/fix_indent.rst

@@ -179,20 +179,25 @@ contains *xlat*\ , *ylat*\ , *zlat* keywords of the
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the energy of interaction between atoms and the indenter to
+this fix to add the energy of interaction between atoms and the
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  The energy of each particle interacting
+indenter to the global potential energy of the system as part of
-with the indenter is K/3 (r - R)\^3.
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify energy no <fix_modify>`. The energy of
+each particle interacting with the indenter is K/3 (r - R)\^3.
 
 The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
-fix. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+fix. This allows to set at which level of the :doc:`r-RESPA
-integrator the fix is adding its forces. Default is the outermost level.
+<run_style>` integrator the fix is adding its forces. Default is the
+outermost level.
 
 This fix computes a global scalar energy and a global 3-vector of
-forces (on the indenter), which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar and vector values calculated
+forces (on the indenter), which can be accessed by various
-by this fix are "extensive".
+:doc:`output commands <Howto_output>`.  The scalar and vector values
+calculated by this fix are "extensive".
 
 The forces due to this fix are imposed during an energy minimization,
 invoked by the :doc:`minimize <minimize>` command.  Note that if you
@@ -204,10 +209,10 @@ check if you have done this.
 
 .. note::
 
-   If you want the atom/indenter interaction energy to be included
+   If you want the atom/indenter interaction energy to be included in
-   in the total potential energy of the system (the quantity being
+   the total potential energy of the system (the quantity being
-   minimized), you must enable the :doc:`fix_modify <fix_modify>` *energy*
+   minimized), you must enable the :doc:`fix_modify <fix_modify>`
-   option for this fix.
+   *energy* option for this fix.
 
 Restrictions
 """"""""""""

doc/src/fix_langevin.rst

@@ -230,7 +230,7 @@ conservation.
 
 .. note::
 
-   this accumulated energy does NOT include kinetic energy removed
+   This accumulated energy does NOT include kinetic energy removed
    by the *zero* flag. LAMMPS will print a warning when both options are
    active.
 
@@ -244,7 +244,8 @@ to zero by subtracting off an equal part of it from each atom in the
 group.  As a result, the center-of-mass of a system with zero initial
 momentum will not drift over time.
 
-The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>` time-discretization of the Langevin model.  As
+The keyword *gjf* can be used to run the :ref:`Gronbech-Jensen/Farago
+<Gronbech-Jensen>` time-discretization of the Langevin model.  As
 described in the papers cited below, the purpose of this method is to
 enable longer timesteps to be used (up to the numerical stability
 limit of the integrator), while still producing the correct Boltzmann
@@ -252,19 +253,20 @@ distribution of atom positions.
 
 The current implementation provides the user with the option to output
 the velocity in one of two forms: *vfull* or *vhalf*\ , which replaces
-the outdated option *yes*\ . The *gjf* option *vfull* outputs the on-site
+the outdated option *yes*\ . The *gjf* option *vfull* outputs the
-velocity given in :ref:`Gronbech-Jensen/Farago <Gronbech-Jensen>`; this velocity
+on-site velocity given in :ref:`Gronbech-Jensen/Farago
-is shown to be systematically lower than the target temperature by a small
+<Gronbech-Jensen>`; this velocity is shown to be systematically lower
-amount, which grows quadratically with the timestep.
+than the target temperature by a small amount, which grows
-The *gjf* option *vhalf* outputs the 2GJ half-step velocity given in
+quadratically with the timestep.  The *gjf* option *vhalf* outputs the
-:ref:`Gronbech Jensen/Gronbech-Jensen <2Gronbech-Jensen>`; for linear systems,
+2GJ half-step velocity given in :ref:`Gronbech Jensen/Gronbech-Jensen
-this velocity is shown to not have any statistical errors for any stable time step.
+<2Gronbech-Jensen>`; for linear systems, this velocity is shown to not
-An overview of statistically correct Boltzmann and Maxwell-Boltzmann
+have any statistical errors for any stable time step.  An overview of
-sampling of true on-site and true half-step velocities is given in
+statistically correct Boltzmann and Maxwell-Boltzmann sampling of true
-:ref:`Gronbech-Jensen <1Gronbech-Jensen>`.
+on-site and true half-step velocities is given in
-Regardless of the choice of output velocity, the sampling of the configurational
+:ref:`Gronbech-Jensen <1Gronbech-Jensen>`.  Regardless of the choice
-distribution of atom positions is the same, and linearly consistent with the
+of output velocity, the sampling of the configurational distribution
-target temperature.
+of atom positions is the same, and linearly consistent with the target
+temperature.
 
 ----------
 
@@ -287,16 +289,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Langevin thermostatting to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+*ecouple* and *econserve*\ , but only if the *tally* keyword to set to
-setting the *tally* keyword to *yes*\ .
+*yes*\ .  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".  Note that calculation of this quantity requires
+paragraph.  The scalar value calculated by this fix is "extensive".
-setting the *tally* keyword to *yes*\ .
+Note that calculation of this quantity also requires setting the
+*tally* keyword to *yes*\ .
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_langevin_eff.rst

@@ -81,16 +81,18 @@ you have defined to this fix which will be used in its thermostatting
 procedure, as described above.  For consistency, the group used by
 this fix and by the compute should be the same.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Langevin thermostatting to the
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.  Note that use of this option requires
+*ecouple* and *econserve*\ , but only if the *tally* keyword to set to
-setting the *tally* keyword to *yes*\ .
+*yes*\ .  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
 This fix computes a global scalar which can be accessed by various
-:doc:`output commands <Howto_output>`.  The scalar is the cumulative
+:doc:`output commands <Howto_output>`.  The scalar is the same
-energy change due to this fix.  The scalar value calculated by this
+cumulative energy change due to this fix described in the previous
-fix is "extensive".  Note that calculation of this quantity requires
+paragraph.  The scalar value calculated by this fix is "extensive".
-setting the *tally* keyword to *yes*\ .
+Note that calculation of this quantity also requires setting the
+*tally* keyword to *yes*\ .
 
 This fix can ramp its target temperature over multiple runs, using the
 *start* and *stop* keywords of the :doc:`run <run>` command.  See the

doc/src/fix_latte.rst

@@ -107,16 +107,27 @@ larger system sizes and longer time scales
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy computed by LATTE to the system's
+this fix to add the potential energy computed by LATTE to the global
-potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+potential energy of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+energy yes <fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *virial* option is supported by this
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
-fix to add the LATTE DFTB contribution to the system's virial as part
+this fix to add the contribution compute by LATTE to the global
-of :doc:`thermodynamic output <thermo_style>`.  The default is *virial
+pressure of the system via the :doc:`compute pressure
-yes*
+<compute_pressure>` command.  This can be accessed by
+:doc:`thermodynamic output <thermo_style>`.  The default setting for
+this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+this fix to add the contribution computed by LATTE to the global
+pressure of the system as part of :doc:`thermodynamic output
+<thermo_style>`.  The default setting for this fix is :doc:`fix_modify
+virial yes <fix_modify>`.
 
 This fix computes a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -127,20 +138,22 @@ No parameter of this fix can be used with the *start/stop* keywords of
 the :doc:`run <run>` command.
 
 The DFTB forces computed by LATTE via this fix are imposed during an
-energy minimization, invoked by the :doc:`minimize <minimize>` command.
+energy minimization, invoked by the :doc:`minimize <minimize>`
+command.
 
 .. note::
 
    If you want the potential energy associated with the DFTB
    forces to be included in the total potential energy of the system (the
-   quantity being minimized), you MUST enable the
+   quantity being minimized), you MUST not disable the
    :doc:`fix_modify <fix_modify>` *energy* option for this fix.
 
 Restrictions
 """"""""""""
 
 This fix is part of the LATTE package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 You must use metal units, as set by the :doc:`units <units>` command to
 use this fix.

doc/src/fix_lb_rigid_pc_sphere.rst

@@ -50,7 +50,8 @@ This fix is based on the :doc:`fix rigid <fix_rigid>` command, and was
 created to be used in place of that fix, to integrate the equations of
 motion of spherical rigid bodies when a lattice-Boltzmann fluid is
 present with a user-specified value of the force-coupling constant.
-The fix uses the integration algorithm described in :ref:`Mackay et al. <Mackay>` to update the positions, velocities, and orientations of
+The fix uses the integration algorithm described in :ref:`Mackay et
+al. <Mackay>` to update the positions, velocities, and orientations of
 a set of spherical rigid bodies experiencing velocity dependent
 hydrodynamic forces.  The spherical bodies are assumed to rotate as
 solid, uniform density spheres, with moments of inertia calculated
@@ -88,9 +89,18 @@ Restart, fix_modify, output, run start/stop, minimize info
 No information about the *rigid* and *rigid/nve* fixes are written to
 :doc:`binary restart files <restart>`.
 
+The :doc:`fix_modify <fix_modify>` *virial* option is supported by
+this fix to add the contribution due to the added forces on atoms to
+both the global pressure and per-atom stress of the system via the
+:doc:`compute pressure <compute_pressure>` and :doc:`compute
+stress/atom <compute_stress_atom>` commands.  The former can be
+accessed by :doc:`thermodynamic output <thermo_style>`.  The default
+setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
+
 Similar to the :doc:`fix rigid <fix_rigid>` command: The rigid fix
-computes a global scalar which can be accessed by various :doc:`output commands <Howto_output>`.  The scalar value calculated by these
+computes a global scalar which can be accessed by various :doc:`output
-fixes is "intensive".  The scalar is the current temperature of the
+commands <Howto_output>`.  The scalar value calculated by these fixes
+is "intensive".  The scalar is the current temperature of the
 collection of rigid bodies.  This is averaged over all rigid bodies
 and their translational and rotational degrees of freedom.  The
 translational energy of a rigid body is 1/2 m v\^2, where m = total
@@ -130,7 +140,8 @@ Restrictions
 """"""""""""
 
 This fix is part of the USER-LB package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Can only be used if a lattice-Boltzmann fluid has been created via the
 :doc:`fix lb/fluid <fix_lb_fluid>` command, and must come after this

doc/src/fix_modify.rst

@@ -59,43 +59,58 @@ define their own compute by default, as described in their
 documentation.  Thus this option allows the user to override the
 default method for computing P.
 
-The *energy* keyword can be used with fixes that support it.
+The *energy* keyword can be used with fixes that support it, which is
-*energy yes* adds a contribution to the potential energy of the
+explained at the bottom of their doc page.  *Energy yes* will add a
-system. The fix's global and per-atom
+contribution to the potential energy of the system.  More
-energy is included in the calculation performed by the :doc:`compute pe <compute_pe>` or :doc:`compute pe/atom <compute_pe_atom>`
+specifically, the fix's global or per-atom energy is included in the
-commands.  See the :doc:`thermo_style <thermo_style>` command for info
+calculation performed by the :doc:`compute pe <compute_pe>` or
-on how potential energy is output.  For fixes that tally a global
+:doc:`compute pe/atom <compute_pe_atom>` commands.  The former is what
-energy, it can be printed by using the keyword f_ID in the
+is used the :doc:`thermo_style <thermo_style>` command for output of
-thermo_style custom command, where ID is the fix-ID of the appropriate
+any quantity that includes the global potential energy of the system.
-fix.
+Note that the :doc:`compute pe <compute_pe>` and :doc:`compute pe/atom
+<compute_pe_atom>` commands also have an option to include or exclude
+the contribution from fixes.  For fixes that tally a global energy, it
+can also be printed with thermodynamic output by using the keyword
+f_ID in the thermo_style custom command, where ID is the fix-ID of the
+appropriate fix.
 
 .. note::
 
-   You must also specify the *energy yes* setting for a fix if you
+   If you are performing an :doc:`energy minimization <minimize>` with
-   are using it when performing an :doc:`energy minimization <minimize>`
+   one of these fixes and want the energy and forces it produces to be
-   and if you want the energy and forces it produces to be part of the
+   part of the optimization criteria, you must specify the *energy
-   optimization criteria.
+   yes* setting.
-
-The *virial* keyword can be used with fixes that support it.
-*virial yes* adds a contribution to the virial of the
-system. The fix's global and per-atom
-virial is included in the calculation performed by the :doc:`compute pressure <compute_pressure>` or
-:doc:`compute stress/atom <compute_stress_atom>`
-commands.  See the :doc:`thermo_style <thermo_style>` command for info
-on how pressure is output.
 
 .. note::
 
-   You must specify the *virial yes* setting for a fix if you
+   For most fixes that support the *energy* keyword, the default
-   are doing :doc:`box relaxation <fix_box_relax>` and
+   setting is *no*.  For a few it is *yes*, when a user would expect
-   if you want virial contribution of the fix to be part of the
+   that to be the case.  The doc page of each fix gives the default.
-   relaxation criteria, although this seems unlikely.
+
+The *virial* keyword can be used with fixes that support it, which is
+explained at the bottom of their doc page.  *Virial yes* will add a
+contribution to the virial of the system.  More specifically, the
+fix's global or per-atom virial is included in the calculation
+performed by the :doc:`compute pressure <compute_pressure>` or
+:doc:`compute stress/atom <compute_stress_atom>` commands.  The former
+is what is used the :doc:`thermo_style <thermo_style>` command for
+output of any quantity that includes the global pressure of the
+system.  Note that the :doc:`compute pressure <compute_pressure>` and
+:doc:`compute stress/atom <compute_stress_atom>` commands also have an
+option to include or exclude the contribution from fixes.
 
 .. note::
 
-   This option is only supported by fixes that explicitly say
+   If you are performing an :doc:`energy minimization <minimize>` with
-   so. For some of these (e.g. the :doc:`fix shake <fix_shake>` command)
+   :doc:`box relaxation <fix_box_relax>` and one of these fixes and
-   the default setting is *virial yes*\ , for others it is *virial no*\ .
+   want the virial contribution of the fix to be part of the
+   optimization criteria, you must specify the *virial yes* setting.
+
+.. note::
+
+   For most fixes that support the *virial* keyword, the default
+   setting is *no*.  For a few it is *yes*, when a user would expect
+   that to be the case.  The doc page of each fix gives the default.
 
 For fixes that set or modify forces, it may be possible to select at
 which :doc:`r-RESPA <run_style>` level the fix operates via the *respa*
@@ -112,13 +127,15 @@ The *dynamic/dof* keyword determines whether the number of atoms N in
 the fix group and their associated degrees of freedom are re-computed
 each time a temperature is computed.  Only fix styles that calculate
 their own internal temperature use this option.  Currently this is
-only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix rigid/npt/small <fix_rigid>` commands for the purpose of
+only the :doc:`fix rigid/nvt/small <fix_rigid>` and :doc:`fix
+rigid/npt/small <fix_rigid>` commands for the purpose of
 thermostatting rigid body translation and rotation.  By default, N and
 their DOF are assumed to be constant.  If you are adding atoms or
-molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
+molecules to the system (see the :doc:`fix pour <fix_pour>`, :doc:`fix
+deposit <fix_deposit>`, and :doc:`fix gcmc <fix_gcmc>` commands) or
 expect atoms or molecules to be lost (e.g. due to exiting the
-simulation box or via :doc:`fix evaporate <fix_evaporate>`), then
+simulation box or via :doc:`fix evaporate <fix_evaporate>`), then this
-this option should be used to insure the temperature is correctly
+option should be used to insure the temperature is correctly
 normalized.
 
 .. note::

doc/src/fix_msst.rst

@@ -131,20 +131,29 @@ command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
 
+The cumulative energy change in the system imposed by this fix is
+included in the :doc:`thermodynamic output <thermo_style>` keywords
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
+
+This fix computes a global scalar which can be accessed by various
+:doc:`output commands <Howto_output>`.  The scalar is the same
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
 The progress of the MSST can be monitored by printing the global
 scalar and global vector quantities computed by the fix.
 
-The scalar is the cumulative energy change due to the fix. This is
+As mentioned above, the scalar is the cumulative energy change due to
-also the energy added to the potential energy by the
+the fix.  By monitoring the thermodynamic *econserve* output, this can
-:doc:`fix_modify <fix_modify>` *energy* command.  With this command, the
+be used to test if the MD timestep is sufficiently small for accurate
-thermo keyword *etotal* prints the conserved quantity of the MSST
+integration of the dynamic equations.
-dynamic equations. This can be used to test if the MD timestep is
-sufficiently small for accurate integration of the dynamic
-equations. See also :doc:`thermo_style <thermo_style>` command.
 
-The global vector contains four values in this order:
+The global vector contains four values in the following order.  The
+vector values output by this fix are "intensive".
 
-[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*, *lagrangian_position*]
+[\ *dhugoniot*\ , *drayleigh*\ , *lagrangian_speed*,
+*lagrangian_position*]
 
 1. *dhugoniot* is the departure from the Hugoniot (temperature units).
 2. *drayleigh* is the departure from the Rayleigh line (pressure units).
@@ -157,17 +166,11 @@ headers, the following LAMMPS commands are suggested:
 .. code-block:: LAMMPS
 
    fix              msst all msst z
-   fix_modify       msst energy yes
    variable dhug    equal f_msst[1]
    variable dray    equal f_msst[2]
    variable lgr_vel equal f_msst[3]
    variable lgr_pos equal f_msst[4]
-   thermo_style     custom step temp ke pe lz pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
+   thermo_style     custom step temp ke pe lz pzz econserve v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
-
-These fixes compute a global scalar and a global vector of 4
-quantities, which can be accessed by various :doc:`output commands
-<Howto_output>`.  The scalar values calculated by this fix are
-"extensive"; the vector values are "intensive".
 
 Restrictions
 """"""""""""

doc/src/fix_nh.rst

@@ -1,8 +1,10 @@
 .. index:: fix nvt
+.. index:: fix nvt/gpu
 .. index:: fix nvt/intel
 .. index:: fix nvt/kk
 .. index:: fix nvt/omp
 .. index:: fix npt
+.. index:: fix npt/gpu
 .. index:: fix npt/intel
 .. index:: fix npt/kk
 .. index:: fix npt/omp
@@ -13,12 +15,12 @@
 fix nvt command
 ===============
 
-Accelerator Variants: *nvt/intel*, *nvt/kk*, *nvt/omp*
+Accelerator Variants: *nvt/gpu*, *nvt/intel*, *nvt/kk*, *nvt/omp*
 
 fix npt command
 ===============
 
-Accelerator Variants: *npt/intel*, *npt/kk*, *npt/omp*
+Accelerator Variants: *npt/gpu*, *npt/intel*, *npt/kk*, *npt/omp*
 
 fix nph command
 ===============
@@ -594,17 +596,20 @@ compute temperature on a subset of atoms.
    specified by the *press* keyword will be unaffected by the *temp*
    setting.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+The cumulative energy change in the system imposed by these fixes, via
-fixes to add the energy change induced by Nose/Hoover thermostatting
+either thermostatting and/or barostatting, is included in the
-and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
-:doc:`thermodynamic output <thermo_style>`.
+*econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
-These fixes compute a global scalar and a global vector of quantities,
+These fixes compute a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by these fixes is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
-values are "intensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
-The scalar is the cumulative energy change due to the fix.
+These fixes compute also compute a global vector of quantities, which
+can be accessed by various :doc:`output commands <Howto_output>`.  The
+vector values are "intensive".
 
 The vector stores internal Nose/Hoover thermostat and barostat
 variables.  The number and meaning of the vector values depends on

doc/src/fix_nph_asphere.rst

@@ -87,7 +87,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary
+restart files <restart>`.  See the :doc:`read_restart <read_restart>`
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
@@ -101,9 +102,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nph_body.rst

@@ -84,7 +84,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary
+restart files <restart>`.  See the :doc:`read_restart <read_restart>`
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
@@ -98,9 +99,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nph_sphere.rst

@@ -100,7 +100,8 @@ It also means that changing attributes of *thermo_temp* or
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover barostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover barostat to :doc:`binary
+restart files <restart>`.  See the :doc:`read_restart <read_restart>`
 command for info on how to re-specify a fix in an input script that
 reads a restart file, so that the operation of the fix continues in an
 uninterrupted fashion.
@@ -114,9 +115,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover barostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nph <fix_nh>` command.

doc/src/fix_nphug.rst

@@ -168,43 +168,47 @@ specified, then the instantaneous value in the system at the start of
 the simulation is used.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
-supported by these fixes.  You can use them to assign a
+supported by this fix.  You can use them to assign a :doc:`compute
-:doc:`compute <compute>` you have defined to this fix which will be used
+<compute>` you have defined to this fix which will be used in its
-in its thermostatting or barostatting procedure, as described above.
+thermostatting or barostatting procedure, as described above.  If you
-If you do this, note that the kinetic energy derived from the compute
+do this, note that the kinetic energy derived from the compute
 temperature should be consistent with the virial term computed using
 all atoms for the pressure.  LAMMPS will warn you if you choose to
 compute temperature on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by these
+The cumulative energy change in the system imposed by this fix is
-fixes to add the energy change induced by Nose/Hoover thermostatting
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-and barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`. Either way, this energy is \*not\*
+doc page for details.  Note that this energy is \*not\* included in
-included in the definition of internal energy E when calculating the value
+the definition of internal energy E when calculating the value of
-of Delta in the above equation.
+Delta in the above equation.
 
-These fixes compute a global scalar and a global vector of quantities,
+This fix computes a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by these fixes is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
-values are "intensive".
+paragraph.  The scalar value calculated by this fix is "extensive".
 
-The scalar is the cumulative energy change due to the fix.
+This fix also computes a global vector of quantities, which can be
+accessed by various :doc:`output commands <Howto_output>`.  The scalar
+The vector values are "intensive".
 
-The vector stores three quantities unique to this fix (:math:`\Delta`, Us, and up),
+The vector stores three quantities unique to this fix (:math:`\Delta`,
-followed by all the internal Nose/Hoover thermostat and barostat
+Us, and up), followed by all the internal Nose/Hoover thermostat and
-variables defined for :doc:`fix npt <fix_nh>`. Delta is the deviation
+barostat variables defined for :doc:`fix npt <fix_nh>`. Delta is the
-of the temperature from the target temperature, given by the above equation.
+deviation of the temperature from the target temperature, given by the
-Us and up are the shock and particle velocity corresponding to a steady
+above equation.  Us and up are the shock and particle velocity
-shock calculated from the RH conditions. They have units of distance/time.
+corresponding to a steady shock calculated from the RH
+conditions. They have units of distance/time.
 
 Restrictions
 """"""""""""
 
 This fix style is part of the SHOCK package.  It is only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` doc page for more info.
 
-All the usual restrictions for :doc:`fix npt <fix_nh>` apply,
+All the usual restrictions for :doc:`fix npt <fix_nh>` apply, plus the
-plus the additional ones mentioned above.
+additional ones mentioned above.
 
 Related commands
 """"""""""""""""

doc/src/fix_npt_asphere.rst

@@ -124,10 +124,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_npt_body.rst

@@ -45,7 +45,8 @@ can also have a bias velocity removed from them before thermostatting
 takes place; see the description below.
 
 Additional parameters affecting the thermostat and barostat are
-specified by keywords and values documented with the :doc:`fix npt <fix_nh>` command.  See, for example, discussion of the *temp*\ ,
+specified by keywords and values documented with the :doc:`fix npt
+<fix_nh>` command.  See, for example, discussion of the *temp*\ ,
 *iso*\ , *aniso*\ , and *dilate* keywords.
 
 The particles in the fix group are the only ones whose velocities and
@@ -121,10 +122,10 @@ consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_npt_cauchy.rst

@@ -487,27 +487,31 @@ compute temperature on a subset of atoms.
 .. note::
 
    If both the *temp* and *press* keywords are used in a single
-   thermo_modify command (or in two separate commands), then the order in
+   thermo_modify command (or in two separate commands), then the order
-   which the keywords are specified is important.  Note that a :doc:`pressure compute <compute_pressure>` defines its own temperature compute as
+   in which the keywords are specified is important.  Note that a
-   an argument when it is specified.  The *temp* keyword will override
+   :doc:`pressure compute <compute_pressure>` defines its own
-   this (for the pressure compute being used by fix npt), but only if the
+   temperature compute as an argument when it is specified.  The
-   *temp* keyword comes after the *press* keyword.  If the *temp* keyword
+   *temp* keyword will override this (for the pressure compute being
-   comes before the *press* keyword, then the new pressure compute
+   used by fix npt), but only if the *temp* keyword comes after the
-   specified by the *press* keyword will be unaffected by the *temp*
+   *press* keyword.  If the *temp* keyword comes before the *press*
-   setting.
+   keyword, then the new pressure compute specified by the *press*
+   keyword will be unaffected by the *temp* setting.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix, due to
-fix to add the energy change induced by Nose/Hoover thermostatting
+thermostatting and/or barostatting, is included in the
-and barostatting to the system's potential energy as part of
+:doc:`thermodynamic output <thermo_style>` keywords *ecouple* and
-:doc:`thermodynamic output <thermo_style>`.
+*econserve*.  See the :doc:`thermo_style <thermo_style>` doc page for
+details.
 
-This fix computes a global scalar and a global vector of quantities,
+This fix computes a global scalar which can be accessed by various
-which can be accessed by various :doc:`output commands <Howto_output>`.
+:doc:`output commands <Howto_output>`.  The scalar is the same
-The scalar value calculated by this fix is "extensive"; the vector
+cumulative energy change due to this fix described in the previous
+paragraph.  The scalar value calculated by this fix is "extensive".
+
+This fix also computes a global vector of quantities, which can be
+accessed by various :doc:`output commands <Howto_output>`.  Rhe vector
 values are "intensive".
 
-The scalar is the cumulative energy change due to the fix.
-
 The vector stores internal Nose/Hoover thermostat and barostat
 variables.  The number and meaning of the vector values depends on
 which fix is used and the settings for keywords *tchain* and *pchain*\ ,

doc/src/fix_npt_sphere.rst

@@ -93,13 +93,14 @@ IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
 since pressure is computed for the entire system.
 
 Note that these are NOT the computes used by thermodynamic output (see
-the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*
+the :doc:`thermo_style <thermo_style>` command) with ID =
-and *thermo_press*.  This means you can change the attributes of this
+*thermo_temp* and *thermo_press*.  This means you can change the
-fix's temperature or pressure via the
+attributes of this fix's temperature or pressure via the
-:doc:`compute_modify <compute_modify>` command or print this temperature
+:doc:`compute_modify <compute_modify>` command or print this
-or pressure during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
+temperature or pressure during thermodynamic output via the
-It also means that changing attributes of *thermo_temp* or
+:doc:`thermo_style custom <thermo_style>` command using the
-*thermo_press* will have no effect on this fix.
+appropriate compute-ID.  It also means that changing attributes of
+*thermo_temp* or *thermo_press* will have no effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
 with :doc:`compute commands <compute>` that calculate a temperature
@@ -129,18 +130,18 @@ a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* and *press* options are
-supported by this fix.  You can use them to assign a
+supported by this fix.  You can use them to assign a :doc:`compute
-:doc:`compute <compute>` you have defined to this fix which will be used
+<compute>` you have defined to this fix which will be used in its
-in its thermostatting or barostatting procedure.  If you do this, note
+thermostatting or barostatting procedure.  If you do this, note that
-that the kinetic energy derived from the compute temperature should be
+the kinetic energy derived from the compute temperature should be
 consistent with the virial term computed using all atoms for the
 pressure.  LAMMPS will warn you if you choose to compute temperature
 on a subset of atoms.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting and
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-barostatting to the system's potential energy as part of
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
-:doc:`thermodynamic output <thermo_style>`.
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix npt <fix_nh>` command.

doc/src/fix_nve.rst

@@ -1,4 +1,5 @@
 .. index:: fix nve
+.. index:: fix nve/gpu
 .. index:: fix nve/intel
 .. index:: fix nve/kk
 .. index:: fix nve/omp
@@ -6,7 +7,7 @@
 fix nve command
 ===============
 
-Accelerator Variants: *nve/intel*, *nve/kk*, *nve/omp*
+Accelerator Variants: *nve/gpu*, *nve/intel*, *nve/kk*, *nve/omp*
 
 Syntax
 """"""

doc/src/fix_nve_asphere.rst

@@ -1,10 +1,11 @@
 .. index:: fix nve/asphere
+.. index:: fix nve/asphere/gpu
 .. index:: fix nve/asphere/intel
 
 fix nve/asphere command
 =======================
 
-Accelerator Variants: *nve/asphere/intel*
+Accelerator Variants: *nve/asphere/gpu*, *nve/asphere/intel*
 
 Syntax
 """"""

doc/src/fix_nvt_asphere.rst

@@ -92,19 +92,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_body.rst

@@ -89,19 +89,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_sllod.rst

@@ -122,19 +122,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_nvt_sllod_eff.rst

@@ -41,19 +41,21 @@ velocity.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt/eff <fix_nh_eff>` command.

doc/src/fix_nvt_sphere.rst

@@ -106,19 +106,21 @@ thermal degrees of freedom, and the bias is added back in.
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-This fix writes the state of the Nose/Hoover thermostat to :doc:`binary restart files <restart>`.  See the :doc:`read_restart <read_restart>`
+This fix writes the state of the Nose/Hoover thermostat to
-command for info on how to re-specify a fix in an input script that
+:doc:`binary restart files <restart>`.  See the :doc:`read_restart
-reads a restart file, so that the operation of the fix continues in an
+<read_restart>` command for info on how to re-specify a fix in an
-uninterrupted fashion.
+input script that reads a restart file, so that the operation of the
+fix continues in an uninterrupted fashion.
 
 The :doc:`fix_modify <fix_modify>` *temp* option is supported by this
 fix.  You can use it to assign a :doc:`compute <compute>` you have
 defined to this fix which will be used in its thermostatting
 procedure.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The cumulative energy change in the system imposed by this fix is
-fix to add the energy change induced by Nose/Hoover thermostatting to
+included in the :doc:`thermodynamic output <thermo_style>` keywords
-the system's potential energy as part of :doc:`thermodynamic output <thermo_style>`.
+*ecouple* and *econserve*.  See the :doc:`thermo_style <thermo_style>`
+doc page for details.
 
 This fix computes the same global scalar and global vector of
 quantities as does the :doc:`fix nvt <fix_nh>` command.

doc/src/fix_orient.rst

@@ -144,16 +144,20 @@ writing the orientation files is given in :ref:`(Wicaksono2) <Wicaksono2>`
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
+<restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-fix to add the potential energy of atom interactions with the grain
+this fix to add the potential energy of atom interactions with the
-boundary driving force to the system's potential energy as part of
+grain boundary driving force to the global potential energy of the
-:doc:`thermodynamic output <thermo_style>`.
+system as part of :doc:`thermodynamic output <thermo_style>`.  The
+default setting for this fix is :doc:`fix_modify energy no
+<fix_modify>`.
 
-The :doc:`fix_modify <fix_modify>` *respa* option is supported by these
+The :doc:`fix_modify <fix_modify>` *respa* option is supported by
-fixes. This allows to set at which level of the :doc:`r-RESPA <run_style>`
+these fixes. This allows to set at which level of the :doc:`r-RESPA
-integrator a fix is adding its forces. Default is the outermost level.
+<run_style>` integrator a fix is adding its forces. Default is the
+outermost level.
 
 This fix calculates a global scalar which can be accessed by various
 :doc:`output commands <Howto_output>`.  The scalar is the potential
@@ -166,13 +170,16 @@ order parameter Xi and normalized order parameter (0 to 1) for each
 atom.  The per-atom values can be accessed on any timestep.
 
 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>`.
+the :doc:`run <run>` command.
+
+This fix is not invoked during :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
 This fix is part of the MISC package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 This fix should only be used with fcc or bcc lattices.
 

doc/src/fix_orient_eco.rst

@@ -26,22 +26,24 @@ Examples
 Description
 """""""""""
 
-The fix applies a synthetic driving force to a grain boundary which can
+The fix applies a synthetic driving force to a grain boundary which
-be used for the investigation of grain boundary motion. The affiliation
+can be used for the investigation of grain boundary motion. The
-of atoms to either of the two grains forming the grain boundary is
+affiliation of atoms to either of the two grains forming the grain
-determined from an orientation-dependent order parameter as described
+boundary is determined from an orientation-dependent order parameter
-in :ref:`(Ulomek) <Ulomek>`. The potential energy of atoms is either increased by an amount
+as described in :ref:`(Ulomek) <Ulomek>`. The potential energy of
-of 0.5*\ *u0* or -0.5*\ *u0* according to the orientation of the surrounding
+atoms is either increased by an amount of 0.5*\ *u0* or -0.5*\ *u0*
-crystal. This creates a potential energy gradient which pushes atoms near
+according to the orientation of the surrounding crystal. This creates
-the grain boundary to orient according to the energetically favorable
+a potential energy gradient which pushes atoms near the grain boundary
-grain orientation. This fix is designed for applications in bicrystal system
+to orient according to the energetically favorable grain
-with one grain boundary and open ends, or two opposite grain boundaries in
+orientation. This fix is designed for applications in bicrystal system
-a periodic system. In either case, the entire system can experience a
+with one grain boundary and open ends, or two opposite grain
-displacement during the simulation which needs to be accounted for in the
+boundaries in a periodic system. In either case, the entire system can
-evaluation of the grain boundary velocity. While the basic method is
+experience a displacement during the simulation which needs to be
-described in :ref:`(Ulomek) <Ulomek>`, the implementation follows the efficient
+accounted for in the evaluation of the grain boundary velocity. While
-implementation from :ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy added to an
+the basic method is described in :ref:`(Ulomek) <Ulomek>`, the
-atom j is given by the following formulas
+implementation follows the efficient implementation from
+:ref:`(Schratt & Mohles) <Schratt>`. The synthetic potential energy
+added to an atom j is given by the following formulas
 
 .. math::
 
@@ -60,60 +62,69 @@ atom j is given by the following formulas
 which are fully explained in :ref:`(Ulomek) <Ulomek>`
 and :ref:`(Schratt & Mohles) <Schratt>`.
 
-The force on each atom is the negative gradient of the synthetic potential energy. It
+The force on each atom is the negative gradient of the synthetic
-depends on the surrounding of this atom. An atom far from the grain boundary does not
+potential energy. It depends on the surrounding of this atom. An atom
-experience a synthetic force as its surrounding is that of an oriented single crystal
+far from the grain boundary does not experience a synthetic force as
-and thermal fluctuations are masked by the parameter *eta*\ . Near the grain boundary
+its surrounding is that of an oriented single crystal and thermal
-however, the gradient is nonzero and synthetic force terms are computed.
+fluctuations are masked by the parameter *eta*\ . Near the grain
-The orientationsFile specifies the perfect oriented crystal basis vectors for the
+boundary however, the gradient is nonzero and synthetic force terms
-two adjoining crystals. The first three lines (line=row vector) for the energetically penalized and the
+are computed.  The orientationsFile specifies the perfect oriented
-last three lines for the energetically favored grain assuming *u0* is positive. For
+crystal basis vectors for the two adjoining crystals. The first three
-negative *u0*, this is reversed. With the *cutoff* parameter, the size of the region around
+lines (line=row vector) for the energetically penalized and the last
-each atom which is used in the order parameter computation is defined. The cutoff must be
+three lines for the energetically favored grain assuming *u0* is
-smaller than the interaction range of the MD potential. It should at
+positive. For negative *u0*, this is reversed. With the *cutoff*
-least include the nearest neighbor shell. For high temperatures or low angle
+parameter, the size of the region around each atom which is used in
-grain boundaries, it might be beneficial to increase the cutoff in order to get a more
+the order parameter computation is defined. The cutoff must be smaller
-precise identification of the atoms surrounding. However, computation time will
+than the interaction range of the MD potential. It should at least
-increase as more atoms are considered in the order parameter and force computation.
+include the nearest neighbor shell. For high temperatures or low angle
-It is also worth noting that the cutoff radius must not exceed the communication
+grain boundaries, it might be beneficial to increase the cutoff in
-distance for ghost atoms in LAMMPS. With orientationsFile, the
+order to get a more precise identification of the atoms
-6 oriented crystal basis vectors is specified. Each line of the input file
+surrounding. However, computation time will increase as more atoms are
-contains the three components of a primitive lattice vector oriented according to
+considered in the order parameter and force computation.  It is also
-the grain orientation in the simulation box. The first (last) three lines correspond
+worth noting that the cutoff radius must not exceed the communication
-to the primitive lattice vectors of the first (second) grain. An example for
+distance for ghost atoms in LAMMPS. With orientationsFile, the 6
-a :math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
+oriented crystal basis vectors is specified. Each line of the input
-
+file contains the three components of a primitive lattice vector
-If no synthetic energy difference between the grains is created, :math:`u0=0`, the
+oriented according to the grain orientation in the simulation box. The
-force computation is omitted. In this case, still, the order parameter of the
+first (last) three lines correspond to the primitive lattice vectors
-driving force is computed and can be used to track the grain boundary motion throughout the
+of the first (second) grain. An example for a
-simulation.
+:math:`\Sigma\langle001\rangle` mis-orientation is given at the end.
-
 
+If no synthetic energy difference between the grains is created,
+:math:`u0=0`, the force computation is omitted. In this case, still,
+the order parameter of the driving force is computed and can be used
+to track the grain boundary motion throughout the simulation.
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc: `binary restart files <restart>`.
+No information about this fix is written to :doc: `binary restart
+files <restart>`.
 
-The :doc:`fix_modify <fix_modify>` *energy* option is supported by this fix to
+The :doc:`fix_modify <fix_modify>` *energy* option is supported by
-add the potential energy of atom interactions with the grain boundary
+this fix to add the potential energy of atom interactions with the
-driving force to the system's potential energy as part of thermodynamic output.
+grain boundary driving force to the global potential energy of the
-The total sum of added synthetic potential energy is computed and can be accessed
+system as part of :doc:`thermodynamic output <thermo_style>`.  The
-by various output options. The order parameter as well as the thermally masked
+default setting for this fix is :doc:`fix_modify energy no
-output parameter are stored in per-atom arrays and can also be accessed by various
+<fix_modify>`.
-:doc:`output commands <Howto_output>`.
 
-No parameter of this fix can be used with the start/stop keywords of the run command. This fix is
+This fix calculates a per-atom array with 2 columns, which can be
-not invoked during energy minimization.
+accessed by indices 1-1 by any command that uses per-atom values from
+a fix as input.  See the :doc:`Howto output <Howto_output>` doc page
+for an overview of LAMMPS output options.
 
+The first column is the order parameter for each atom; the second is
+the thermal masking value for each atom.  Both are described above.
 
+No parameter of this fix can be used with the start/stop keywords of
+the run command. This fix is not invoked during energy minimization.
 
 Restrictions
 """"""""""""
 
-This fix is part of the USER-MISC package. It is only enabled if LAMMPS was
+This fix is part of the USER-MISC package. It is only enabled if
-built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
-
+<Build_package>` doc page for more info.
 
 
 Related commands