Merge pull request #3122 from akohlmey/maintenance-2021-09-29

Third round of maintenance fixes for the stable release

.github/CODEOWNERS

@@ -83,7 +83,7 @@ src/library.*             @sjplimp
 src/main.cpp              @sjplimp
 src/min_*.*               @sjplimp
 src/memory.*              @sjplimp
-src/modify.*              @sjplimp @stanmoore1
+src/modify.*              @sjplimp
 src/molecule.*            @sjplimp
 src/my_page.h             @sjplimp
 src/my_pool_chunk.h       @sjplimp

.github/workflows/codeql-analysis.yml

@@ -3,7 +3,7 @@ name: "CodeQL Code Analysis"
 
 on:
   push:
-    branches: [develop]
+    branches: [master]
 
 jobs:
   analyze:

.github/workflows/compile-msvc.yml

@@ -1,33 +0,0 @@
-# GitHub action to build LAMMPS on Windows with Visual C++
-name: "Native Windows Compilation"
-
-on:
-  push:
-    branches: [develop]
-
-jobs:
-  build:
-    name: Windows Compilation Test
-    if: ${{ github.repository == 'lammps/lammps' }}
-    runs-on: windows-latest
-
-    steps:
-    - name: Checkout repository
-      uses: actions/checkout@v2
-      with:
-        fetch-depth: 2
-
-    - name: Building LAMMPS via CMake
-      shell: bash
-      run: |
-        cmake -C cmake/presets/windows.cmake \
-              -S cmake -B build \
-              -D BUILD_SHARED_LIBS=on \
-              -D LAMMPS_EXCEPTIONS=on
-        cmake --build build --config Release
-
-    - name: Run LAMMPS executable
-      shell: bash
-      run: |
-        ./build/Release/lmp.exe -h
-        ./build/Release/lmp.exe -in bench/in.lj

.github/workflows/unittest-macos.yml

@@ -3,7 +3,7 @@ name: "Unittest for MacOS"
 
 on:
   push:
-    branches: [develop]
+    branches: [master]
 
 jobs:
   build:

.gitignore

@@ -37,8 +37,8 @@ vgcore.*
 .Trashes
 ehthumbs.db
 Thumbs.db
+.clang-format
 .lammps_history
-.vs
 
 #cmake
 /build*
@@ -49,8 +49,3 @@ Thumbs.db
 /Testing
 /cmake_install.cmake
 /lmp
-out/Debug
-out/RelWithDebInfo
-out/Release
-out/x86
-out/x64

cmake/CMakeLists.txt

@@ -81,40 +81,22 @@ check_for_autogen_files(${LAMMPS_SOURCE_DIR})
 include(CheckIncludeFileCXX)
 
 # set required compiler flags and compiler/CPU arch specific optimizations
-if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-  if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-    if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
-      set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /Qrestrict")
-    endif()
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "/QxCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "/QxHost")
-    endif()
+if((CMAKE_CXX_COMPILER_ID STREQUAL "Intel") OR (CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM"))
+  set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
+  if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
+    set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
   else()
-    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -restrict")
-    if(CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.3 OR CMAKE_CXX_COMPILER_VERSION VERSION_EQUAL 17.4)
-      set(CMAKE_TUNE_DEFAULT "-xCOMMON-AVX512")
-    else()
-      set(CMAKE_TUNE_DEFAULT "-xHost")
-    endif()
+    set(CMAKE_TUNE_DEFAULT "-xHost")
   endif()
 endif()
 
-# we require C++11 without extensions. Kokkos requires at least C++14 (currently)
+# we require C++11 without extensions
 set(CMAKE_CXX_STANDARD 11)
-if(PKG_KOKKOS AND (CMAKE_CXX_STANDARD LESS 14))
-  set(CMAKE_CXX_STANDARD 14)
-endif()
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF CACHE BOOL "Use compiler extensions")
-# ugly hacks for MSVC which by default always reports an old C++ standard in the __cplusplus macro
-# and prints lots of pointless warnings about "unsafe" functions
+# ugly hack for MSVC which by default always reports an old C++ standard in the __cplusplus macro
 if(MSVC)
   add_compile_options(/Zc:__cplusplus)
-  add_compile_options(/wd4244)
-  add_compile_options(/wd4267)
-  add_compile_definitions(_CRT_SECURE_NO_WARNINGS)
 endif()
 
 # export all symbols when building a .dll file on windows
@@ -299,11 +281,6 @@ else()
   target_include_directories(mpi_stubs PUBLIC $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
   if(BUILD_SHARED_LIBS)
     target_link_libraries(lammps PRIVATE mpi_stubs)
-    if(MSVC)
-      target_link_libraries(lmp PRIVATE mpi_stubs)
-      target_include_directories(lmp INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
-      target_compile_definitions(lmp INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
-    endif(MSVC)
     target_include_directories(lammps INTERFACE $<BUILD_INTERFACE:${LAMMPS_SOURCE_DIR}/STUBS>)
     target_compile_definitions(lammps INTERFACE $<INSTALL_INTERFACE:LAMMPS_LIB_NO_MPI>)
   else()
@@ -491,12 +468,9 @@ foreach(HEADER cmath)
   endif(NOT FOUND_${HEADER})
 endforeach(HEADER)
 
-# make the standard math library overrideable and autodetected (for systems that don't have it)
-find_library(STANDARD_MATH_LIB m DOC "Standard Math library")
-mark_as_advanced(STANDARD_MATH_LIB)
-if(STANDARD_MATH_LIB)
-  target_link_libraries(lammps PRIVATE ${STANDARD_MATH_LIB})
-endif()
+set(MATH_LIBRARIES "m" CACHE STRING "math library")
+mark_as_advanced( MATH_LIBRARIES )
+target_link_libraries(lammps PRIVATE ${MATH_LIBRARIES})
 
 ######################################
 # Generate Basic Style files
@@ -617,12 +591,15 @@ foreach(PKG_WITH_INCL CORESHELL QEQ OPENMP DPD-SMOOTH KOKKOS OPT INTEL GPU)
 endforeach()
 
 if(PKG_PLUGIN)
-  target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
-endif()
-
-# link with -ldl or equivalent for plugin loading; except on Windows
-if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
-   target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  if(BUILD_SHARED_LIBS)
+    target_compile_definitions(lammps PRIVATE -DLMP_PLUGIN)
+  else()
+    message(WARNING "Plugin loading will not work unless BUILD_SHARED_LIBS is enabled")
+  endif()
+  # link with -ldl or equivalent for plugin loading; except on Windows
+  if(NOT ${CMAKE_SYSTEM_NAME} STREQUAL "Windows")
+    target_link_libraries(lammps PRIVATE ${CMAKE_DL_LIBS})
+  endif()
 endif()
 
 ######################################################################
@@ -631,7 +608,7 @@ endif()
 # and after everything else that is compiled locally
 ######################################################################
 if(CMAKE_SYSTEM_NAME STREQUAL "Windows")
-  target_link_libraries(lammps PRIVATE "wsock32;psapi")
+  target_link_libraries(lammps PRIVATE -lwsock32 -lpsapi)
 endif()
 
 ######################################################

cmake/CMakeSettings.json

@@ -1,55 +0,0 @@
-{
-    "configurations": [
-        {
-            "name": "x64-Debug-MSVC",
-            "generator": "Ninja",
-            "configurationType": "Debug",
-            "buildRoot": "${workspaceRoot}\\build\\${name}",
-            "installRoot": "${workspaceRoot}\\install\\${name}",
-            "cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
-            "buildCommandArgs": "",
-            "ctestCommandArgs": "",
-            "inheritEnvironments": [ "msvc_x64_x64" ],
-            "variables": [
-                {
-                    "name": "BUILD_SHARED_LIBS",
-                    "value": "True",
-                    "type": "BOOL"
-                },
-                {
-                    "name": "BUILD_TOOLS",
-                    "value": "True",
-                    "type": "BOOL"
-                },
-                {
-                    "name": "LAMMPS_EXCEPTIONS",
-                    "value": "True",
-                    "type": "BOOL"
-                }
-            ]
-        },
-        {
-            "name": "x64-Debug-Clang",
-            "generator": "Ninja",
-            "configurationType": "Debug",
-            "buildRoot": "${workspaceRoot}\\build\\${name}",
-            "installRoot": "${workspaceRoot}\\install\\${name}",
-            "cmakeCommandArgs": "-S ${workspaceRoot}\\cmake -C ${workspaceRoot}\\cmake\\presets\\windows.cmake",
-            "buildCommandArgs": "",
-            "ctestCommandArgs": "",
-            "inheritEnvironments": [ "clang_cl_x64" ],
-            "variables": [
-                {
-                    "name": "BUILD_TOOLS",
-                    "value": "True",
-                    "type": "BOOL"
-                },
-                {
-                    "name": "LAMMPS_EXCEPTIONS",
-                    "value": "True",
-                    "type": "BOOL"
-                }
-            ]
-        }
-    ]
-}

cmake/Modules/GTest.cmake

@@ -7,8 +7,8 @@ else()
 endif()
 
 include(ExternalProject)
-set(GTEST_URL "https://github.com/google/googletest/archive/release-1.11.0.tar.gz" CACHE STRING "URL of googletest source")
-set(GTEST_MD5 "e8a8df240b6938bb6384155d4c37d937" CACHE STRING "MD5 sum for googletest source")
+set(GTEST_URL "https://github.com/google/googletest/archive/release-1.10.0.tar.gz" CACHE STRING "URL for GTest tarball")
+set(GTEST_MD5 "ecd1fa65e7de707cd5c00bdac56022cd" CACHE STRING "MD5 checksum of GTest tarball")
 mark_as_advanced(GTEST_URL)
 mark_as_advanced(GTEST_MD5)
 ExternalProject_Add(googletest

cmake/Modules/LAMMPSUtils.cmake

@@ -25,7 +25,7 @@ function(validate_option name values)
 endfunction(validate_option)
 
 function(get_lammps_version version_header variable)
-    file(READ ${version_header} line)
+    file(STRINGS ${version_header} line REGEX LAMMPS_VERSION)
     set(MONTHS x Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec)
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\1" day "${line}")
     string(REGEX REPLACE "#define LAMMPS_VERSION \"([0-9]+) ([A-Za-z]+) ([0-9]+)\"" "\\2" month "${line}")
@@ -85,7 +85,7 @@ endfunction(GenerateBinaryHeader)
 
 # fetch missing potential files
 function(FetchPotentials pkgfolder potfolder)
-  if(EXISTS "${pkgfolder}/potentials.txt")
+  if (EXISTS "${pkgfolder}/potentials.txt")
     file(STRINGS "${pkgfolder}/potentials.txt" linelist REGEX "^[^#].")
     foreach(line ${linelist})
       string(FIND ${line} " " blank)

cmake/Modules/Packages/COMPRESS.cmake

@@ -1,10 +1,11 @@
 find_package(ZLIB REQUIRED)
 target_link_libraries(lammps PRIVATE ZLIB::ZLIB)
 
-find_package(PkgConfig REQUIRED)
-pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
-
-if(Zstd_FOUND)
+find_package(PkgConfig QUIET)
+if(PkgConfig_FOUND)
+  pkg_check_modules(Zstd IMPORTED_TARGET libzstd>=1.4)
+  if(Zstd_FOUND)
     target_compile_definitions(lammps PRIVATE -DLAMMPS_ZSTD)
     target_link_libraries(lammps PRIVATE PkgConfig::Zstd)
+  endif()
 endif()

cmake/Modules/Packages/GPU.cmake

@@ -30,7 +30,15 @@ file(GLOB GPU_LIB_SOURCES ${LAMMPS_LIB_SOURCE_DIR}/gpu/[^.]*.cpp)
 file(MAKE_DIRECTORY ${LAMMPS_LIB_BINARY_DIR}/gpu)
 
 if(GPU_API STREQUAL "CUDA")
-  find_package(CUDA REQUIRED)
+  find_package(CUDA QUIET)
+  # augment search path for CUDA toolkit libraries to include the stub versions. Needed to find libcuda.so on machines without a CUDA driver installation
+  if(CUDA_FOUND)
+    set(CMAKE_LIBRARY_PATH "${CUDA_TOOLKIT_ROOT_DIR}/lib64/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib/stubs;${CUDA_TOOLKIT_ROOT_DIR}/lib64;${CUDA_TOOLKIT_ROOT_DIR}/lib;${CMAKE_LIBRARY_PATH}")
+    find_package(CUDA REQUIRED)
+  else()
+    message(FATAL_ERROR "CUDA Toolkit not found")
+  endif()
+
   find_program(BIN2C bin2c)
   if(NOT BIN2C)
     message(FATAL_ERROR "Could not find bin2c, use -DBIN2C=/path/to/bin2c to help cmake finding it.")
@@ -306,12 +314,12 @@ elseif(GPU_API STREQUAL "HIP")
 
         if(HIP_COMPILER STREQUAL "clang")
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco --offload-arch=${HIP_ARCH} -O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         else()
           add_custom_command(OUTPUT ${CUBIN_FILE}
-            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -ffast-math -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
+            VERBATIM COMMAND ${HIP_HIPCC_EXECUTABLE} --genco -t="${HIP_ARCH}" -f=\"-O3 -DUSE_HIP -D_${GPU_PREC_SETTING} -DLAMMPS_${LAMMPS_SIZES} -I${LAMMPS_LIB_SOURCE_DIR}/gpu\" -o ${CUBIN_FILE} ${CU_CPP_FILE}
             DEPENDS ${CU_CPP_FILE}
             COMMENT "Generating ${CU_NAME}.cubin")
         endif()

cmake/Modules/Packages/KOKKOS.cmake

@@ -1,7 +1,7 @@
 ########################################################################
 # As of version 3.3.0 Kokkos requires C++14
 if(CMAKE_CXX_STANDARD LESS 14)
-  message(FATAL_ERROR "The KOKKOS package requires the C++ standard to be set to at least C++14")
+  set(CMAKE_CXX_STANDARD 14)
 endif()
 ########################################################################
 # consistency checks and Kokkos options/settings required by LAMMPS

cmake/Modules/Packages/MACHDYN.cmake

@@ -8,7 +8,7 @@ option(DOWNLOAD_EIGEN3 "Download Eigen3 instead of using an already installed on
 if(DOWNLOAD_EIGEN3)
   message(STATUS "Eigen3 download requested - we will build our own")
 
-  set(EIGEN3_URL "${LAMMPS_THIRDPARTY_URL}/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
+  set(EIGEN3_URL "https://download.lammps.org/thirdparty/eigen-3.4.0.tar.gz" CACHE STRING "URL for Eigen3 tarball")
   set(EIGEN3_MD5 "4c527a9171d71a72a9d4186e65bea559" CACHE STRING "MD5 checksum of Eigen3 tarball")
   mark_as_advanced(EIGEN3_URL)
   mark_as_advanced(EIGEN3_MD5)

cmake/Modules/Packages/ML-PACE.cmake

@@ -1,11 +1,11 @@
-set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.10.25.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
 
-set(PACELIB_MD5 "a2ac3315c41a1a4a5c912bcb1bc9c5cc" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
+set(PACELIB_URL "https://github.com/ICAMS/lammps-user-pace/archive/refs/tags/v.2021.4.9.tar.gz" CACHE STRING "URL for PACE evaluator library sources")
+set(PACELIB_MD5 "4db54962fbd6adcf8c18d46e1798ceb5" CACHE STRING "MD5 checksum of PACE evaluator library tarball")
 mark_as_advanced(PACELIB_URL)
 mark_as_advanced(PACELIB_MD5)
 
 # download library sources to build folder
-file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz EXPECTED_HASH MD5=${PACELIB_MD5}) #SHOW_PROGRESS
+file(DOWNLOAD ${PACELIB_URL} ${CMAKE_BINARY_DIR}/libpace.tar.gz SHOW_PROGRESS EXPECTED_HASH MD5=${PACELIB_MD5})
 
 # uncompress downloaded sources
 execute_process(
@@ -14,19 +14,12 @@ execute_process(
   WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
 )
 
-file(GLOB lib-pace ${CMAKE_BINARY_DIR}/lammps-user-pace-*)
-add_subdirectory(${lib-pace}/yaml-cpp build-yaml-cpp)
-set(YAML_CPP_INCLUDE_DIR ${lib-pace}/yaml-cpp/include)
-
-file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${lib-pace}/ML-PACE)
-file(GLOB PACE_EVALUATOR_SOURCES ${lib-pace}/ML-PACE/*.cpp)
+file(GLOB PACE_EVALUATOR_INCLUDE_DIR ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE)
+file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PACE/*.cpp)
 list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
 
 add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
 set_target_properties(pace PROPERTIES CXX_EXTENSIONS ON OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
-target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR})
-
-
-target_link_libraries(pace PRIVATE yaml-cpp-pace)
-
+target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
 target_link_libraries(lammps PRIVATE pace)
+

cmake/Modules/Packages/ML-QUIP.cmake

@@ -32,7 +32,8 @@ if(DOWNLOAD_QUIP)
   foreach(flag ${LAPACK_LIBRARIES})
     set(temp "${temp} ${flag}")
   endforeach()
-  set(temp "${temp}\n")
+  # Fix cmake crashing when MATH_LINKOPTS not set, required for e.g. recent Cray Programming Environment
+  set(temp "${temp} -L/_DUMMY_PATH_\n")
   set(temp "${temp}PYTHON=python\nPIP=pip\nEXTRA_LINKOPTS=\n")
   set(temp "${temp}HAVE_CP2K=0\nHAVE_VASP=0\nHAVE_TB=0\nHAVE_PRECON=1\nHAVE_LOTF=0\nHAVE_ONIOM=0\n")
   set(temp "${temp}HAVE_LOCAL_E_MIX=0\nHAVE_QC=0\nHAVE_GAP=1\nHAVE_DESCRIPTORS_NONCOMMERCIAL=1\n")
@@ -50,6 +51,7 @@ if(DOWNLOAD_QUIP)
     GIT_TAG origin/public
     GIT_SHALLOW YES
     GIT_PROGRESS YES
+    GIT_SUBMODULES "src/fox;src/GAP"
     PATCH_COMMAND ${CMAKE_COMMAND} -E copy_if_different ${CMAKE_BINARY_DIR}/quip.config <SOURCE_DIR>/arch/Makefile.lammps
     CONFIGURE_COMMAND env QUIP_ARCH=lammps make config
     BUILD_COMMAND env QUIP_ARCH=lammps make libquip

cmake/Modules/Packages/PLUMED.cmake

@@ -54,8 +54,8 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.2/plumed-src-2.7.2.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "cfa0b4dd90a81c25d3302e8d97bfeaea" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.4/plumed-src-2.7.4.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_MD5 "858e0b6aed173748fc85b6bc8a9dcb3e" CACHE STRING "MD5 checksum of PLUMED tarball")
 
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)

cmake/Modules/Tools.cmake

@@ -25,9 +25,7 @@ if(BUILD_TOOLS)
   get_filename_component(MSI2LMP_SOURCE_DIR ${LAMMPS_TOOLS_DIR}/msi2lmp/src ABSOLUTE)
   file(GLOB MSI2LMP_SOURCES ${MSI2LMP_SOURCE_DIR}/[^.]*.c)
   add_executable(msi2lmp ${MSI2LMP_SOURCES})
-  if(STANDARD_MATH_LIB)
-    target_link_libraries(msi2lmp PRIVATE ${STANDARD_MATH_LIB})
-  endif()
+  target_link_libraries(msi2lmp PRIVATE ${MATH_LIBRARIES})
   install(TARGETS msi2lmp DESTINATION ${CMAKE_INSTALL_BINDIR})
   install(FILES ${LAMMPS_DOC_DIR}/msi2lmp.1 DESTINATION ${CMAKE_INSTALL_MANDIR}/man1)
 endif()

cmake/presets/most.cmake

@@ -48,7 +48,6 @@ set(ALL_PACKAGES
   PHONON
   PLUGIN
   POEMS
-  PYTHON
   QEQ
   REACTION
   REAXFF

cmake/presets/windows.cmake

@@ -1,64 +0,0 @@
-set(WIN_PACKAGES
-  ASPHERE
-  BOCS
-  BODY
-  BROWNIAN
-  CG-DNA
-  CG-SDK
-  CLASS2
-  COLLOID
-  COLVARS
-  CORESHELL
-  DIELECTRIC
-  DIFFRACTION
-  DIPOLE
-  DPD-BASIC
-  DPD-MESO
-  DPD-REACT
-  DPD-SMOOTH
-  DRUDE
-  EFF
-  EXTRA-COMPUTE
-  EXTRA-DUMP
-  EXTRA-FIX
-  EXTRA-MOLECULE
-  EXTRA-PAIR
-  FEP
-  GRANULAR
-  INTERLAYER
-  KSPACE
-  MANIFOLD
-  MANYBODY
-  MC
-  MEAM
-  MISC
-  ML-IAP
-  ML-SNAP
-  MOFFF
-  MOLECULE
-  MOLFILE
-  OPENMP
-  ORIENT
-  PERI
-  PHONON
-  POEMS
-  PTM
-  QEQ
-  QTB
-  REACTION
-  REAXFF
-  REPLICA
-  RIGID
-  SHOCK
-  SMTBQ
-  SPH
-  SPIN
-  SRD
-  TALLY
-  UEF
-  YAFF)
-
-foreach(PKG ${WIN_PACKAGES})
-  set(PKG_${PKG} ON CACHE BOOL "" FORCE)
-endforeach()
-

doc/Makefile

@@ -230,7 +230,7 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.2.0 -c advice.detachedHead=0 --depth 1 https://github.com/mathjax/MathJax.git $@
 
 $(ANCHORCHECK): $(VENV)
 	@( \

doc/doxygen/Doxyfile.in

@@ -435,8 +435,6 @@ INPUT                  = @LAMMPS_SOURCE_DIR@/utils.cpp                 \
                          @LAMMPS_SOURCE_DIR@/my_pool_chunk.cpp         \
                          @LAMMPS_SOURCE_DIR@/my_pool_chunk.h           \
                          @LAMMPS_SOURCE_DIR@/math_eigen.h              \
-                         @LAMMPS_SOURCE_DIR@/platform.h                \
-                         @LAMMPS_SOURCE_DIR@/platform.cpp              \
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

doc/lammps.1

@@ -1,4 +1,4 @@
-.TH LAMMPS "1" "27 October 2021" "2021-10-27"
+.TH LAMMPS "29 September 2021" "2021-09-29"
 .SH NAME
 .B LAMMPS
 \- Molecular Dynamics Simulator.

doc/msi2lmp.1

@@ -1,4 +1,4 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "v3.9.9" "2018-11-05"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS

doc/src/Build_settings.rst

@@ -321,7 +321,9 @@ following settings:
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_JPEG -DLAMMPS_PNG -DLAMMPS_FFMPEG  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_JPEG
+         LMP_INC = -DLAMMPS_PNG
+         LMP_INC = -DLAMMPS_FFMPEG
 
          JPG_INC = -I/usr/local/include   # path to jpeglib.h, png.h, zlib.h header files if make cannot find them
          JPG_PATH = -L/usr/lib            # paths to libjpeg.a, libpng.a, libz.a (.so) files if make cannot find them
@@ -352,10 +354,8 @@ Read or write compressed files
 -----------------------------------------
 
 If this option is enabled, large files can be read or written with
-compression by ``gzip`` or similar tools by several LAMMPS commands,
-including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
-:doc:`dump <dump>`.  Currently supported compression tools are:
-``gzip``, ``bzip2``, ``zstd``, and ``lzma``.
+gzip compression by several LAMMPS commands, including
+:doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and :doc:`dump <dump>`.
 
 .. tabs::
 
@@ -364,23 +364,23 @@ including :doc:`read_data <read_data>`, :doc:`rerun <rerun>`, and
       .. code-block:: bash
 
          -D WITH_GZIP=value       # yes or no
-                                  # default is yes if CMake can find the gzip program, else no
+                                  # default is yes if CMake can find gzip, else no
+         -D GZIP_EXECUTABLE=path  # path to gzip executable if CMake cannot find it
 
    .. tab:: Traditional make
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_GZIP   <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_GZIP
 
-This option requires that your operating system fully supports the
-"popen()" function in the standard runtime library and that a ``gzip``
-or other executable can be found by LAMMPS in the standard search path
-during a run.
+This option requires that your operating system fully supports the "popen()"
+function in the standard runtime library and that a ``gzip`` executable can be
+found by LAMMPS during a run.
 
 .. note::
 
-   On clusters with high-speed networks, using the "fork()" library call
-   (required by "popen()") can interfere with the fast communication
+   On some clusters with high-speed networks, using the "fork()" library
+   call (required by "popen()") can interfere with the fast communication
    library and lead to simulations using compressed output or input to
    hang or crash. For selected operations, compressed file I/O is also
    available using a compression library instead, which is what the
@@ -452,7 +452,7 @@ those systems:
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_LONGLONG_TO_LONG  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_LONGLONG_TO_LONG
 
 ----------
 
@@ -479,7 +479,7 @@ e.g. to Python. Of course, the calling code has to be set up to
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_EXCEPTIONS   <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_EXCEPTIONS
 
 .. note::
 
@@ -520,7 +520,7 @@ executable, not the library.
 
       .. code-block:: make
 
-         LMP_INC = -DLAMMPS_TRAP_FPE  <other LMP_INC settings>
+         LMP_INC = -DLAMMPS_TRAP_FPE
 
 After compilation with this flag set, the LAMMPS executable will stop
 and produce a core dump when a division by zero, overflow, illegal math

doc/src/Build_windows.rst

@@ -4,7 +4,6 @@ Notes for building LAMMPS on Windows
 * :ref:`General remarks <generic>`
 * :ref:`Running Linux on Windows <linux>`
 * :ref:`Using GNU GCC ported to Windows <gnu>`
-* :ref:`Using Visual Studio <msvc>`
 * :ref:`Using a cross-compiler <cross>`
 
 ----------
@@ -32,13 +31,13 @@ pre-compiled Windows binary packages are sufficient for your needs.  If
 it is necessary for you to compile LAMMPS on a Windows machine
 (e.g. because it is your main desktop), please also consider using a
 virtual machine software and compile and run LAMMPS in a Linux virtual
-machine, or - if you have a sufficiently up-to-date Windows 10 or
-Windows 11 installation - consider using the Windows subsystem for
-Linux.  This optional Windows feature allows you to run the bash shell
-from Ubuntu from within Windows and from there on, you can pretty much
-use that shell like you are running on an Ubuntu Linux machine
-(e.g. installing software via apt-get and more).  For more details on
-that, please see :doc:`this tutorial <Howto_wsl>`.
+machine, or - if you have a sufficiently up-to-date Windows 10
+installation - consider using the Windows subsystem for Linux.  This
+optional Windows feature allows you to run the bash shell from Ubuntu
+from within Windows and from there on, you can pretty much use that
+shell like you are running on an Ubuntu Linux machine (e.g. installing
+software via apt-get and more).  For more details on that, please see
+:doc:`this tutorial <Howto_wsl>`.
 
 .. _gnu:
 
@@ -68,35 +67,6 @@ requiring changes to the LAMMPS source code, or figure out corrections
 yourself, please report them on the lammps-users mailing list, or file
 them as an issue or pull request on the LAMMPS GitHub project.
 
-.. _msvc:
-
-Using Microsoft Visual Studio
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-Following the integration of the :doc:`platform namespace
-<Developer_platform>` into the LAMMPS code base, portability of LAMMPS
-to be compiled on Windows using Visual Studio has been significantly
-improved.  This has been tested with Visual Studio 2019 (aka version
-16).  Not all features and packages in LAMMPS are currently supported
-out of the box, but a preset ``cmake/presets/windows.cmake`` is provided
-that contains the packages that have been compiled successfully.  You
-must use the CMake based build procedure, and either use the integrated
-CMake support of Visual Studio or use an external CMake installation to
-create build files for the Visual Studio build system.  Please note that
-on launching Visual Studio it will scan the directory tree and likely
-miss the correct master ``CMakeLists.txt``.  Try to open the
-``cmake/CMakeSettings.json`` and use those CMake configurations as a
-starting point.  It is also possible to configure and compile LAMMPS
-from the command line with a CMake binary from `cmake.org <https://cmake.org>`_.
-
-To support running in parallel you can compile with OpenMP enabled using
-the OPENMP package or install Microsoft MPI (including the SDK) and compile
-LAMMPS with MPI enabled.
-
-This is work in progress and you should contact the LAMMPS developers
-via GitHub, the forum, or the mailing list, if you have questions or
-LAMMPS specific problems.
-
 .. _cross:
 
 Using a cross-compiler

doc/src/Commands_fix.rst

@@ -23,7 +23,6 @@ OPT.
    :columns: 5
 
    * :doc:`accelerate/cos <fix_accelerate_cos>`
-   * :doc:`acks2/reaxff (k) <fix_acks2_reaxff>`
    * :doc:`adapt <fix_adapt>`
    * :doc:`adapt/fep <fix_adapt_fep>`
    * :doc:`addforce <fix_addforce>`
@@ -104,7 +103,6 @@ OPT.
    * :doc:`manifoldforce <fix_manifoldforce>`
    * :doc:`mdi/engine <fix_mdi_engine>`
    * :doc:`meso/move <fix_meso_move>`
-   * :doc:`mol/swap <fix_mol_swap>`
    * :doc:`momentum (k) <fix_momentum>`
    * :doc:`momentum/chunk <fix_momentum>`
    * :doc:`move <fix_move>`

doc/src/Developer.rst

@@ -18,5 +18,4 @@ of time and requests from the LAMMPS user community.
    Developer_plugins
    Developer_unittest
    Classes
-   Developer_platform
    Developer_utils

doc/src/Developer_platform.rst

@@ -1,152 +0,0 @@
-Platform abstraction functions
-------------------------------
-
-The ``platform`` sub-namespace inside the ``LAMMPS_NS`` namespace
-provides a collection of wrapper and convenience functions and utilities
-that perform common tasks for which platform specific code would be
-required or for which a more high-level abstraction would be convenient
-and reduce duplicated code.  This reduces redundant implementations and
-encourages consistent behavior and thus has some overlap with the
-:doc:`"utils" sub-namespace <Developer_utils>`.
-
-Time functions
-^^^^^^^^^^^^^^
-
-.. doxygenfunction:: cputime
-   :project: progguide
-
-.. doxygenfunction:: walltime
-   :project: progguide
-
-.. doxygenfunction:: usleep
-   :project: progguide
-
-Platform information functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: os_info
-   :project: progguide
-
-.. doxygenfunction:: compiler_info
-   :project: progguide
-
-.. doxygenfunction:: cxx_standard
-   :project: progguide
-
-.. doxygenfunction:: openmp_standard
-   :project: progguide
-
-.. doxygenfunction:: mpi_vendor
-   :project: progguide
-
-.. doxygenfunction:: mpi_info
-   :project: progguide
-
-.. doxygenfunction:: compress_info
-   :project: progguide
-
-
-File and path functions and global constants
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenvariable:: filepathsep
-   :project: progguide
-
-.. doxygenvariable:: pathvarsep
-   :project: progguide
-
-.. doxygenfunction:: guesspath
-   :project: progguide
-
-.. doxygenfunction:: path_basename
-   :project: progguide
-
-.. doxygenfunction:: path_join
-   :project: progguide
-
-.. doxygenfunction:: file_is_readable
-   :project: progguide
-
-.. doxygenfunction:: is_console
-   :project: progguide
-
-.. doxygenfunction:: path_is_directory
-   :project: progguide
-
-.. doxygenfunction:: current_directory
-   :project: progguide
-
-.. doxygenfunction:: list_directory
-   :project: progguide
-
-.. doxygenfunction:: chdir
-   :project: progguide
-
-.. doxygenfunction:: mkdir
-   :project: progguide
-
-.. doxygenfunction:: rmdir
-   :project: progguide
-
-.. doxygenfunction:: unlink
-   :project: progguide
-
-Standard I/O function wrappers
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenvariable:: END_OF_FILE
-   :project: progguide
-
-.. doxygenfunction:: ftell
-   :project: progguide
-
-.. doxygenfunction:: fseek
-   :project: progguide
-
-.. doxygenfunction:: ftruncate
-   :project: progguide
-
-.. doxygenfunction:: popen
-   :project: progguide
-
-.. doxygenfunction:: pclose
-   :project: progguide
-
-Environment variable functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: putenv
-   :project: progguide
-
-.. doxygenfunction:: list_pathenv
-   :project: progguide
-
-.. doxygenfunction:: find_exe_path
-   :project: progguide
-
-Dynamically loaded object or library functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: dlopen
-   :project: progguide
-
-.. doxygenfunction:: dlclose
-   :project: progguide
-
-.. doxygenfunction:: dlsym
-   :project: progguide
-
-.. doxygenfunction:: dlerror
-   :project: progguide
-
-Compressed file I/O functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. doxygenfunction:: has_compress_extension
-   :project: progguide
-
-.. doxygenfunction:: compressed_read
-   :project: progguide
-
-.. doxygenfunction:: compressed_write
-   :project: progguide

doc/src/Developer_utils.rst

@@ -7,9 +7,7 @@ a collection of convenience functions and utilities that perform common
 tasks that are required repeatedly throughout the LAMMPS code like
 reading or writing to files with error checking or translation of
 strings into specific types of numbers with checking for validity.  This
-reduces redundant implementations and encourages consistent behavior and
-thus has some overlap with the :doc:`"platform" sub-namespace
-<Developer_platform>`.
+reduces redundant implementations and encourages consistent behavior.
 
 I/O with status check and similar functions
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
@@ -62,9 +60,6 @@ silently returning the result of a partial conversion or zero in cases
 where the string is not a valid number.  This behavior allows to more
 easily detect typos or issues when processing input files.
 
-Similarly the :cpp:func:`logical() <LAMMPS_NS::utils::logical>` function
-will convert a string into a boolean and will only accept certain words.
-
 The *do_abort* flag should be set to ``true`` in case  this function
 is called only on a single MPI rank, as that will then trigger the
 a call to ``Error::one()`` for errors instead of ``Error::all()``
@@ -88,9 +83,6 @@ strings for compliance without conversion.
 .. doxygenfunction:: tnumeric
    :project: progguide
 
-.. doxygenfunction:: logical
-   :project: progguide
-
 
 String processing
 ^^^^^^^^^^^^^^^^^
@@ -103,12 +95,6 @@ and parsing files or arguments.
 .. doxygenfunction:: strdup
    :project: progguide
 
-.. doxygenfunction:: lowercase
-   :project: progguide
-
-.. doxygenfunction:: uppercase
-   :project: progguide
-
 .. doxygenfunction:: trim
    :project: progguide
 
@@ -151,6 +137,21 @@ and parsing files or arguments.
 .. doxygenfunction:: is_double
    :project: progguide
 
+File and path functions
+^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. doxygenfunction:: guesspath
+   :project: progguide
+
+.. doxygenfunction:: path_basename
+   :project: progguide
+
+.. doxygenfunction:: path_join
+   :project: progguide
+
+.. doxygenfunction:: file_is_readable
+   :project: progguide
+
 Potential file functions
 ^^^^^^^^^^^^^^^^^^^^^^^^
 

doc/src/Developer_write.rst

@@ -29,9 +29,7 @@ of code in the header before include guards:
 .. code-block:: c
 
    #ifdef FIX_CLASS
-   // clang-format off
-   FixStyle(print/vel,FixPrintVel);
-   // clang-format on
+   FixStyle(print/vel,FixPrintVel)
    #else
    /* the definition of the FixPrintVel class comes here */
    ...
@@ -55,7 +53,7 @@ of each timestep. First of all, implement a constructor:
      if (narg < 4)
        error->all(FLERR,"Illegal fix print/vel command");
 
-     nevery = force->inumeric(FLERR,arg[3]);
+     nevery = utils::inumeric(FLERR,arg[3],false,lmp);
      if (nevery <= 0)
        error->all(FLERR,"Illegal fix print/vel command");
    }

doc/src/Examples.rst

@@ -80,7 +80,7 @@ Lowercase directories
 +-------------+------------------------------------------------------------------+
 | friction    | frictional contact of spherical asperities between 2d surfaces   |
 +-------------+------------------------------------------------------------------+
-| mc          | Monte Carlo features via fix gcmc, widom and other commands      |
+| gcmc        | Grand Canonical Monte Carlo (GCMC) via the fix gcmc command      |
 +-------------+------------------------------------------------------------------+
 | granregion  | use of fix wall/region/gran as boundary on granular particles    |
 +-------------+------------------------------------------------------------------+
@@ -205,7 +205,7 @@ Uppercase directories
 +------------+--------------------------------------------------------------------------------------------------+
 | KAPPA      | compute thermal conductivity via several methods                                                 |
 +------------+--------------------------------------------------------------------------------------------------+
-| MC-LOOP    | using LAMMPS in a Monte Carlo mode to relax the energy of a system in a input script loop        |
+| MC         | using LAMMPS in a Monte Carlo mode to relax the energy of a system                               |
 +------------+--------------------------------------------------------------------------------------------------+
 | PACKAGES   | examples for specific packages and contributed commands                                          |
 +------------+--------------------------------------------------------------------------------------------------+

doc/src/Howto_github.rst

@@ -141,7 +141,8 @@ unrelated feature, you should switch branches!
    Committing changes to the *develop*, *release*, or *stable* branches
    is strongly discouraged.  While it may be convenient initially, it
    will create more work in the long run.  Various texts and tutorials
-   on using git effectively discuss the motivation for this.
+   on using git effectively discuss the motivation for using feature
+   branches instead.
 
 **After changes are made**
 

doc/src/Howto_thermostat.rst

@@ -2,8 +2,8 @@ Thermostats
 ===========
 
 Thermostatting means controlling the temperature of particles in an MD
-simulation.  :doc:`Barostatting <Howto_barostat>` means controlling
-the pressure.  Since the pressure includes a kinetic component due to
+simulation.  :doc:`Barostatting <Howto_barostat>` means controlling the
+pressure.  Since the pressure includes a kinetic component due to
 particle velocities, both these operations require calculation of the
 temperature.  Typically a target temperature (T) and/or pressure (P)
 is specified by the user, and the thermostat or barostat attempts to
@@ -26,13 +26,11 @@ can be invoked via the *dpd/tstat* pair style:
 * :doc:`pair_style dpd/tstat <pair_dpd>`
 
 :doc:`Fix nvt <fix_nh>` only thermostats the translational velocity of
-particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this,
-except that it subtracts out a velocity bias due to a deforming box
-and integrates the SLLOD equations of motion.  See the :doc:`Howto
-nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere
-<fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>`
-thermostat not only translation velocities but also rotational
-velocities for spherical and aspherical particles.
+particles.  :doc:`Fix nvt/sllod <fix_nvt_sllod>` also does this, except
+that it subtracts out a velocity bias due to a deforming box and
+integrates the SLLOD equations of motion.  See the :doc:`Howto nemd <Howto_nemd>` page for further details.  :doc:`Fix nvt/sphere <fix_nvt_sphere>` and :doc:`fix nvt/asphere <fix_nvt_asphere>` thermostat not only translation
+velocities but also rotational velocities for spherical and aspherical
+particles.
 
 .. note::
 
@@ -42,31 +40,25 @@ velocities for spherical and aspherical particles.
    e.g. molecular systems.  The latter can be tricky to do correctly.
 
 DPD thermostatting alters pairwise interactions in a manner analogous
-to the per-particle thermostatting of :doc:`fix langevin
-<fix_langevin>`.
+to the per-particle thermostatting of :doc:`fix langevin <fix_langevin>`.
 
-Any of the thermostatting fixes can be instructed to use custom
-temperature computes that remove bias which has two effects: first,
-the current calculated temperature, which is compared to the requested
-target temperature, is calculated with the velocity bias removed;
-second, the thermostat adjusts only the thermal temperature component
-of the particle's velocities, which are the velocities with the bias
-removed.  The removed bias is then added back to the adjusted
-velocities.  See the doc pages for the individual fixes and for the
-:doc:`fix_modify <fix_modify>` command for instructions on how to
-assign a temperature compute to a thermostatting fix.
+Any of the thermostatting fixes can be instructed to use custom temperature
+computes that remove bias which has two effects:  first, the current
+calculated temperature, which is compared to the requested target temperature,
+is calculated with the velocity bias removed;  second, the thermostat adjusts
+only the thermal temperature component of the particle's velocities, which are
+the velocities with the bias removed.  The removed bias is then added back
+to the adjusted velocities.  See the doc pages for the individual
+fixes and for the :doc:`fix_modify <fix_modify>` command for
+instructions on how to assign a temperature compute to a
+thermostatting fix.  For example, you can apply a thermostat to only
+the x and z components of velocity by using it in conjunction with
+:doc:`compute temp/partial <compute_temp_partial>`.  Of you could
+thermostat only the thermal temperature of a streaming flow of
+particles without affecting the streaming velocity, by using
+:doc:`compute temp/profile <compute_temp_profile>`.
 
-For example, you can apply a thermostat only to atoms in a spatial
-region by using it in conjunction with :doc:`compute temp/region
-<compute_temp_region>`.  Or you can apply a thermostat to only the x
-and z components of velocity by using it with :doc:`compute
-temp/partial <compute_temp_partial>`.  Of you could thermostat only
-the thermal temperature of a streaming flow of particles without
-affecting the streaming velocity, by using :doc:`compute temp/profile
-<compute_temp_profile>`.
-
-Below is a list of custom temperature computes that can be used like
-that:
+Below is a list of some custom temperature computes that can be used like that:
 
 * :doc:`compute_temp_asphere`
 * :doc:`compute_temp_body`
@@ -80,6 +72,8 @@ that:
 * :doc:`compute_temp_rotate`
 * :doc:`compute_temp_sphere`
 
+
+
 .. note::
 
    Only the nvt fixes perform time integration, meaning they update
@@ -92,17 +86,17 @@ that:
 * :doc:`fix nve/sphere <fix_nve_sphere>`
 * :doc:`fix nve/asphere <fix_nve_asphere>`
 
-Thermodynamic output, which can be setup via the :doc:`thermo_style
-<thermo_style>` command, often includes temperature values.  As
-explained on the page for the :doc:`thermo_style <thermo_style>`
-command, the default temperature is setup by the thermo command
-itself.  It is NOT the temperature associated with any thermostatting
-fix you have defined or with any compute you have defined that
-calculates a temperature.  The doc pages for the thermostatting fixes
-explain the ID of the temperature compute they create.  Thus if you
-want to view these temperatures, you need to specify them explicitly
-via the :doc:`thermo_style custom <thermo_style>` command.  Or you can
-use the :doc:`thermo_modify <thermo_modify>` command to re-define what
+Thermodynamic output, which can be setup via the
+:doc:`thermo_style <thermo_style>` command, often includes temperature
+values.  As explained on the page for the
+:doc:`thermo_style <thermo_style>` command, the default temperature is
+setup by the thermo command itself.  It is NOT the temperature
+associated with any thermostatting fix you have defined or with any
+compute you have defined that calculates a temperature.  The doc pages
+for the thermostatting fixes explain the ID of the temperature compute
+they create.  Thus if you want to view these temperatures, you need to
+specify them explicitly via the :doc:`thermo_style custom <thermo_style>` command.  Or you can use the
+:doc:`thermo_modify <thermo_modify>` command to re-define what
 temperature compute is used for default thermodynamic output.
 
 ----------

doc/src/Install_git.rst

@@ -28,8 +28,9 @@ provides `limited support for subversion clients <svn_>`_.
 
 You can follow the LAMMPS development on 3 different git branches:
 
-* **stable**   :  this branch is updated with every stable release;
-  updates are always "fast forward" merges from *develop*
+* **stable**   :  this branch is updated from the *release* branch with
+  every stable release version and also has selected bug fixes and updates
+  back-ported from the *develop* branch
 * **release**  :  this branch is updated with every patch release;
   updates are always "fast forward" merges from *develop*
 * **develop**  :  this branch follows the ongoing development and
@@ -47,20 +48,22 @@ your machine and "release" is one of the 3 branches listed above.
 (Note that you actually download all 3 branches; you can switch
 between them at any time using "git checkout <branch name>".)
 
-.. note::
+.. admonition:: Saving time and disk space when using ``git clone``
 
    The complete git history of the LAMMPS project is quite large because
    it contains the entire commit history of the project since fall 2006,
-   which includes the time when LAMMPS was managed with subversion. This
-   also includes commits that have added and removed some large files
-   (mostly by accident).  If you do not need access to the entire commit
-   history, you can speed up the "cloning" process and reduce local disk
-   space requirements by using the *--depth* git command line flag thus
-   create a "shallow clone" of the repository that contains only a
-   subset of the git history. Using a depth of 1000 is usually sufficient
-   to include the head commits of the *develop* and the *release* branches.
-   To include the head commit of the *stable* branch you may need a depth
-   of up to 10000.
+   which includes the time when LAMMPS was managed with subversion.
+   This includes a few commits that have added and removed some large
+   files (mostly by accident).  If you do not need access to the entire
+   commit history (most people don't), you can speed up the "cloning"
+   process and reduce local disk space requirements by using the
+   *--depth* git command line flag.  That will create a "shallow clone"
+   of the repository containing only a subset of the git history.  Using
+   a depth of 1000 is usually sufficient to include the head commits of
+   the *develop* and the *release* branches.  To include the head commit
+   of the *stable* branch you may need a depth of up to 10000.  If you
+   later need more of the git history, you can always convert the
+   shallow clone into a "full clone".
 
 Once the command completes, your directory will contain the same files
 as if you unpacked a current LAMMPS tarball, with the exception, that
@@ -156,9 +159,9 @@ changed.  How to do this depends on the build system you are using.
 .. admonition:: Git protocols
    :class: note
 
-   The servers at github.com support the "git://" and "https://" access
-   protocols for anonymous, read-only access.  If you have a suitably
-   configured GitHub account, you may also use SSH protocol with the
+   The servers at github.com support the "https://" access protocol for
+   anonymous, read-only access.  If you have a suitably configured GitHub
+   account, you may also use SSH protocol with the
    URL "git@github.com:lammps/lammps.git".
 
 The LAMMPS GitHub project is currently managed by Axel Kohlmeyer

doc/src/Intro_citing.rst

@@ -16,7 +16,7 @@ source code design, the program structure, the spatial decomposition
 approach, the neighbor finding, basic communications algorithms, and how
 users and developers have contributed to LAMMPS is:
 
-  `LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. (accepted 09/2021), DOI:10.1016/j.cpc.2021.108171 <https://doi.org/10.1016/j.cpc.2021.108171>`_
+  `LAMMPS - A flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales, Comp. Phys. Comm. 271, 108171 (2022) <https://doi.org/10.1016/j.cpc.2021.108171>`_
 
 So a project using LAMMPS or a derivative application that uses LAMMPS
 as a simulation engine should cite this paper.  The paper is expected to

doc/src/Manual_version.rst

@@ -10,23 +10,31 @@ Whenever we fix a bug or update or add a feature, it will be merged into
 the *develop* branch of the git repository.  When a sufficient number of
 changes have accumulated *and* the software passes a set of automated
 tests, we release it in the next *patch* release, which are made every
-few weeks.  Info on patch releases are on `this website page
+few weeks.  The *release* branch of the git repository is updated with
+every such release.  Info on patch releases are on `this website page
 <https://www.lammps.org/bug.html>`_.
 
-Once or twice a year, only bug fixes and small, non-intrusive changes are
-included for a period of time, and the code is subjected to more detailed
+Once or twice a year, we apply only bug fixes and small, non-intrusive
+changes to the *develop* branch and the code is subjected to more detailed
 and thorough testing than the default automated testing.  The latest
-patch release after such a period is then labeled as a *stable* version.
+patch release after such a period is then also labeled as a *stable* version
+and the *stable* branch is updated with it.  Between stable releases
+we occasionally release some updates to the stable release containing
+only bug fixes and updates back-ported from *develop* but no new features
+and update the *stable* branch accordingly.
 
-Each version of LAMMPS contains all the features and bug-fixes up to
-and including its version date.
+Each version of LAMMPS contains all the documented features up to and
+including its version date.
 
 The version date is printed to the screen and logfile every time you
 run LAMMPS. It is also in the file src/version.h and in the LAMMPS
 directory name created when you unpack a tarball.  And it is on the
 first page of the :doc:`manual <Manual>`.
 
-* If you browse the HTML pages on the LAMMPS WWW site, they always
-  describe the most current patch release of LAMMPS.
+* If you browse the HTML pages on the LAMMPS WWW site, they will by
+  default describe the most current patch release version of LAMMPS.
+  In the navigation bar on the bottom left, there is the option to
+  view instead the documentation for the most recent *stable* version
+  or the latest version from the current development branch.
 * If you browse the HTML pages included in your tarball, they
   describe the version you have, which may be older.

doc/src/Modify_pair.rst

@@ -12,24 +12,24 @@ includes some optional methods to enable its use with rRESPA.
 
 Here is a brief description of the class methods in pair.h:
 
-+---------------------------------+-------------------------------------------------------------------+
-| compute                         | workhorse routine that computes pairwise interactions             |
-+---------------------------------+-------------------------------------------------------------------+
-| settings                        | reads the input script line with arguments you define             |
-+---------------------------------+-------------------------------------------------------------------+
-| coeff                           | set coefficients for one i,j type pair                            |
-+---------------------------------+-------------------------------------------------------------------+
-| init_one                        | perform initialization for one i,j type pair                      |
-+---------------------------------+-------------------------------------------------------------------+
-| init_style                      | initialization specific to this pair style                        |
-+---------------------------------+-------------------------------------------------------------------+
-| write & read_restart            | write/read i,j pair coeffs to restart files                       |
-+---------------------------------+-------------------------------------------------------------------+
-| write & read_restart_settings   | write/read global settings to restart files                       |
-+---------------------------------+-------------------------------------------------------------------+
-| single                          | force and energy of a single pairwise interaction between 2 atoms |
-+---------------------------------+-------------------------------------------------------------------+
-| compute_inner/middle/outer      | versions of compute used by rRESPA                                |
-+---------------------------------+-------------------------------------------------------------------+
++---------------------------------+---------------------------------------------------------------------+
+| compute                         | workhorse routine that computes pairwise interactions               |
++---------------------------------+---------------------------------------------------------------------+
+| settings                        | reads the input script line with arguments you define               |
++---------------------------------+---------------------------------------------------------------------+
+| coeff                           | set coefficients for one i,j type pair                              |
++---------------------------------+---------------------------------------------------------------------+
+| init_one                        | perform initialization for one i,j type pair                        |
++---------------------------------+---------------------------------------------------------------------+
+| init_style                      | initialization specific to this pair style                          |
++---------------------------------+---------------------------------------------------------------------+
+| write & read_restart            | write/read i,j pair coeffs to restart files                         |
++---------------------------------+---------------------------------------------------------------------+
+| write & read_restart_settings   | write/read global settings to restart files                         |
++---------------------------------+---------------------------------------------------------------------+
+| single                          | force/r and energy of a single pairwise interaction between 2 atoms |
++---------------------------------+---------------------------------------------------------------------+
+| compute_inner/middle/outer      | versions of compute used by rRESPA                                  |
++---------------------------------+---------------------------------------------------------------------+
 
 The inner/middle/outer routines are optional.

doc/src/Speed.rst

@@ -14,7 +14,7 @@ Intel Xeon Phi co-processors.
 
 The `Benchmark page <https://www.lammps.org/bench.html>`_ of the LAMMPS
 website gives performance results for the various accelerator
-packages discussed on the :doc:`Accelerator packages <Speed_packages>`
+packages discussed on the :doc:`Speed packages <Speed_packages>` doc
 page, for several of the standard LAMMPS benchmark problems, as a
 function of problem size and number of compute nodes, on different
 hardware platforms.

doc/src/Tools.rst

@@ -278,16 +278,20 @@ eam database tool
 -----------------------------
 
 The tools/eam_database directory contains a Fortran program that will
-generate EAM alloy setfl potential files for any combination of 16
+generate EAM alloy setfl potential files for any combination of 17
 elements: Cu, Ag, Au, Ni, Pd, Pt, Al, Pb, Fe, Mo, Ta, W, Mg, Co, Ti,
-Zr.  The files can then be used with the :doc:`pair_style eam/alloy <pair_eam>` command.
+Zr, Cr.  The files can then be used with the :doc:`pair_style eam/alloy <pair_eam>` command.
 
 The tool is authored by Xiaowang Zhou (Sandia), xzhou at sandia.gov,
-and is based on his paper:
+with updates from Lucas Hale (NIST) lucas.hale at nist.gov and is based on his paper:
 
 X. W. Zhou, R. A. Johnson, and H. N. G. Wadley, Phys. Rev. B, 69,
 144113 (2004).
 
+The parameters for Cr were taken from:
+
+Lin Z B, Johnson R A and Zhigilei L V, Phys. Rev. B 77 214108 (2008).
+
 ----------
 
 .. _eamgn:

doc/src/accel_styles.rst

@@ -1,7 +1,7 @@
 Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
 functionally the same as the corresponding style without the suffix.
 They have been optimized to run faster, depending on your available
-hardware, as discussed on the :doc:`Accelerator packages <Speed_packages>`
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
 page.  The accelerated styles take the same arguments and should
 produce the same results, except for round-off and precision issues.
 
@@ -13,5 +13,5 @@ You can specify the accelerated styles explicitly in your input script
 by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
 :doc:`suffix <suffix>` command in your input script.
 
-See the :doc:`Accelerator packages <Speed_packages>` page for more
+See the :doc:`Speed packages <Speed_packages>` page for more
 instructions on how to use the accelerated styles effectively.

doc/src/angle_charmm.rst

@@ -56,7 +56,23 @@ radian\^2.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, INTEL, KOKKOS,
+OPENMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/atom_style.rst

@@ -319,9 +319,28 @@ styles; see the :doc:`Modify <Modify>` doc page.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *kk* suffix are functionally the same as the
+corresponding style without the suffix.  They have been optimized to
+run faster, depending on your available hardware, as discussed in on
+the :doc:`Speed packages <Speed_packages>` doc page.  The accelerated
+styles take the same arguments and should produce the same results,
+except for round-off and precision issues.
 
-----------
+Note that other acceleration packages in LAMMPS, specifically the GPU,
+INTEL, OPENMP, and OPT packages do not use accelerated atom
+styles.
+
+The accelerated styles are part of the KOKKOS package.  They are only
+enabled if LAMMPS was built with those packages.  See the :doc:`Build
+package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line
+switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 Restrictions
 """"""""""""

doc/src/dump_modify.rst

@@ -1011,7 +1011,9 @@ can be disabled with the :code:`checksum` parameter.
 
 Restrictions
 """"""""""""
- none
+
+*dump_modify sort* is not supported for dumps of groups containing
+more than 2 billion atoms.
 
 Related commands
 """"""""""""""""

doc/src/fix.rst

@@ -166,7 +166,6 @@ page are followed by one or more of (g,i,k,o,t) to indicate which
 accelerated styles exist.
 
 * :doc:`accelerate/cos <fix_accelerate_cos>` - apply cosine-shaped acceleration to atoms
-* :doc:`acks2/reaxff <fix_acks2_reaxff>` - apply ACKS2 charge equilibration
 * :doc:`adapt <fix_adapt>` - change a simulation parameter over time
 * :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
 * :doc:`addforce <fix_addforce>` - add a force to each atom
@@ -247,7 +246,6 @@ accelerated styles exist.
 * :doc:`manifoldforce <fix_manifoldforce>` - restrain atoms to a manifold during minimization
 * :doc:`mdi/engine <fix_mdi_engine>` - connect LAMMPS to external programs via the MolSSI Driver Interface (MDI)
 * :doc:`meso/move <fix_meso_move>` - move mesoscopic SPH/SDPD particles in a prescribed fashion
-* :doc:`mol/swap <fix_mol_swap>` - Monte Carlo atom type swapping with a molecule
 * :doc:`momentum <fix_momentum>` - zero the linear and/or angular momentum of a group of atoms
 * :doc:`momentum/chunk <fix_momentum>` - zero the linear and/or angular momentum of a chunk of atoms
 * :doc:`move <fix_move>` - move atoms in a prescribed fashion

doc/src/fix_acks2_reaxff.rst

@@ -1,118 +0,0 @@
-.. index:: fix acks2/reaxff
-.. index:: fix acks2/reaxff/kk
-
-fix acks2/reaxff command
-========================
-
-Accelerator Variants: *acks2/reaxff/kk*
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID acks2/reaxff Nevery cutlo cuthi tolerance params args
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* acks2/reaxff = style name of this fix command
-* Nevery = perform ACKS2 every this many steps
-* cutlo,cuthi = lo and hi cutoff for Taper radius
-* tolerance = precision to which charges will be equilibrated
-* params = reaxff or a filename
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
-   fix 1 all acks2/reaxff 1 0.0 10.0 1.0e-6 param.acks2
-
-Description
-"""""""""""
-
-Perform the atom-condensed Kohn-Sham DFT to second order (ACKS2) charge
-equilibration method as described in :ref:`(Verstraelen) <Verstraelen>`.
-ACKS2 impedes unphysical long-range charge transfer sometimes seen with
-QEq (e.g. for dissociation of molecules), at increased computational
-cost.  It is typically used in conjunction with the ReaxFF force field
-model as implemented in the :doc:`pair_style reaxff <pair_reaxff>`
-command, but it can be used with any potential in LAMMPS, so long as it
-defines and uses charges on each atom.  For more technical details about
-the charge equilibration performed by fix acks2/reaxff, see the
-:ref:`(O'Hearn) <O'Hearn>` paper.
-
-The ACKS2 method minimizes the electrostatic energy of the system by
-adjusting the partial charge on individual atoms based on interactions
-with their neighbors. It requires some parameters for each atom type.
-If the *params* setting above is the word "reaxff", then these are
-extracted from the :doc:`pair_style reaxff <pair_reaxff>` command and
-the ReaxFF force field file it reads in.  If a file name is specified
-for *params*\ , then the parameters are taken from the specified file
-and the file must contain one line for each atom type.  The latter form
-must be used when performing QeQ with a non-ReaxFF potential.  The lines
-should be formatted as follows:
-
-.. parsed-literal::
-
-   bond_softness
-   itype chi eta gamma bcut
-
-where the first line is the global parameter *bond_softness*. The
-remaining 1 to Ntypes lines include *itype*, the atom type from 1 to
-Ntypes, *chi*, the electronegativity in eV, *eta*, the self-Coulomb
-potential in eV, *gamma*, the valence orbital exponent, and *bcut*, the
-bond cutoff distance.  Note that these 4 quantities are also in the
-ReaxFF potential file, except that eta is defined here as twice the eta
-value in the ReaxFF file. Note that unlike the rest of LAMMPS, the units
-of this fix are hard-coded to be A, eV, and electronic charge.
-
-**Restart, fix_modify, output, run start/stop, minimize info:**
-
-No information about this fix is written to :doc:`binary restart files
-<restart>`.  No global scalar or vector or per-atom quantities are
-stored by this fix for access by various :doc:`output commands
-<Howto_output>`.  No parameter of this fix can be used with the
-*start/stop* keywords of the :doc:`run <run>` command.
-
-This fix is invoked during :doc:`energy minimization <minimize>`.
-
-----------
-
-.. include:: accel_styles.rst
-
-----------
-
-Restrictions
-""""""""""""
-
-This fix is part of the REAXFF package.  It is only enabled if LAMMPS
-was built with that package.  See the :doc:`Build package
-<Build_package>` doc page for more info.
-
-This fix does not correctly handle interactions involving multiple
-periodic images of the same atom. Hence, it should not be used for
-periodic cell dimensions less than 10 angstroms.
-
-This fix may be used in combination with :doc:`fix efield <fix_efield>`
-and will apply the external electric field during charge equilibration,
-but there may be only one fix efield instance used, it may only use a
-constant electric field, and the electric field vector may only have
-components in non-periodic directions.
-
-Related commands
-""""""""""""""""
-
-:doc:`pair_style reaxff <pair_reaxff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`
-
-**Default:** none
-
-----------
-
-.. _O'Hearn:
-
-**(O'Hearn)** O'Hearn, Alperen, Aktulga, SIAM J. Sci. Comput., 42(1), C1-C22 (2020).
-
-.. _Verstraelen:
-
-**(Verstraelen)** Verstraelen, Ayers, Speybroeck, Waroquier, J. Chem. Phys. 138, 074108 (2013).

doc/src/fix_atom_swap.rst

@@ -73,51 +73,51 @@ is the same after the swap as it was before the swap, even though the
 atom masses have changed.
 
 The *semi-grand* keyword can be set to *yes* to switch to the
-semi-grand canonical ensemble as discussed in :ref:`(Sadigh)
-<Sadigh>`. This means that the total number of each particle type does
-not need to be conserved. The default is *no*, which means that the
-only kind of swap allowed exchanges an atom of one type with an atom
-of a different given type. In other words, the relative mole fractions
-of the swapped atoms remains constant. Whereas in the semi-grand
-canonical ensemble, the composition of the system can change. Note
-that when using *semi-grand*, atoms in the fix group whose type is not
-listed in the *types* keyword are ineligible for attempted
-conversion. An attempt is made to switch the selected atom (if
-eligible) to one of the other listed types with equal
-probability. Acceptance of each attempt depends upon the Metropolis
-criterion.
+semi-grand canonical ensemble as discussed in :ref:`(Sadigh) <Sadigh>`. This
+means that the total number of each particle type does not need to be
+conserved. The default is *no*, which means that the only kind of swap
+allowed exchanges an atom of one type with an atom of a different
+given type. In other words, the relative mole fractions of the swapped
+atoms remains constant. Whereas in the semi-grand canonical ensemble,
+the composition of the system can change. Note that when using
+*semi-grand*, atoms in the fix group whose type is not listed
+in the *types* keyword are ineligible for attempted
+conversion. An attempt is made to switch
+the selected atom (if eligible) to one of the other listed types
+with equal probability. Acceptance of each attempt depends upon the Metropolis criterion.
 
-The *mu* keyword allows users to specify chemical potentials. This is
-required and allowed only when using *semi-grand*\ .  All chemical
-potentials are absolute, so there is one for each swap type listed
-following the *types* keyword.  In semi-grand canonical ensemble
-simulations the chemical composition of the system is controlled by
-the difference in these values. So shifting all values by a constant
-amount will have no effect on the simulation.
+The *mu* keyword allows users to specify chemical
+potentials. This is required and allowed only when using *semi-grand*\ .
+All chemical potentials are absolute, so there is one for
+each swap type listed following the *types* keyword.
+In semi-grand canonical ensemble simulations the chemical composition
+of the system is controlled by the difference in these values. So
+shifting all values by a constant amount will have no effect
+on the simulation.
 
 This command may optionally use the *region* keyword to define swap
 volume.  The specified region must have been previously defined with a
-:doc:`region <region>` command.  It must be defined with side = *in*\
-.  Swap attempts occur only between atoms that are both within the
+:doc:`region <region>` command.  It must be defined with side = *in*\ .
+Swap attempts occur only between atoms that are both within the
 specified region. Swaps are not otherwise attempted.
 
 You should ensure you do not swap atoms belonging to a molecule, or
-LAMMPS will eventually generate an error when it tries to find those
-atoms.  LAMMPS will warn you if any of the atoms eligible for swapping
-have a non-zero molecule ID, but does not check for this at the time of
+LAMMPS will soon generate an error when it tries to find those atoms.
+LAMMPS will warn you if any of the atoms eligible for swapping have a
+non-zero molecule ID, but does not check for this at the time of
 swapping.
 
 If not using *semi-grand* this fix checks to ensure all atoms of the
 given types have the same atomic charge. LAMMPS does not enforce this
-in general, but it is needed for this fix to simplify the swapping
-procedure. Successful swaps will swap the atom type and charge of the
-swapped atoms. Conversely, when using *semi-grand*, it is assumed that
-all the atom types involved in switches have the same
-charge. Otherwise, charge would not be conserved. As a consequence, no
-checks on atomic charges are performed, and successful switches update
-the atom type but not the atom charge. While it is possible to use
-*semi-grand* with groups of atoms that have different charges, these
-charges will not be changed when the atom types change.
+in general, but it is needed for this fix to simplify the
+swapping procedure. Successful swaps will swap the atom type and charge
+of the swapped atoms. Conversely, when using *semi-grand*, it is assumed that all the atom
+types involved in switches have the same charge. Otherwise, charge
+would not be conserved. As a consequence, no checks on atomic charges are
+performed, and successful switches update the atom type but not the
+atom charge. While it is possible to use *semi-grand* with groups of
+atoms that have different charges, these charges will not be changed when the
+atom types change.
 
 Since this fix computes total potential energies before and after
 proposed swaps, so even complicated potential energy calculations are
@@ -133,24 +133,23 @@ OK, including the following:
 Some fixes have an associated potential energy. Examples of such fixes
 include: :doc:`efield <fix_efield>`, :doc:`gravity <fix_gravity>`,
 :doc:`addforce <fix_addforce>`, :doc:`langevin <fix_langevin>`,
-:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen
-<fix_temp_berendsen>`, :doc:`temp/rescale <fix_temp_rescale>`, and
-:doc:`wall fixes <fix_wall>`.  For that energy to be included in the
-total potential energy of the system (the quantity used when
-performing GCMC moves), you MUST enable the :doc:`fix_modify
-<fix_modify>` *energy* option for that fix.  The doc pages for
-individual :doc:`fix <fix>` commands specify if this should be done.
+:doc:`restrain <fix_restrain>`, :doc:`temp/berendsen <fix_temp_berendsen>`,
+:doc:`temp/rescale <fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.
+For that energy to be included in the total potential energy of the
+system (the quantity used when performing GCMC moves),
+you MUST enable the :doc:`fix_modify <fix_modify>` *energy* option for
+that fix.  The doc pages for individual :doc:`fix <fix>` commands
+specify if this should be done.
 
 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 number
-generator seed, the next timestep for MC exchanges, the number of
-exchange attempts and successes etc.  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.
+This fix writes the state of the fix to :doc:`binary restart files <restart>`.  This includes information about the random
+number generator seed, the next timestep for MC exchanges, the number
+of exchange attempts and successes etc.  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.
 
 .. note::
 
@@ -166,13 +165,12 @@ by various :doc:`output commands <Howto_output>`.  The vector values are
 the following global cumulative quantities:
 
 * 1 = swap attempts
-* 2 = swap accepts
+* 2 = swap successes
 
 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
 """"""""""""
@@ -186,8 +184,7 @@ Related commands
 
 :doc:`fix nvt <fix_nh>`, :doc:`neighbor <neighbor>`,
 :doc:`fix deposit <fix_deposit>`, :doc:`fix evaporate <fix_evaporate>`,
-:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`,
-:doc:`fix mol/swap <fix_mol_swap>`
+:doc:`delete_atoms <delete_atoms>`, :doc:`fix gcmc <fix_gcmc>`
 
 Default
 """""""

doc/src/fix_langevin.rst

@@ -138,18 +138,16 @@ temperature with optional time-dependence as well.
 
 Like other fixes that perform thermostatting, this fix can be used
 with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+atom velocities.  E.g. removing the center-of-mass velocity from a
+group of atoms or removing the x-component of velocity from the
+calculation.  This is not done by default, but only if the
+:doc:`fix_modify <fix_modify>` command is used to assign a temperature
+compute to this fix that includes such a bias term.  See the doc pages
+for individual :doc:`compute commands <compute>` to determine which ones
+include a bias.  In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostatting is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in.
 
 The *damp* parameter is specified in time units and determines how
 rapidly the temperature is relaxed.  For example, a value of 100.0 means
@@ -185,8 +183,7 @@ omega (which is derived from the angular momentum in the case of
 aspherical particles).
 
 The rotational temperature of the particles can be monitored by the
-:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute
-temp/asphere <compute_temp_asphere>` commands with their rotate
+:doc:`compute temp/sphere <compute_temp_sphere>` and :doc:`compute temp/asphere <compute_temp_asphere>` commands with their rotate
 options.
 
 For the *omega* keyword there is also a scale factor of

doc/src/fix_langevin_drude.rst

@@ -167,20 +167,17 @@ functions, and include :doc:`thermo_style <thermo_style>` command
 keywords for the simulation box parameters and timestep and elapsed
 time.  Thus it is easy to specify a time-dependent temperature.
 
-Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+Like other fixes that perform thermostatting, this fix can be used with
+:doc:`compute commands <compute>` that remove a "bias" from the atom
+velocities.  E.g. removing the center-of-mass velocity from a group of
+atoms.  This is not done by default, but only if the
+:doc:`fix_modify <fix_modify>` command is used to assign a temperature
+compute to this fix that includes such a bias term.  See the doc pages
+for individual :doc:`compute commands <compute>` to determine which ones
+include a bias.  In this case, the thermostat works in the following
+manner: bias is removed from each atom, thermostatting is performed on
+the remaining thermal degrees of freedom, and the bias is added back
+in.  NOTE: this feature has not been tested.
 
 Note: The temperature thermostatting the core-Drude particle pairs
 should be chosen low enough, so as to mimic as closely as possible the

doc/src/fix_mol_swap.rst

@@ -1,170 +0,0 @@
-.. index:: fix mol/swap
-
-fix mol/swap command
-=====================
-
-Syntax
-""""""
-
-.. parsed-literal::
-
-   fix ID group-ID mol/swap N X itype jtype seed T keyword value ...
-
-* ID, group-ID are documented in :doc:`fix <fix>` command
-* atom/swap = style name of this fix command
-* N = invoke this fix every N steps
-* X = number of swaps to attempt every N steps
-* itype,jtype = two atom types to swap with each other
-* seed = random # seed (positive integer)
-* T = scaling temperature of the MC swaps (temperature units)
-* zero or more keyword/value pairs may be appended to args
-* keyword = *ke*
-
-  .. parsed-literal::
-
-       *ke* value = *no* or *yes*
-         *no* = no conservation of kinetic energy after atom swaps
-         *yes* = kinetic energy is conserved after atom swaps
-
-Examples
-""""""""
-
-.. code-block:: LAMMPS
-
-   fix 2 all mol/swap 100 1 2 3 29494 300.0 ke no
-   fix mySwap fluid mol/swap 500 10 1 2 482798 1.0
-
-Description
-"""""""""""
-
-This fix performs Monte Carlo swaps of two specified atom types within
-a randomly selected molecule.  Two possible use cases are as follows.
-
-First, consider a mixture of some molecules with atoms of itype and
-other molecules with atoms of jtype.  The fix will select a random
-molecule and attempt to swap all the itype atoms to jtype for the
-first kind of molecule, or all the jtype atoms to itype for the second
-kind.  Because the swap will only take place if it is energetically
-favorable, the fix can be used to determine the miscibility of 2
-different kinds of molecules much more quickly than just dynamics
-would do it.
-
-Second, consider diblock co-polymers with two types of monomers itype
-and jtype.  The fix will select a random molecule and attempt to do a
-itype <--> jtype swap of all those monomers within the molecule.  Thus
-the fix can be used to find the energetically favorable fractions of
-two flavors of diblock co-polymers.
-
-Intra-molecular swaps of atom types are attempted every N timesteps.  On
-that timestep, X swaps are attempted.  For each attempt a single
-molecule ID is randomly selected.  The range of possible molecule IDs
-from loID to hiID is pre-computed before each run begins.  The
-loID/hiID is set for the molecule with the smallest/largest ID which
-has any itype or jtype atoms in it.  Note that if you define a system
-with many molecule IDs between loID and hiID which have no itype or
-jtype atoms, then the fix will be inefficient at performing swaps.
-Also note that if atoms with molecule ID = 0 exist, they are not
-considered molecules by this fix; they are assumed to be solvent atoms
-or molecules.
-
-Candidate atoms for swapping must also be in the fix group.  Atoms
-within the selected molecule which are not itype or jtype are ignored.
-
-When an atom is swapped from itype to jtype (or vice versa), if
-charges are defined, the charge values for itype versus jtype atoms
-are also swapped.  This requires that all itype atoms in the system
-have the same charge value.  Likewise all jtype atoms in the system
-must have the same charge value.  If this is not the case, LAMMPS
-issues a warning that it cannot swap charge values.
-
-If the *ke* keyword is set to yes, which is the default, and the
-masses of itype and jtype atoms are different, then when a swap
-occurs, the velocity of the swapped atom is rescaled by the sqrt of
-the mass ratio, so as to conserve the kinetic energy of the atom.
-
-----------
-
-The potential energy of the entire system is computed before and after
-each swap is performed within a single molecule.  The specified
-temperature T is used in the Metropolis criterion to accept or reject
-the attempted swap.  If the swap is rejected all swapped values are
-reversed.
-
-The potential energy calculations can include systems and models with
-the following features:
-
-* manybody pair styles, including EAM
-* hybrid pair styles
-* long-range electrostatics (kspace)
-* triclinic systems
-* potential energy contributions from other fixes
-
-For the last bullet point, fixes can have an associated potential
-energy. Examples of such fixes include: :doc:`efield <fix_efield>`,
-:doc:`gravity <fix_gravity>`, :doc:`addforce <fix_addforce>`,
-:doc:`langevin <fix_langevin>`, :doc:`restrain <fix_restrain>`,
-:doc:`temp/berendsen <fix_temp_berendsen>`, :doc:`temp/rescale
-<fix_temp_rescale>`, and :doc:`wall fixes <fix_wall>`.  For that
-energy to be included in the total potential energy of the system (the
-quantity used for the swap accept/reject decision), you MUST enable
-the :doc:`fix_modify <fix_modify>` *energy* option for that fix.  The
-doc pages for individual :doc:`fix <fix>` commands specify if this
-should be done.
-
-.. note::
-
-  One comment on computational efficiency.  If the cutoff lengths
-  defined for the pair style are different for itype versus jtype
-  atoms (for any of their interactions with any other atom type), then
-  a new neighbor list needs to be generated for every attempted swap.
-  This is potentially expensive if N is small or X is large.
-
-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 number
-generator seed, the next timestep for MC exchanges, the number of
-exchange attempts and successes etc.  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.
-
-.. note::
-
-   For this to work correctly, the timestep must **not** be changed
-   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
-fix.
-
-This fix computes a global vector of length 2, which can be accessed
-by various :doc:`output commands <Howto_output>`.  The vector values are
-the following global cumulative quantities:
-
-* 1 = swap attempts
-* 2 = swap accepts
-
-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>`.
-
-Restrictions
-""""""""""""
-
-This fix is part of the MC package.  It is only enabled if LAMMPS was
-built with that package.  See the :doc:`Build package <Build_package>`
-doc page for more info.
-
-Related commands
-""""""""""""""""
-
-:doc:`fix atom/swap <fix_atom_swap>`, :doc:`fix gcmc <fix_gcmc>`
-
-Default
-"""""""
-
-The option default is ke = yes.

doc/src/fix_nh.rst

@@ -486,20 +486,19 @@ temperature or pressure during thermodynamic output via the
 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 remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+Like other fixes that perform thermostatting, fix nvt and fix npt can
+be used with :doc:`compute commands <compute>` that calculate a
+temperature after removing a "bias" from the atom velocities.
+E.g. removing the center-of-mass velocity from a group of atoms or
+only calculating temperature on the x-component of velocity or only
+calculating temperature for atoms in a geometric region.  This is not
+done by default, but only if the :doc:`fix_modify <fix_modify>` command
+is used to assign a temperature compute to this fix that includes such
+a bias term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_npt_asphere.rst

@@ -48,9 +48,8 @@ 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*, *iso*,
-*aniso*, and *dilate* keywords.
+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
 positions are updated by the velocity/position update portion of the
@@ -90,19 +89,18 @@ 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 remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_npt_body.rst

@@ -87,19 +87,18 @@ 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 remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_npt_cauchy.rst

@@ -400,20 +400,19 @@ temperature or pressure during thermodynamic output via the
 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 remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+Like other fixes that perform thermostatting, fix npt/cauchy can
+be used with :doc:`compute commands <compute>` that calculate a
+temperature after removing a "bias" from the atom velocities.
+E.g. removing the center-of-mass velocity from a group of atoms or
+only calculating temperature on the x-component of velocity or only
+calculating temperature for atoms in a geometric region.  This is not
+done by default, but only if the :doc:`fix_modify <fix_modify>` command
+is used to assign a temperature compute to this fix that includes such
+a bias term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_npt_sphere.rst

@@ -103,19 +103,18 @@ 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 remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_nvt_asphere.rst

@@ -72,19 +72,18 @@ It also means that changing attributes of *thermo_temp* will have no
 effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_nvt_body.rst

@@ -69,19 +69,18 @@ It also means that changing attributes of *thermo_temp* will have no
 effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_nvt_sllod.rst

@@ -37,16 +37,15 @@ trajectory consistent with the canonical ensemble.
 
 This thermostat is used for a simulation box that is changing size
 and/or shape, for example in a non-equilibrium MD (NEMD) simulation.
-The size/shape change is induced by use of the :doc:`fix deform
-<fix_deform>` command, so each point in the simulation box can be
-thought of as having a "streaming" velocity.  This position-dependent
-streaming velocity is subtracted from each atom's actual velocity to
-yield a thermal velocity which is used for temperature computation and
-thermostatting.  For example, if the box is being sheared in x,
-relative to y, then points at the bottom of the box (low y) have a
-small x velocity, while points at the top of the box (hi y) have a
-large x velocity.  These velocities do not contribute to the thermal
-"temperature" of the atom.
+The size/shape change is induced by use of the :doc:`fix deform <fix_deform>` command, so each point in the simulation box
+can be thought of as having a "streaming" velocity.  This
+position-dependent streaming velocity is subtracted from each atom's
+actual velocity to yield a thermal velocity which is used for
+temperature computation and thermostatting.  For example, if the box
+is being sheared in x, relative to y, then points at the bottom of the
+box (low y) have a small x velocity, while points at the top of the
+box (hi y) have a large x velocity.  These velocities do not
+contribute to the thermal "temperature" of the atom.
 
 .. note::
 
@@ -61,15 +60,13 @@ large x velocity.  These velocities do not contribute to the thermal
    consistent.
 
 The SLLOD equations of motion, originally proposed by Hoover and Ladd
-(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be
-equivalent to Newton's equations of motion for shear flow by
-:ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate
-the desired velocity gradient and the correct production of work by
-stresses for all forms of homogeneous flow by :ref:`(Daivis and Todd)
-<Daivis>`.  As implemented in LAMMPS, they are coupled to a
-Nose/Hoover chain thermostat in a velocity Verlet formulation, closely
-following the implementation used for the :doc:`fix nvt <fix_nh>`
-command.
+(see :ref:`(Evans and Morriss) <Evans3>`), were proven to be equivalent to
+Newton's equations of motion for shear flow by :ref:`(Evans and Morriss) <Evans3>`. They were later shown to generate the desired
+velocity gradient and the correct production of work by stresses for
+all forms of homogeneous flow by :ref:`(Daivis and Todd) <Daivis>`.  As
+implemented in LAMMPS, they are coupled to a Nose/Hoover chain
+thermostat in a velocity Verlet formulation, closely following the
+implementation used for the :doc:`fix nvt <fix_nh>` command.
 
 .. note::
 
@@ -97,28 +94,27 @@ underscore + "temp", and the group for the new compute is the same as
 the fix group.
 
 Note that this is NOT the compute used by thermodynamic output (see
-the :doc:`thermo_style <thermo_style>` command) with ID =
-*thermo_temp*.  This means you can change the attributes of this fix's
-temperature (e.g. its degrees-of-freedom) via the :doc:`compute_modify
-<compute_modify>` command or print this temperature during
-thermodynamic output via the :doc:`thermo_style custom <thermo_style>`
-command using the appropriate compute-ID.  It also means that changing
-attributes of *thermo_temp* will have no effect on this fix.
+the :doc:`thermo_style <thermo_style>` command) with ID = *thermo_temp*.
+This means you can change the attributes of this fix's temperature
+(e.g. its degrees-of-freedom) via the
+:doc:`compute_modify <compute_modify>` command or print this temperature
+during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` command using the appropriate compute-ID.
+It also means that changing attributes of *thermo_temp* will have no
+effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_nvt_sphere.rst

@@ -86,19 +86,18 @@ It also means that changing attributes of *thermo_temp* will have no
 effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_qeq.rst

@@ -230,10 +230,7 @@ These fixes are part of the QEQ package.  They are only enabled if
 LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-These qeq fixes are not compatible with the GPU and USER-INTEL packages.
-
-These qeq fixes will ignore electric field contributions from
-:doc:`fix efield <fix_efield>`.
+The qeq fixes are not compatible with the GPU and USER-INTEL packages.
 
 Related commands
 """"""""""""""""

doc/src/fix_qeq_reaxff.rst

@@ -116,12 +116,6 @@ This fix does not correctly handle interactions involving multiple
 periodic images of the same atom.  Hence, it should not be used for
 periodic cell dimensions less than 10 angstroms.
 
-This fix may be used in combination with :doc:`fix efield <fix_efield>`
-and will apply the external electric field during charge equilibration,
-but there may be only one fix efield instance used, it may only use a
-constant electric field, and the electric field vector may only have
-components in non-periodic directions.
-
 Related commands
 """"""""""""""""
 

doc/src/fix_reaxff_species.rst

@@ -56,17 +56,6 @@ number of molecules of each species.  In this context, "species" means
 a unique molecule.  The chemical formula of each species is given in
 the first line.
 
-.. warning::
-
-   In order to compute averaged data, it is required that there are no
-   neighbor list rebuilds between the *Nfreq* steps. For that reason, fix
-   *reaxff/species* may change your neighbor list settings.  There will
-   be a warning message showing the new settings. Having an *Nfreq*
-   setting that is larger than what is required for correct computation
-   of the ReaxFF force field interactions can thus lead to incorrect
-   results.  For typical ReaxFF calculations a value of 100 is already
-   quite large.
-
 If the filename ends with ".gz", the output file is written in gzipped
 format.  A gzipped dump file will be about 3x smaller than the text version,
 but will also take longer to write.

doc/src/fix_saed_vtk.rst

@@ -28,6 +28,7 @@ Syntax
          Nstart = start averaging on this timestep
        *file* arg = filename
          filename = name of file to output time averages to
+       *overwrite* arg = none = overwrite output file with only latest output
 
 Examples
 """"""""
@@ -160,6 +161,10 @@ the *file* keyword and this string is appended with _N.vtk where N is
 an index (0,1,2...) to account for situations with multiple diffraction
 intensity outputs.
 
+The *overwrite* keyword will continuously overwrite the output file
+with the latest output, so that it only contains one timestep worth of
+output.  This option can only be used with the *ave running* setting.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 

doc/src/fix_setforce.rst

@@ -89,13 +89,26 @@ precession vectors instead of the forces.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
 
-.. note::
+The region keyword is also supported by Kokkos, but a Kokkos-enabled
+region must be used. See the region :doc:`region <region>` command for
+more information.
 
-  The region keyword is supported by Kokkos, but a Kokkos-enabled
-  region must be used. See the region :doc:`region <region>` command for
-  more information.
+These accelerated styles are part of the r Kokkos package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/fix_temp_berendsen.rst

@@ -102,19 +102,18 @@ It also means that changing attributes of *thermo_temp* will have no
 effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_temp_csvr.rst

@@ -110,29 +110,28 @@ during thermodynamic output via the :doc:`thermo_style custom <thermo_style>` co
 It also means that changing attributes of *thermo_temp* will have no
 effect on this fix.
 
-Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+Like other fixes that perform thermostatting, these fixes can be used
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is used
+to assign a temperature compute to this fix that includes such a bias
+term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal degrees of freedom, and the bias is added back in.
 
 An important feature of these thermostats is that they have an
-associated effective energy that is a constant of motion.  The
-effective energy is the total energy (kinetic + potential) plus the
-accumulated kinetic energy changes due to the thermostat. The latter
-quantity is the global scalar computed by these fixes. This feature is
-useful to check the integration of the equations of motion against
-discretization errors. In other words, the conservation of the
-effective energy can be used to choose an appropriate integration
+associated effective energy that is a constant of motion.
+The effective energy is the total energy (kinetic + potential) plus
+the accumulated kinetic energy changes due to the thermostat. The
+latter quantity is the global scalar computed by these fixes. This
+feature is useful to check the integration of the equations of motion
+against discretization errors. In other words, the conservation of
+the effective energy can be used to choose an appropriate integration
 :doc:`timestep <timestep>`. This is similar to the usual paradigm of
 checking the conservation of the total energy in the microcanonical
 ensemble.

doc/src/fix_temp_rescale.rst

@@ -109,19 +109,19 @@ command using the appropriate compute-ID.  It also means that changing
 attributes of *thermo_temp* will have no effect on this fix.
 
 Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+with :doc:`compute commands <compute>` that calculate a temperature
+after removing a "bias" from the atom velocities.  E.g. removing the
+center-of-mass velocity from a group of atoms or only calculating
+temperature on the x-component of velocity or only calculating
+temperature for atoms in a geometric region.  This is not done by
+default, but only if the :doc:`fix_modify <fix_modify>` command is
+used to assign a temperature compute to this fix that includes such a
+bias term.  See the doc pages for individual :doc:`compute commands
+<compute>` to determine which ones include a bias.  In this case, the
+thermostat works in the following manner: the current temperature is
+calculated taking the bias into account, bias is removed from each
+atom, thermostatting is performed on the remaining thermal degrees of
+freedom, and the bias is added back in.
 
 ----------
 

doc/src/fix_tgnh_drude.rst

@@ -187,32 +187,26 @@ barostatting.
 
 ----------
 
-Like other fixes that perform thermostatting, this fix can be used
-with :doc:`compute commands <compute>` that remove a "bias" from the
-atom velocities.  E.g. to apply the thermostat only to atoms within a
-spatial :doc:`region <region>`, or to remove the center-of-mass
-velocity from a group of atoms, or to remove the x-component of
-velocity from the calculation.
-
-This is not done by default, but only if the :doc:`fix_modify
-<fix_modify>` command is used to assign a temperature compute to this
-fix that includes such a bias term.  See the doc pages for individual
-:doc:`compute temp commands <compute>` to determine which ones include
-a bias.  In this case, the thermostat works in the following manner:
-bias is removed from each atom, thermostatting is performed on the
-remaining thermal degrees of freedom, and the bias is added back in.
+Like other fixes that perform thermostatting, these fixes can
+be used with :doc:`compute commands <compute>` that calculate a
+temperature after removing a "bias" from the atom velocities.
+This is not done by default, but only if the :doc:`fix_modify <fix_modify>` command
+is used to assign a temperature compute to this fix that includes such
+a bias term.  See the doc pages for individual :doc:`compute commands <compute>` to determine which ones include a bias.  In
+this case, the thermostat works in the following manner: the current
+temperature is calculated taking the bias into account, bias is
+removed from each atom, thermostatting is performed on the remaining
+thermal DOF, and the bias is added back in.
 
 .. note::
 
-   However, not all temperature compute commands are valid to be used
-   with these fixes.  Precisely, only temperature compute that does
-   not modify the DOF of the group can be used.  E.g. :doc:`compute
-   temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos
-   <compute_viscosity_cos>` compute the kinetic energy after remove a
-   velocity gradient without affecting the DOF of the group, then they
-   can be invoked in this way.  In contrast, :doc:`compute
-   temp/partial <compute_temp_partial>` may remove the DOF at one or
-   more dimensions, therefore it cannot be used with these fixes.
+   However, not all temperature compute commands are valid to be used with these fixes.
+   Precisely, only temperature compute that does not modify the DOF of the group can be used.
+   E.g. :doc:`compute temp/ramp <compute_temp_ramp>` and :doc:`compute viscosity/cos <compute_viscosity_cos>`
+   compute the kinetic energy after remove a velocity gradient without affecting the DOF of the group,
+   then they can be invoked in this way.
+   In contrast, :doc:`compute temp/partial <compute_temp_partial>` may remove the DOF at one or more dimensions,
+   therefore it cannot be used with these fixes.
 
 ----------
 

doc/src/improper_harmonic.rst

@@ -64,7 +64,25 @@ radian\^2.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
+
+These accelerated styles are part of the GPU, INTEL, KOKKOS,
+OPENMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package
+<Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix
+command-line switch <Run_options>` when you invoke LAMMPS, or you can
+use the :doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/kspace_style.rst

@@ -310,7 +310,7 @@ Forschungszentrum Juelich.
 
 The library is available for download at "http://scafacos.de" or can
 be cloned from the git-repository
-"git://github.com/scafacos/scafacos.git".
+"https://github.com/scafacos/scafacos.git".
 
 In order to use this KSpace style, you must download and build the
 ScaFaCoS library, then build LAMMPS with the SCAFACOS package
@@ -414,26 +414,33 @@ relative RMS error.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
 
-.. note::
+More specifically, the *pppm/gpu* style performs charge assignment and
+force interpolation calculations on the GPU.  These processes are
+performed either in single or double precision, depending on whether
+the -DFFT_SINGLE setting was specified in your low-level Makefile, as
+discussed above.  The FFTs themselves are still calculated on the CPU.
+If *pppm/gpu* is used with a GPU-enabled pair style, part of the PPPM
+calculation can be performed concurrently on the GPU while other
+calculations for non-bonded and bonded force calculation are performed
+on the CPU.
 
-  For the GPU package, the *pppm/gpu* style performs charge assignment
-  and force interpolation calculations on the GPU.  These processes
-  are performed either in single or double precision, depending on
-  whether the -DFFT_SINGLE setting was specified in your low-level
-  Makefile, as discussed above.  The FFTs themselves are still
-  calculated on the CPU.  If *pppm/gpu* is used with a GPU-enabled
-  pair style, part of the PPPM calculation can be performed
-  concurrently on the GPU while other calculations for non-bonded and
-  bonded force calculation are performed on the CPU.
+The *pppm/kk* style performs charge assignment and force interpolation
+calculations, along with the FFTs themselves, on the GPU or (optionally) threaded
+on the CPU when using OpenMP and FFTW3.
 
-.. note::
+These accelerated styles are part of the GPU, INTEL, KOKKOS,
+OPENMP, and OPT packages respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
-  For the KOKKOS package, the *pppm/kk* style performs charge
-  assignment and force interpolation calculations, along with the FFTs
-  themselves, on the GPU or (optionally) threaded on the CPU when
-  using OpenMP and FFTW3.
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/package.rst

@@ -166,7 +166,7 @@ intel", or "package omp" command with default settings.
    set, either to default values or to specified settings.  I.e. settings
    from previous invocations do not persist across multiple invocations.
 
-See the :doc:`Accelerator packages <Speed_packages>` page for more details
+See the :doc:`Speed packages <Speed_packages>` page for more details
 about using the various accelerator packages for speeding up LAMMPS
 simulations.
 

doc/src/pair_agni.rst

@@ -67,7 +67,21 @@ and input files are provided in the examples/PACKAGES/agni directory.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with *omp* suffix is functionally the same as the corresponding
+style without the suffix. They have been optimized to run faster,
+depending on your available hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc page.  The accelerated style takes
+the same arguments and should produce the same results, except for
+round-off and precision issues.
+
+The accelerated style is part of the OPENMP.  They are only enabled
+if LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
+
+You can specify the accelerated style explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/pair_granular.rst

@@ -205,7 +205,7 @@ For *damping mass_velocity*, the normal damping is given by:
    \eta_n = \eta_{n0} m_{eff}
 
 Here, :math:`\eta_{n0}` is the damping coefficient specified for the normal
-contact model, in units of *mass*\ /\ *time* and
+contact model, in units of 1/\ *time* and
 :math:`m_{eff} = m_i m_j/(m_i + m_j)` is the effective mass.
 Use *damping mass_velocity* to reproduce the damping behavior of
 *pair gran/hooke/\**.

doc/src/pair_hybrid.rst

@@ -383,19 +383,30 @@ coefficients to 0.0.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  Pair style *hybrid/scaled* does (currently) not support the
+*gpu*, *omp*, *kk*, or *intel* suffix.
 
-.. note::
+Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles delegate
+computation to the individual sub-styles, the suffix versions of the
+*hybrid* and *hybrid/overlay* styles are used to propagate the
+corresponding suffix to all sub-styles, if those versions
+exist. Otherwise the non-accelerated version will be used.
 
-  Since the *hybrid*, *hybrid/overlay*, *hybrid/scaled* styles
-  delegate computation to the individual sub-styles, the suffix
-  versions of the *hybrid* and *hybrid/overlay* styles are used to
-  propagate the corresponding suffix to all sub-styles, if those
-  versions exist. Otherwise the non-accelerated version will be used.
-  The individual accelerated sub-styles are part of the GPU, KOKKOS,
-  INTEL, OPENMP, and OPT packages, respectively.  They are only
-  enabled if LAMMPS was built with those packages.  See the
-  :doc:`Build package <Build_package>` page for more info.
+The individual accelerated sub-styles are part of the GPU, KOKKOS,
+INTEL, OPENMP, and OPT packages, respectively.  They are only
+enabled if LAMMPS was built with those packages.  See the :doc:`Build
+package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/pair_lebedeva_z.rst

@@ -26,15 +26,29 @@ Examples
 Description
 """""""""""
 
-The *lebedeva/z* style computes the Lebedeva interaction
-potential as described in :ref:`(Lebedeva et al.) <Leb01>`. An important simplification is made,
-which is to take all normals along the z-axis.
+The *lebedeva/z* pair style computes the Lebedeva interaction potential
+as described in :ref:`(Lebedeva1) <Leb01>` and :ref:`(Lebedeva2)
+<Leb02>`.  An important simplification is made, which is to take all
+normals along the z-axis.
+
+The Lebedeva potential is intended for the description of the interlayer
+interaction between graphene layers.  To perform a realistic simulation,
+this potential must be used in combination with an intralayer potential
+such as :doc:`AIREBO <pair_airebo>` or :doc:`Tersoff <pair_tersoff>`
+facilitated by using pair style :doc:`hybrid/overlay <pair_hybrid>`.  To
+keep the intralayer properties unaffected, the interlayer interaction
+within the same layers should be avoided.  This can be achieved by
+assigning different atom types to atoms of different layers (e.g. 1 and
+2 in the examples above).
+
+Other interactions can be set to zero using pair_style *none*\ .
+
 
 .. math::
 
-   E       = & \frac{1}{2} \sum_i \sum_{i \neq j} V_{ij}\\
+   E       = & \frac{1}{2} \sum_i \sum_{j \neq i} V_{ij}\\
    V_{ij}  = & B e^{-\alpha(r_{ij} - z_0)} \\
-             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij} e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
+             & + C(1 + D_1\rho^2_{ij} + D_2\rho^4_{ij}) e^{-\lambda_1\rho^2_{ij}} e^{-\lambda_2 (z^2_{ij} - z^2_0)} \\
              & - A \left(\frac{z_0}{r_ij}\right)^6 + A \left( \frac{z_0}{r_c} \right)^6 \\
    \rho^2_{ij} = & x^2_{ij} + y^2_{ij} \qquad (\mathbf{n_i} \equiv \mathbf{\hat{z}})
 
@@ -43,12 +57,15 @@ Energies are shifted so that they go continuously to zero at the cutoff assuming
 that the exponential part of :math:`V_{ij}` (first term) decays sufficiently fast.
 This shift is achieved by the last term in the equation for :math:`V_{ij}` above.
 
-The parameter file (e.g. CC.Lebedeva), is intended for use with metal
-:doc:`units <units>`, with energies in meV. An additional parameter, *S*,
-is available to facilitate scaling of energies.
+The provided parameter file (CC.Lebedeva) contains two sets of parameters.
 
-This potential must be used in combination with hybrid/overlay.
-Other interactions can be set to zero using pair_style *none*\ .
+- The first set (element name "C") is suitable for normal conditions and
+  is taken from :ref:`(Popov1) <Popov>`
+- The second set (element name "C1") is suitable for high-pressure
+  conditions and is taken from :ref:`(Koziol1) <Koziol>`
+
+Both sets contain an additional parameter, *S*, that can be used to
+facilitate scaling of energies and is set to 1.0 by default.
 
 Restrictions
 """"""""""""
@@ -77,4 +94,16 @@ none
 
 .. _Leb01:
 
-**(Lebedeva et al.)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+**(Lebedeva1)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Phys. Rev. B, 84, 245437 (2011)
+
+.. _Leb02:
+
+**(Lebedeva2)** I. V. Lebedeva, A. A. Knizhnik, A. M. Popov, Y. E. Lozovik, B. V. Potapkin, Physica E: 44, 949-954 (2012)
+
+.. _Popov:
+
+**(Popov1)** A.M. Popov, I. V. Lebedeva, A. A. Knizhnik, Y. E. Lozovik and B. V. Potapkin, Chem. Phys. Lett. 536, 82-86 (2012).
+
+.. _Koziol:
+
+**(Koziol1)** Z. Koziol, G. Gawlik and J. Jagielski, Chinese Phys. B 28, 096101 (2019).

doc/src/pair_local_density.rst

@@ -26,23 +26,25 @@ Examples
 Description
 """""""""""
 
-The local density (LD) potential is a mean-field manybody potential, and, in some
-sense,a generalization of embedded atom models (EAM). The name "local density
-potential" arises from the fact that it assigns an energy to an atom depending
-on the number of neighboring atoms of given type around it within a predefined
-spherical volume (i.e., within a cutoff). The bottom-up coarse-graining (CG)
-literature suggests that such potentials can be widely useful  in capturing
-effective multibody forces in a computationally efficient manner so as to
-improve the quality of CG models of implicit solvation:ref:`(Sanyal1) <Sanyal1>` and
-phase-segregation in liquid mixtures:ref:`(Sanyal2) <Sanyal2>`, and provide guidelines
-to determine the extent of manybody correlations present in a CG
-model.:ref:`(Rosenberger) <Rosenberger>` The LD potential in LAMMPS is primarily
-intended to be used as a corrective potential over traditional pair potentials
-in bottom-up CG models, i.e., as a hybrid pair style with
-other explicit pair interaction terms (e.g., table spline, Lennard Jones, etc.).
-Because the LD potential is not a pair potential per se,  it is implemented
-simply as a single auxiliary file with all specifications that will be read
-upon initialization.
+The local density (LD) potential is a mean-field manybody potential,
+and, in some way, a generalization of embedded atom models (EAM).  The
+name "local density potential" arises from the fact that it assigns an
+energy to an atom depending on the number of neighboring atoms of a
+given type around it within a predefined spherical volume (i.e., within
+the cutoff).  The bottom-up coarse-graining (CG) literature suggests
+that such potentials can be widely useful in capturing effective
+multibody forces in a computationally efficient manner and thus improve
+the quality of CG models of implicit solvation :ref:`(Sanyal1)
+<Sanyal1>` and phase-segregation in liquid mixtures :ref:`(Sanyal2)
+<Sanyal2>`, and provide guidelines to determine the extent of manybody
+correlations present in a CG model :ref:`(Rosenberger) <Rosenberger>`.
+The LD potential in LAMMPS is primarily intended to be used as a
+corrective potential over traditional pair potentials in bottom-up CG
+models via :doc:`hybrid/overlay pair style <pair_hybrid>` with other
+explicit pair interaction terms (e.g., tabulated, Lennard-Jones, Morse
+etc.).  Because the LD potential is not a pair potential per se, it is
+implemented simply as a single auxiliary file with all specifications
+that will be read upon initialization.
 
 .. note::
 

doc/src/pair_python.rst

@@ -126,11 +126,11 @@ and *compute_energy*, which both take 3 numerical arguments:
 * itype = the (numerical) type of the first atom
 * jtype = the (numerical) type of the second atom
 
-This functions need to compute the force and the energy, respectively,
-and use the result as return value. The functions need to use the
-*pmap* dictionary to convert the LAMMPS atom type number to the symbolic
-value of the internal potential parameter data structure. Following
-the *LJCutMelt* example, here are the two functions:
+This functions need to compute the (scaled) force and the energy,
+respectively, and use the result as return value. The functions need
+to use the *pmap* dictionary to convert the LAMMPS atom type number
+to the symbolic value of the internal potential parameter data structure.
+Following the *LJCutMelt* example, here are the two functions:
 
 .. code-block:: python
 
@@ -154,10 +154,10 @@ the *LJCutMelt* example, here are the two functions:
 
    for consistency with the C++ pair styles in LAMMPS, the
    *compute_force* function follows the conventions of the Pair::single()
-   methods and does not return the full force, but the force scaled by
-   the distance between the two atoms, so this value only needs to be
-   multiplied by delta x, delta y, and delta z to conveniently obtain the
-   three components of the force vector between these two atoms.
+   methods and does not return the pairwise force directly, but the force
+   divided by the distance between the two atoms, so this value only needs
+   to be  multiplied by delta x, delta y, and delta z to conveniently obtain
+   the three components of the force vector between these two atoms.
 
 ----------
 

doc/src/pair_reaxff.rst

@@ -20,7 +20,7 @@ Syntax
   .. parsed-literal::
 
      keyword = *checkqeq* or *lgvdw* or *safezone* or *mincap* or *minhbonds*
-       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff or acks2/reaxff fix
+       *checkqeq* value = *yes* or *no* = whether or not to require qeq/reaxff fix
        *enobonds* value = *yes* or *no* = whether or not to tally energy of atoms with no bonds
        *lgvdw* value = *yes* or *no* = whether or not to use a low gradient vdW correction
        *safezone* = factor used for array allocation
@@ -119,8 +119,7 @@ The ReaxFF parameter files provided were created using a charge
 equilibration (QEq) model for handling the electrostatic interactions.
 Therefore, by default, LAMMPS requires that either the
 :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or the
-:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
-command be used with
+:doc:`fix qeq/shielded <fix_qeq>` command be used with
 *pair_style reaxff* when simulating a ReaxFF model, to equilibrate
 the charges each timestep.
 
@@ -129,8 +128,7 @@ for the QEq fixes, allowing a simulation to be run without charge
 equilibration. In this case, the static charges you assign to each
 atom will be used for computing the electrostatic interactions in
 the system. See the :doc:`fix qeq/reaxff <fix_qeq_reaxff>` or
-:doc:`fix qeq/shielded <fix_qeq>` or :doc:`fix acks2/reaxff <fix_acks2_reaxff>`
-command documentation for more details.
+:doc:`fix qeq/shielded <fix_qeq>` command documentation for more details.
 
 Using the optional keyword *lgvdw* with the value *yes* turns on the
 low-gradient correction of ReaxFF for long-range London Dispersion,
@@ -354,8 +352,7 @@ Related commands
 """"""""""""""""
 
 :doc:`pair_coeff <pair_coeff>`, :doc:`fix qeq/reaxff <fix_qeq_reaxff>`,
-:doc:`fix acks2/reaxff <fix_acks2_reaxff>`, :doc:`fix reaxff/bonds <fix_reaxff_bonds>`,
-:doc:`fix reaxff/species <fix_reaxff_species>`
+:doc:`fix reaxff/bonds <fix_reaxff_bonds>`, :doc:`fix reaxff/species <fix_reaxff_species>`
 
 Default
 """""""

doc/src/pair_sw.rst

@@ -159,14 +159,28 @@ taken from the ij and ik pairs (:math:`\sigma`, *a*, :math:`\gamma`)
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
 
-.. note::
+These accelerated styles are part of the GPU, INTEL, KOKKOS,
+OPENMP and OPT packages, respectively.  They are only enabled if
+LAMMPS was built with those packages.  See the :doc:`Build package <Build_package>` page for more info.
 
-  When using the INTEL package with this style, there is an additional
-  5 to 10 percent performance improvement when the Stillinger-Weber
-  parameters p and q are set to 4 and 0 respectively.  These
-  parameters are common for modeling silicon and water.
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+When using the INTEL package with this style, there is an
+additional 5 to 10 percent performance improvement when the
+Stillinger-Weber parameters p and q are set to 4 and 0 respectively.
+These parameters are common for modeling silicon and water.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/plugin.rst

@@ -65,8 +65,10 @@ only enabled if LAMMPS was built with that package.
 See the :doc:`Build package <Build_package>` page for
 more info. Plugins are not available on Windows.
 
-If plugins access functions or classes from a package, LAMMPS must
-have been compiled with that package included.
+For the loading of plugins to work the LAMMPS library must be
+:ref:`compiled as a shared library <library>`.  If plugins
+access functions or classes from a package, LAMMPS must have
+been compiled with that package included.
 
 Plugins are dependent on the LAMMPS binary interface (ABI)
 and particularly the MPI library used. So they are not guaranteed

doc/src/region.rst

@@ -371,13 +371,26 @@ sub-regions can be defined with the *open* keyword.
 
 ----------
 
-.. include:: accel_styles.rst
+Styles with a *gpu*, *intel*, *kk*, *omp*, or *opt* suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed on the :doc:`Speed packages <Speed_packages>` doc
+page.  The accelerated styles take the same arguments and should
+produce the same results, except for round-off and precision issues.
 
-.. note::
+The code using the region (such as a fix or compute) must also be supported
+by Kokkos or no acceleration will occur. Currently, only *block* style
+regions are supported by Kokkos.
 
-  Currently, only *block* style regions are supported by Kokkos.  The
-  code using the region (such as a fix or compute) must also be
-  supported by Kokkos or no acceleration will occur.
+These accelerated styles are part of the Kokkos package.  They are
+only enabled if LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` page for more info.
+
+You can specify the accelerated styles explicitly in your input script
+by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the
+:doc:`suffix <suffix>` command in your input script.
+
+See the :doc:`Speed packages <Speed_packages>` page for more
+instructions on how to use the accelerated styles effectively.
 
 ----------
 

doc/src/run_style.rst

@@ -125,13 +125,12 @@ screen.0 by default; see the :doc:`-plog and -pscreen command-line switches <Run
 for the second partition will not contain thermodynamic output beyond the
 first timestep of the run.
 
-See the :doc:`Accelerator packages <Speed_packages>` page for
-performance details of the speed-up offered by the *verlet/split*
-style.  One important performance consideration is the assignment of
-logical processors in the 2 partitions to the physical cores of a
-parallel machine.  The :doc:`processors <processors>` command has
-options to support this, and strategies are discussed in :doc:`Section
-5 <Speed>` of the manual.
+See the :doc:`Speed packages <Speed_packages>` page for performance
+details of the speed-up offered by the *verlet/split* style.  One
+important performance consideration is the assignment of logical
+processors in the 2 partitions to the physical cores of a parallel
+machine.  The :doc:`processors <processors>` command has options to
+support this, and strategies are discussed in :doc:`Section 5 <Speed>` of the manual.
 
 ----------
 
@@ -296,10 +295,10 @@ except for round-off and precision issues.
 
 You can specify *respa/omp* explicitly in your input script, or you
 can use the :doc:`-suffix command-line switch <Run_options>` when you
-invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in
-your input script.
+invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your
+input script.
 
-See the :doc:`Accelerator packages <Speed_packages>` page for more
+See the :doc:`Speed packages <Speed_packages>` page for more
 instructions on how to use the accelerated styles effectively.
 
 ----------
@@ -309,8 +308,7 @@ Restrictions
 
 The *verlet/split* style can only be used if LAMMPS was built with the
 REPLICA package. Correspondingly the *respa/omp* style is available
-only if the OPENMP package was included. See the :doc:`Build package
-<Build_package>` page for more info.
+only if the OPENMP package was included. See the :doc:`Build package <Build_package>` page for more info.
 
 Whenever using rRESPA, the user should experiment with trade-offs in
 speed and accuracy for their system, and verify that they are

doc/utils/check-styles.py

@@ -254,7 +254,7 @@ for command_type, entries in index.items():
 
 print("Total number of style index entries:", total_index)
 
-skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
+skip_fix = ('python', 'NEIGH_HISTORY/omp','qeq/reax','reax/c/bonds','reax/c/species')
 skip_pair = ('meam/c','lj/sf','reax/c')
 
 counter = 0
@@ -282,7 +282,7 @@ if counter:
 counter = 0
 
 counter += check_style_index("compute", compute, index["compute"])
-counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
+counter += check_style_index("fix", fix, index["fix"], skip=['python','qeq/reax','reax/c/bonds','reax/c/species'])
 counter += check_style_index("angle_style", angle, index["angle_style"])
 counter += check_style_index("bond_style", bond, index["bond_style"])
 counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])

doc/utils/requirements.txt

@@ -1,7 +1,7 @@
-Sphinx
-sphinxcontrib-spelling
-git+git://github.com/akohlmey/sphinx-fortran@parallel-read
-sphinx_tabs
-breathe
-Pygments
-six
+Sphinx==4.2.0
+sphinxcontrib-spelling==7.2.1
+git+https://github.com/akohlmey/sphinx-fortran@parallel-read
+sphinx_tabs==3.2.0
+breathe==4.31.0
+Pygments==2.10.0
+six==1.16.0

doc/utils/sphinx-config/false_positives.txt

@@ -19,7 +19,6 @@ accuracies
 ach
 ackland
 Ackland
-acks
 acolor
 acos
 Acta
@@ -78,7 +77,6 @@ allocators
 allosws
 AlO
 Alonso
-Alperen
 alphak
 alphashrink
 amap
@@ -687,7 +685,6 @@ diagonalized
 diagonalizers
 diagonalizing
 Diallo
-diblock
 Dickel
 diel
 differentiable
@@ -1125,6 +1122,7 @@ gaussian
 gaussians
 Gaussians
 Gavhane
+Gawlik
 gayberne
 gcc
 gcmc
@@ -1138,7 +1136,6 @@ Germann
 Germano
 gerolf
 Gerolf
-getrusage
 Gershgorin
 getter
 gettimeofday
@@ -1226,7 +1223,6 @@ Guo
 gw
 gyromagnetic
 gz
-gzip
 gzipped
 Haak
 Hafskjold
@@ -1257,7 +1253,6 @@ hbond
 hcp
 hdnnp
 HDNNP
-Hearn
 heatconduction
 Hebbeker
 Hebenstreit
@@ -1284,7 +1279,6 @@ hgrid
 hhmrr
 Hibbs
 Higdon
-hiID
 Hijazi
 Hilger
 Hinestrosa
@@ -1483,6 +1477,7 @@ Izz
 Jacobsen
 Jadhao
 Jadhav
+Jagielski
 jagreat
 Jahn
 Jalalvand
@@ -1609,6 +1604,7 @@ Koslowski
 Kosovan
 Koster
 Kosztin
+Koziol
 Kp
 kradius
 Kraker
@@ -1781,7 +1777,6 @@ Loewen
 logfile
 logfreq
 logicals
-loID
 Lomdahl
 Lond
 lookup
@@ -1817,7 +1812,6 @@ lyon
 Lysogorskiy
 Lyulin
 lz
-lzma
 Maaravi
 MACHDYN
 machdyn
@@ -2271,7 +2265,6 @@ Nmols
 nn
 nnodes
 Nocedal
-nO
 nocite
 nocoeff
 nodeless
@@ -2771,7 +2764,6 @@ REAXFF
 ReaxFF
 reaxff
 rebo
-recurse
 recursing
 Ree
 refactored
@@ -3086,7 +3078,6 @@ Spearot
 specular
 spellcheck
 Spellmeyer
-Speybroeck
 sph
 SPH
 Spickermann
@@ -3452,7 +3443,6 @@ usec
 uSemiParallel
 userguide
 username
-usleep
 usr
 util
 utils
@@ -3500,7 +3490,6 @@ Verlag
 verlet
 Verlet
 versa
-Verstraelen
 ves
 vflag
 vhi
@@ -3567,7 +3556,6 @@ vzcm
 vzi
 Waals
 Wadley
-Waroquier
 wallstyle
 walltime
 Waltham
@@ -3672,7 +3660,6 @@ Yc
 ycm
 Yeh
 yellowgreen
-yEs
 Yethiraj
 yflag
 yhi

examples/PACKAGES/extep/BN.extep

@@ -0,0 +1 @@
+../../../potentials/BN.extep

examples/PACKAGES/extep/in.extep-bn

@@ -15,7 +15,7 @@ neigh_modify    check yes
 
 # Potential
 pair_style      extep
-pair_coeff      * * ../../../../potentials/BN.extep B N
+pair_coeff      * * BN.extep B N
 
 # Output 
 thermo          10

examples/PACKAGES/local_density/benzene_water/log.04Sep19.g++.1

@@ -1,267 +0,0 @@
-LAMMPS (7 Aug 2019)
-# LAMMPS input file for 26.5% benzene mole fraction solution
-# with 380 benzene and 1000 water molecules,
-# using all possible local density potentials
-# between benzene and water
-#
-# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
-#
-# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
-
-
-
-# Initialize simulation box
-dimension       3
-boundary        p p p
-units           real
-atom_style      molecular
-
-# Set potential styles
-pair_style      hybrid/overlay table spline 500 local/density
-
-# Read molecule data and set initial velocities
-read_data       benzene_water.data
-  orthogonal box = (-12.865 -12.865 -64.829) to (12.865 12.865 64.829)
-  1 by 1 by 8 MPI processor grid
-  reading atoms ...
-  1380 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-  special bonds CPU = 0.000566959 secs
-  read_data CPU = 0.00661397 secs
-velocity        all create  3.0000e+02 16611 rot yes dist gaussian
-
-# Assign potentials
-pair_coeff          1     1    table          benzene_water.pair.table      PairBB
-WARNING: 33 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 150 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          1     2    table          benzene_water.pair.table      PairWW
-WARNING: 61 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 90 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          2     2    table          benzene_water.pair.table      PairBW
-WARNING: 108 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 135 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          *     *    local/density  benzene_water.localdensity.table
-
-# Recentering during minimization and equilibration
-fix recentering all recenter 0.0 0.0 0.0 units box
-
-# Thermostat & time integration
-timestep        2.0
-thermo          100
-thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
-
-# Minimization
-minimize        1.e-4 0.0 10000 10000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 15.25
-  ghost atom cutoff = 15.25
-  binsize = 7.625, bins = 4 4 18
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair local/density, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 8.061 | 8.32 | 8.674 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-         300    1233.1611    4162.3053    5395.4665            0            0            0    4162.3053 
-         300    1233.1611     2275.526    3508.6871            0            0            0     2275.526 
-Loop time of 0.352822 on 8 procs for 40 steps with 1380 atoms
-
-71.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-Minimization stats:
-  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
-         4162.30533361      2208.86525108      2275.52597861
-  Force two-norm initial, final = 259.364 69.3915
-  Force max component initial, final = 22.2077 8.31436
-  Final line search alpha, max atom move = 2.90022e-12 2.41135e-11
-  Iterations, force evaluations = 40 110
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.053192   | 0.23903    | 0.32779    |  17.2 | 67.75
-Bond    | 9.0599e-06 | 1.6302e-05 | 2.5272e-05 |   0.0 |  0.00
-Neigh   | 0.00044513 | 0.0023614  | 0.0063851  |   5.1 |  0.67
-Comm    | 0.015469   | 0.090432   | 0.20295    |  20.0 | 25.63
-Output  | 0          | 0          | 0          |   0.0 |  0.00
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.02098    |            |       |  5.95
-
-Nlocal:    172.5 ave 348 max 72 min
-Histogram: 5 0 0 0 0 0 0 0 1 2
-Nghost:    2193.62 ave 4352 max 932 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    9700.5 ave 20535 max 3685 min
-Histogram: 5 0 0 0 0 0 0 1 0 2
-
-Total # of neighbors = 77604
-Ave neighs/atom = 56.2348
-Ave special neighs/atom = 0
-Neighbor list builds = 2
-Dangerous builds = 0
-
-# Set up integration parameters
-fix             timeintegration all nve
-fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
-
-# Equilibration (for realistic results, run for 5000000 steps)
-reset_timestep  0
-run             5000
-WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
-Per MPI rank memory allocation (min/avg/max) = 6.936 | 7.195 | 7.552 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-         300    1233.1611    2866.9109    4100.0721            0            0            0    2866.9109 
-   273.33541    1123.5553    3983.2007     5106.756            0            0            0    3983.2007 
-   293.68078    1207.1857    3319.6601    4526.8458            0            0            0    3319.6601 
-   314.21462    1291.5908    3389.2178    4680.8086            0            0            0    3389.2178 
-   323.77563    1330.8917    3332.9828    4663.8745            0            0            0    3332.9828 
-    302.5902    1243.8082    3461.7692    4705.5774            0            0            0    3461.7692 
-   295.39324    1214.2249    3411.5727    4625.7976            0            0            0    3411.5727 
-   320.52341    1317.5234    3453.1931    4770.7164            0            0            0    3453.1931 
-   312.00777    1282.5195    3403.3443    4685.8638            0            0            0    3403.3443 
-   307.96774    1265.9128    3429.7809    4695.6937            0            0            0    3429.7809 
-   294.75922    1211.6187    3388.8404    4600.4591            0            0            0    3388.8404 
-   311.24567    1279.3869    3514.9603    4794.3472            0            0            0    3514.9603 
-    306.6152    1260.3531    3447.2011    4707.5542            0            0            0    3447.2011 
-   305.23306    1254.6718    3375.5092     4630.181            0            0            0    3375.5092 
-   321.62889    1322.0675    3460.2581    4782.3256            0            0            0    3460.2581 
-   316.37725    1300.4804    3437.0312    4737.5116            0            0            0    3437.0312 
-   322.90522    1327.3139    3389.1262      4716.44            0            0            0    3389.1262 
-   307.57893    1264.3146    3359.8491    4624.1637            0            0            0    3359.8491 
-   302.22607    1242.3115    3406.1711    4648.4826            0            0            0    3406.1711 
-   302.73997    1244.4239    3220.2582    4464.6821            0            0            0    3220.2582 
-   303.66194    1248.2137    3318.4629    4566.6765            0            0            0    3318.4629 
-   308.73862    1269.0815    3369.5894     4638.671            0            0            0    3369.5894 
-   315.60294    1297.2976    3411.2405    4708.5381            0            0            0    3411.2405 
-    310.0113    1274.3129    3360.1054    4634.4183            0            0            0    3360.1054 
-   302.36229    1242.8714    3326.9845    4569.8559            0            0            0    3326.9845 
-   317.78659    1306.2735    3355.4976    4661.7711            0            0            0    3355.4976 
-   302.50479    1243.4571    3317.6846    4561.1417            0            0            0    3317.6846 
-   304.29249    1250.8056    3423.5068    4674.3124            0            0            0    3423.5068 
-   305.99948    1257.8222    3432.9395    4690.7617            0            0            0    3432.9395 
-   309.93363    1273.9937     3393.657    4667.6506            0            0            0     3393.657 
-   316.14884    1299.5415    3463.0636    4762.6051            0            0            0    3463.0636 
-   300.38817    1234.7567    3309.2495    4544.0062            0            0            0    3309.2495 
-   311.05735    1278.6128    3304.4418    4583.0546            0            0            0    3304.4418 
-   311.11872     1278.865    3291.1891    4570.0542            0            0            0    3291.1891 
-   315.74338    1297.8749    3341.3063    4639.1812            0            0            0    3341.3063 
-    297.5658    1223.1552    3316.3862    4539.5414            0            0            0    3316.3862 
-   311.79033    1281.6257    3357.4556    4639.0813            0            0            0    3357.4556 
-   310.93666    1278.1167    3414.7694    4692.8861            0            0            0    3414.7694 
-   307.37298     1263.468    3337.3889    4600.8569            0            0            0    3337.3889 
-   298.84185    1228.4005    3329.6173    4558.0178            0            0            0    3329.6173 
-   310.54684    1276.5143    3351.0852    4627.5995            0            0            0    3351.0852 
-    300.0871    1233.5191    3302.2315    4535.7506            0            0            0    3302.2315 
-   304.69078    1252.4427    3324.2508    4576.6935            0            0            0    3324.2508 
-   313.50714    1288.6827    3330.4088    4619.0915            0            0            0    3330.4088 
-   329.80018    1355.6559      3301.86    4657.5159            0            0            0      3301.86 
-   304.57609    1251.9713    3365.2938    4617.2652            0            0            0    3365.2938 
-   308.73584    1269.0701    3344.4155    4613.4856            0            0            0    3344.4155 
-   306.90951    1261.5629    3304.4698    4566.0327            0            0            0    3304.4698 
-   308.85761    1269.5707    3392.1511    4661.7218            0            0            0    3392.1511 
-   302.78788    1244.6208    3317.0849    4561.7057            0            0            0    3317.0849 
-   321.68092    1322.2813    3321.5755    4643.8568            0            0            0    3321.5755 
-Loop time of 16.3061 on 8 procs for 5000 steps with 1380 atoms
-
-Performance: 52.986 ns/day, 0.453 hours/ns, 306.634 timesteps/s
-69.6% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 2.1872     | 10.542     | 14.607     | 116.7 | 64.65
-Bond    | 0.00044084 | 0.00069669 | 0.00095081 |   0.0 |  0.00
-Neigh   | 0.026948   | 0.15225    | 0.44344    |  42.0 |  0.93
-Comm    | 0.63452    | 4.2953     | 9.49       | 133.9 | 26.34
-Output  | 0.0016391  | 0.012378   | 0.050919   |  13.9 |  0.08
-Modify  | 0.45894    | 1.2107     | 4.4629     | 116.4 |  7.42
-Other   |            | 0.09292    |            |       |  0.57
-
-Nlocal:    172.5 ave 380 max 70 min
-Histogram: 5 0 0 0 0 0 0 1 1 1
-Nghost:    2213 ave 4440 max 903 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    10042.5 ave 24051 max 3500 min
-Histogram: 5 0 0 0 0 0 0 1 1 1
-
-Total # of neighbors = 80340
-Ave neighs/atom = 58.2174
-Ave special neighs/atom = 0
-Neighbor list builds = 123
-Dangerous builds = 1
-
-# Turn off recentering during production phase
-unfix recentering
-
-# Setup trajectory output
-dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
-dump_modify     myDump element B W
-dump_modify     myDump sort id
-
-# Production (for realistic results, run for 10000000 steps)
-reset_timestep  0
-run             1000
-Per MPI rank memory allocation (min/avg/max) = 8.232 | 8.492 | 8.851 Mbytes
-Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
-   321.68092    1322.2813    3784.0834    5106.3647            0            0            0    3784.0834 
-   310.59763    1276.7231    3318.3283    4595.0513            0            0            0    3318.3283 
-   303.39445    1247.1141    3324.1191    4571.2332            0            0            0    3324.1191 
-   311.37275    1279.9092    3305.0901    4584.9993            0            0            0    3305.0901 
-   311.29071     1279.572     3248.216     4527.788            0            0            0     3248.216 
-   314.53456     1292.906    3283.4563    4576.3623            0            0            0    3283.4563 
-   316.52595    1301.0916    3258.9171    4560.0087            0            0            0    3258.9171 
-   318.92447    1310.9509    3235.6256    4546.5765            0            0            0    3235.6256 
-   311.79212    1281.6331     3308.099    4589.7321            0            0            0     3308.099 
-   305.52477    1255.8709    3267.6907    4523.5616            0            0            0    3267.6907 
-   301.07457    1237.5782    3206.3997    4443.9779            0            0            0    3206.3997 
-Loop time of 4.44139 on 8 procs for 1000 steps with 1380 atoms
-
-Performance: 38.907 ns/day, 0.617 hours/ns, 225.155 timesteps/s
-60.8% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.656      | 2.5078     | 3.5775     |  57.7 | 56.46
-Bond    | 0.00013375 | 0.0001854  | 0.0002377  |   0.0 |  0.00
-Neigh   | 0.0048757  | 0.029188   | 0.090432   |  18.9 |  0.66
-Comm    | 0.51836    | 1.4427     | 2.6285     |  56.9 | 32.48
-Output  | 0.083084   | 0.089199   | 0.10333    |   2.3 |  2.01
-Modify  | 0.0087376  | 0.019705   | 0.038437   |   8.4 |  0.44
-Other   |            | 0.3526     |            |       |  7.94
-
-Nlocal:    172.5 ave 388 max 69 min
-Histogram: 5 0 0 0 0 0 0 2 0 1
-Nghost:    2207.88 ave 4429 max 896 min
-Histogram: 3 0 0 2 0 0 2 0 0 1
-Neighs:    10094.1 ave 24847 max 3403 min
-Histogram: 5 0 0 0 0 0 1 1 0 1
-
-Total # of neighbors = 80753
-Ave neighs/atom = 58.5167
-Ave special neighs/atom = 0
-Neighbor list builds = 23
-Dangerous builds = 0
-
-
-Total wall time: 0:00:21

examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.1

@@ -0,0 +1,300 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+Reading data file ...
+  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  1380 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.006 seconds
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 150 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 90 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 135 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 15.25
+  ghost atom cutoff = 15.25
+  binsize = 7.625, bins = 4 4 18
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.754 | 8.754 | 8.754 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
+         300    1233.1611    985.54829    2218.7094            0            0            0    985.54829 
+         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
+Loop time of 0.812343 on 1 procs for 134 steps with 1380 atoms
+
+99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+      2374.67491482358   962.664796664787   962.660357218268
+  Force two-norm initial, final = 263.77519 15.741017
+  Force max component initial, final = 22.412654 7.9360139
+  Final line search alpha, max atom move = 0.014975513 0.11884588
+  Iterations, force evaluations = 134 240
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.78539    | 0.78539    | 0.78539    |   0.0 | 96.68
+Bond    | 2.0149e-05 | 2.0149e-05 | 2.0149e-05 |   0.0 |  0.00
+Neigh   | 0.016759   | 0.016759   | 0.016759   |   0.0 |  2.06
+Comm    | 0.0045     | 0.0045     | 0.0045     |   0.0 |  0.55
+Output  | 2.9402e-05 | 2.9402e-05 | 2.9402e-05 |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.005647   |            |       |  0.70
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5832.00 ave        5832 max        5832 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        78165.0 ave       78165 max       78165 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 78165
+Ave neighs/atom = 56.641304
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 5
+Dangerous builds = 0
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 7.629 | 7.629 | 7.629 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    962.66036    2195.8215            0            0            0    962.66036 
+    253.1913    1040.7522     1803.711    2844.4633            0            0            0     1803.711 
+   290.31049     1193.332    2059.0637    3252.3958            0            0            0    2059.0637 
+   299.30778    1230.3157     2140.226    3370.5417            0            0            0     2140.226 
+   309.81524     1273.507    2178.3782    3451.8853            0            0            0    2178.3782 
+   299.79526    1232.3195    2229.9248    3462.2444            0            0            0    2229.9248 
+   299.24909    1230.0745    2260.7129    3490.7874            0            0            0    2260.7129 
+    299.5898     1231.475    2244.2384    3475.7134            0            0            0    2244.2384 
+   297.81223    1224.1682      2320.27    3544.4382            0            0            0      2320.27 
+   301.53975    1239.4903    2277.0431    3516.5334            0            0            0    2277.0431 
+   292.00572    1200.3003    2292.3073    3492.6076            0            0            0    2292.3073 
+   309.19709    1270.9661    2303.6055    3574.5716            0            0            0    2303.6055 
+   297.54933    1223.0876     2304.127    3527.2146            0            0            0     2304.127 
+   303.48106    1247.4702    2303.5673    3551.0375            0            0            0    2303.5673 
+   296.46047    1218.6118    2256.1591    3474.7709            0            0            0    2256.1591 
+    299.4835     1231.038    2280.0452    3511.0832            0            0            0    2280.0452 
+   306.25958    1258.8914    2307.9795    3566.8709            0            0            0    2307.9795 
+   304.67335    1252.3711    2284.8252    3537.1963            0            0            0    2284.8252 
+   298.33637    1226.3227    2289.8499    3516.1726            0            0            0    2289.8499 
+    303.1338    1246.0427    2342.2148    3588.2575            0            0            0    2342.2148 
+   305.86051     1257.251    2341.0106    3598.2616            0            0            0    2341.0106 
+   297.75418    1223.9296    2303.5613    3527.4909            0            0            0    2303.5613 
+   296.79348    1219.9806    2327.5207    3547.5013            0            0            0    2327.5207 
+   307.25403    1262.9791    2288.4219     3551.401            0            0            0    2288.4219 
+   301.26976    1238.3805    2291.2465     3529.627            0            0            0    2291.2465 
+   297.17249    1221.5385    2283.3926    3504.9311            0            0            0    2283.3926 
+   313.99072    1290.6705    2293.9661    3584.6366            0            0            0    2293.9661 
+   301.70804    1240.1821    2331.1694    3571.3515            0            0            0    2331.1694 
+   300.62599    1235.7343    2325.4367     3561.171            0            0            0    2325.4367 
+   292.13495    1200.8316     2315.631    3516.4626            0            0            0     2315.631 
+    313.9981    1290.7008    2286.0536    3576.7545            0            0            0    2286.0536 
+   300.25311    1234.2015    2324.2379    3558.4394            0            0            0    2324.2379 
+    309.3746    1271.6958    2322.2298    3593.9256            0            0            0    2322.2298 
+   300.23041    1234.1082    2332.7521    3566.8603            0            0            0    2332.7521 
+   302.97054    1245.3716    2303.1689    3548.5405            0            0            0    2303.1689 
+   294.77155    1211.6694    2334.5087    3546.1781            0            0            0    2334.5087 
+   296.81476    1220.0681    2322.5932    3542.6613            0            0            0    2322.5932 
+   301.83238    1240.6932    2345.4841    3586.1773            0            0            0    2345.4841 
+    295.0399    1212.7724    2312.3889    3525.1614            0            0            0    2312.3889 
+   300.73565     1236.185    2338.8384    3575.0235            0            0            0    2338.8384 
+   303.02264    1245.5858    2310.0868    3555.6726            0            0            0    2310.0868 
+   302.86404    1244.9339    2332.2001     3577.134            0            0            0    2332.2001 
+   293.77916    1207.5901    2293.2799    3500.8701            0            0            0    2293.2799 
+   299.30072    1230.2867    2317.5065    3547.7933            0            0            0    2317.5065 
+   311.05029    1278.5837    2311.0476    3589.6313            0            0            0    2311.0476 
+   293.25646    1205.4416    2314.7398    3520.1814            0            0            0    2314.7398 
+   310.49018    1276.2814    2337.4909    3613.7723            0            0            0    2337.4909 
+   302.37336    1242.9169    2340.3197    3583.2366            0            0            0    2340.3197 
+   297.06862    1221.1116    2323.9136    3545.0252            0            0            0    2323.9136 
+   300.54817    1235.4144    2315.2405    3550.6549            0            0            0    2315.2405 
+   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
+Loop time of 15.2696 on 1 procs for 5000 steps with 1380 atoms
+
+Performance: 56.583 ns/day, 0.424 hours/ns, 327.447 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 14.432     | 14.432     | 14.432     |   0.0 | 94.51
+Bond    | 0.00032375 | 0.00032375 | 0.00032375 |   0.0 |  0.00
+Neigh   | 0.41541    | 0.41541    | 0.41541    |   0.0 |  2.72
+Comm    | 0.0975     | 0.0975     | 0.0975     |   0.0 |  0.64
+Output  | 0.0013044  | 0.0013044  | 0.0013044  |   0.0 |  0.01
+Modify  | 0.30336    | 0.30336    | 0.30336    |   0.0 |  1.99
+Other   |            | 0.01973    |            |       |  0.13
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5843.00 ave        5843 max        5843 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        76949.0 ave       76949 max       76949 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 76949
+Ave neighs/atom = 55.760145
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 121
+Dangerous builds = 1
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 9.022 | 9.022 | 9.022 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+   309.10643    1270.5934    2333.1848    3603.7783            0            0            0    2333.1848 
+   300.84572    1236.6375    2331.3493    3567.9868            0            0            0    2331.3493 
+   300.90599    1236.8852    2337.6775    3574.5627            0            0            0    2337.6775 
+   302.77895    1244.5841    2341.7778     3586.362            0            0            0    2341.7778 
+   291.66639    1198.9055    2320.3512    3519.2567            0            0            0    2320.3512 
+    298.7003    1227.8187    2292.8195    3520.6382            0            0            0    2292.8195 
+   301.11163    1237.7305     2310.017    3547.7475            0            0            0     2310.017 
+   305.22515    1254.6393    2315.1355    3569.7748            0            0            0    2315.1355 
+   295.15921    1213.2629     2310.184    3523.4468            0            0            0     2310.184 
+    299.2024    1229.8826    2332.2118    3562.0943            0            0            0    2332.2118 
+   302.80078    1244.6738    2320.3763    3565.0502            0            0            0    2320.3763 
+Loop time of 3.07208 on 1 procs for 1000 steps with 1380 atoms
+
+Performance: 56.249 ns/day, 0.427 hours/ns, 325.512 timesteps/s
+99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8993     | 2.8993     | 2.8993     |   0.0 | 94.37
+Bond    | 6.5327e-05 | 6.5327e-05 | 6.5327e-05 |   0.0 |  0.00
+Neigh   | 0.083502   | 0.083502   | 0.083502   |   0.0 |  2.72
+Comm    | 0.019967   | 0.019967   | 0.019967   |   0.0 |  0.65
+Output  | 0.012268   | 0.012268   | 0.012268   |   0.0 |  0.40
+Modify  | 0.052801   | 0.052801   | 0.052801   |   0.0 |  1.72
+Other   |            | 0.004203   |            |       |  0.14
+
+Nlocal:        1380.00 ave        1380 max        1380 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        5860.00 ave        5860 max        5860 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        77055.0 ave       77055 max       77055 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 77055
+Ave neighs/atom = 55.836957
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 24
+Dangerous builds = 0
+
+
+Total wall time: 0:00:19

examples/PACKAGES/local_density/benzene_water/log.27Oct21.benzene_water.g++.4

@@ -0,0 +1,299 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 26.5% benzene mole fraction solution
+# with 380 benzene and 1000 water molecules,
+# using all possible local density potentials
+# between benzene and water
+#
+# Author: Tanmoy Sanyal, Shell Group, UC Santa Barbara
+#
+# Refer: Sanyal and Shell, JPC-B, 2018, 122 (21), 5678-5693
+
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       benzene_water.data
+Reading data file ...
+  orthogonal box = (-12.865000 -12.865000 -64.829000) to (12.865000 12.865000 64.829000)
+  1 by 1 by 4 MPI processor grid
+  reading atoms ...
+  1380 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.007 seconds
+velocity        all create  3.0000e+02 16611 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1    table          benzene_water.pair.table      PairBB
+WARNING: 33 of 500 force values in table PairBB are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 150 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBB to re-computed values (src/pair_table.cpp:473)
+pair_coeff          1     2    table          benzene_water.pair.table      PairWW
+WARNING: 61 of 500 force values in table PairWW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 90 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairWW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          2     2    table          benzene_water.pair.table      PairBW
+WARNING: 108 of 500 force values in table PairBW are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 135 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairBW to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     *    local/density  benzene_water.localdensity.table
+
+# Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+# Thermostat & time integration
+timestep        2.0
+thermo          100
+thermo_style    custom temp ke pe etotal ebond eangle edihed evdwl
+
+# Minimization
+minimize        1.e-4 0.0 10000 10000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 15.25
+  ghost atom cutoff = 15.25
+  binsize = 7.625, bins = 4 4 18
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 8.441 | 8.589 | 8.688 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    2374.6749     3607.836            0            0            0    2374.6749 
+         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
+Loop time of 0.240559 on 4 procs for 74 steps with 1380 atoms
+
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+      2374.67491482358   1024.89407898645   1024.81130011575
+  Force two-norm initial, final = 263.77519 20.459697
+  Force max component initial, final = 22.412654 8.6082349
+  Final line search alpha, max atom move = 0.027790997 0.23923143
+  Iterations, force evaluations = 74 118
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.15928    | 0.1873     | 0.22814    |   6.5 | 77.86
+Bond    | 3.857e-06  | 4.4012e-06 | 5.496e-06  |   0.0 |  0.00
+Neigh   | 0.00064142 | 0.0028761  | 0.0058864  |   4.2 |  1.20
+Comm    | 0.0040776  | 0.039595   | 0.074187   |  12.6 | 16.46
+Output  | 0          | 0          | 0          |   0.0 |  0.00
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.01078    |            |       |  4.48
+
+Nlocal:        345.000 ave         664 max         147 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+Nghost:        2850.50 ave        4438 max        1208 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19377.5 ave       37718 max        7456 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 77510
+Ave neighs/atom = 56.166667
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 3
+Dangerous builds = 0
+
+# Set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 81890
+
+# Equilibration (for realistic results, run for 5000000 steps)
+reset_timestep  0
+run             5000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 7.316 | 7.465 | 7.563 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+         300    1233.1611    1024.8113    2257.9724            0            0            0    1024.8113 
+   263.61917    1083.6164     1866.745    2950.3614            0            0            0     1866.745 
+    296.0253     1216.823    2122.8463    3339.6692            0            0            0    2122.8463 
+   301.93846    1241.1292    2172.9802    3414.1095            0            0            0    2172.9802 
+    293.9491    1208.2887    2205.4892    3413.7779            0            0            0    2205.4892 
+   286.33795    1177.0027    2204.8908    3381.8935            0            0            0    2204.8908 
+   295.48217    1214.5904    2230.8849    3445.4753            0            0            0    2230.8849 
+   293.88908    1208.0419    2218.7563    3426.7982            0            0            0    2218.7563 
+   295.13798    1213.1756    2277.4515    3490.6271            0            0            0    2277.4515 
+   290.39538     1193.681    2273.4385    3467.1195            0            0            0    2273.4385 
+   297.56782    1223.1635    2268.7182    3491.8817            0            0            0    2268.7182 
+   306.45578    1259.6978    2289.1507    3548.8486            0            0            0    2289.1507 
+   308.54582     1268.289    2284.8514    3553.1404            0            0            0    2284.8514 
+   302.17353    1242.0955    2262.5577    3504.6532            0            0            0    2262.5577 
+   295.30087    1213.8452    2315.8853    3529.7305            0            0            0    2315.8853 
+   308.59197    1268.4787    2291.8314    3560.3101            0            0            0    2291.8314 
+   297.75618    1223.9378    2287.2003    3511.1381            0            0            0    2287.2003 
+   303.43395    1247.2765    2297.7158    3544.9923            0            0            0    2297.7158 
+   307.16233    1262.6021    2255.9769    3518.5791            0            0            0    2255.9769 
+   301.34428    1238.6868     2284.416    3523.1028            0            0            0     2284.416 
+   295.43209    1214.3846    2294.1043    3508.4889            0            0            0    2294.1043 
+   287.86904    1183.2963    2257.0204    3440.3168            0            0            0    2257.0204 
+    297.2661    1221.9233    2251.4194    3473.3428            0            0            0    2251.4194 
+   298.90221    1228.6486     2261.834    3490.4826            0            0            0     2261.834 
+   288.07202    1184.1307    2284.1918    3468.3225            0            0            0    2284.1918 
+   300.41201    1234.8547    2303.9573     3538.812            0            0            0    2303.9573 
+   283.91279     1167.034    2329.7936    3496.8277            0            0            0    2329.7936 
+   297.27507    1221.9602    2337.0516    3559.0118            0            0            0    2337.0516 
+   296.22263    1217.6341    2335.6424    3553.2765            0            0            0    2335.6424 
+   296.13784    1217.2856    2364.7034     3581.989            0            0            0    2364.7034 
+   308.17642    1266.7706    2320.2753    3587.0459            0            0            0    2320.2753 
+   310.26592    1275.3596    2301.9318    3577.2914            0            0            0    2301.9318 
+   292.97391    1204.2801    2289.8116    3494.0917            0            0            0    2289.8116 
+   294.81231    1211.8369    2315.0388    3526.8757            0            0            0    2315.0388 
+   298.66155    1227.6594    2317.2844    3544.9437            0            0            0    2317.2844 
+   302.77939    1244.5859    2301.2063    3545.7922            0            0            0    2301.2063 
+   291.47597    1198.1228    2285.1757    3483.2985            0            0            0    2285.1757 
+   286.19045    1176.3964    2265.2665    3441.6629            0            0            0    2265.2665 
+   295.58144    1214.9984    2272.3165     3487.315            0            0            0    2272.3165 
+   283.86988    1166.8577    2320.6142    3487.4719            0            0            0    2320.6142 
+    300.0576    1233.3979    2330.8962    3564.2941            0            0            0    2330.8962 
+   299.86413    1232.6026    2321.2281    3553.8308            0            0            0    2321.2281 
+   292.79017    1203.5248    2334.2308    3537.7557            0            0            0    2334.2308 
+    291.5027    1198.2327    2335.2119    3533.4446            0            0            0    2335.2119 
+   299.55471    1231.3307    2332.5216    3563.8524            0            0            0    2332.5216 
+   293.29613    1205.6046    2295.3263    3500.9309            0            0            0    2295.3263 
+   303.13151    1246.0333    2310.0548    3556.0881            0            0            0    2310.0548 
+   298.83954     1228.391    2297.3117    3525.7027            0            0            0    2297.3117 
+   297.44775      1222.67    2307.2483    3529.9183            0            0            0    2307.2483 
+   309.59874    1272.6171    2309.2439     3581.861            0            0            0    2309.2439 
+   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
+Loop time of 11.2235 on 4 procs for 5000 steps with 1380 atoms
+
+Performance: 76.982 ns/day, 0.312 hours/ns, 445.495 timesteps/s
+98.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 7.1444     | 8.5074     | 10.534     |  44.9 | 75.80
+Bond    | 0.00017048 | 0.00020672 | 0.00030488 |   0.0 |  0.00
+Neigh   | 0.026174   | 0.12108    | 0.26052    |  28.2 |  1.08
+Comm    | 0.21788    | 1.8597     | 3.3375     |  81.2 | 16.57
+Output  | 0.0008989  | 0.0069895  | 0.021647   |  10.2 |  0.06
+Modify  | 0.19418    | 0.7044     | 2.1378     |  98.6 |  6.28
+Other   |            | 0.02368    |            |       |  0.21
+
+Nlocal:        345.000 ave         678 max         148 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        2854.25 ave        4464 max        1181 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19366.8 ave       38533 max        7481 min
+Histogram: 2 0 0 0 0 1 0 0 0 1
+
+Total # of neighbors = 77467
+Ave neighs/atom = 56.135507
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 121
+Dangerous builds = 1
+
+# Turn off recentering during production phase
+unfix recentering
+
+# Setup trajectory output
+dump            myDump all custom 100 benzene_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element B W
+dump_modify     myDump sort id
+
+# Production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+run             1000
+  generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.640 | 8.791 | 8.894 Mbytes
+Temp KinEng PotEng TotEng E_bond E_angle E_dihed E_vdwl 
+   307.47844    1263.9015     2274.998    3538.8995            0            0            0     2274.998 
+   309.46142    1272.0526    2274.8499    3546.9026            0            0            0    2274.8499 
+   300.70977    1236.0787    2301.0588    3537.1374            0            0            0    2301.0588 
+   300.53659    1235.3668    2316.1008    3551.4675            0            0            0    2316.1008 
+   300.48582    1235.1581    2296.3009     3531.459            0            0            0    2296.3009 
+    299.2618    1230.1267    2325.7501    3555.8768            0            0            0    2325.7501 
+   303.00905    1245.5299    2321.8238    3567.3537            0            0            0    2321.8238 
+   300.07018    1233.4496    2339.2833    3572.7329            0            0            0    2339.2833 
+   304.20292    1250.4374    2353.1018    3603.5392            0            0            0    2353.1018 
+   304.19487    1250.4043    2334.5087     3584.913            0            0            0    2334.5087 
+   294.24283    1209.4961    2335.0535    3544.5496            0            0            0    2335.0535 
+Loop time of 2.90512 on 4 procs for 1000 steps with 1380 atoms
+
+Performance: 59.481 ns/day, 0.403 hours/ns, 344.220 timesteps/s
+98.4% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 1.8627     | 2.2082     | 2.7289     |  22.6 | 76.01
+Bond    | 4.042e-05  | 5.3677e-05 | 8.4044e-05 |   0.0 |  0.00
+Neigh   | 0.0066184  | 0.030172   | 0.064523   |  13.9 |  1.04
+Comm    | 0.05914    | 0.51145    | 0.86887    |  40.7 | 17.61
+Output  | 0.0057814  | 0.0073478  | 0.011158   |   2.6 |  0.25
+Modify  | 0.0085337  | 0.020869   | 0.042248   |   9.4 |  0.72
+Other   |            | 0.127      |            |       |  4.37
+
+Nlocal:        345.000 ave         682 max         147 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        2836.25 ave        4427 max        1175 min
+Histogram: 1 0 0 1 0 0 1 0 0 1
+Neighs:        19249.8 ave       38683 max        7433 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+
+Total # of neighbors = 76999
+Ave neighs/atom = 55.796377
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 23
+Dangerous builds = 0
+
+
+Total wall time: 0:00:14

examples/PACKAGES/local_density/methanol_implicit_water/log.04Sep19.g++.1

@@ -1,226 +0,0 @@
-LAMMPS (7 Aug 2019)
-# LAMMPS input file for 50.0% methanol mole fraction solution
-# with 2500 methanol molecules in implicit water.
-#
-#
-# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
-#
-# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
-
-
-# Initialize simulation box
-dimension       3
-boundary        p p p
-units           real
-atom_style      molecular
-
-# Set potential styles
-pair_style      hybrid/overlay table spline 500 local/density
-
-# Read molecule data and set initial velocities
-read_data       methanol_implicit_water.data
-  orthogonal box = (-31.123 -31.123 -31.123) to (31.123 31.123 31.123)
-  2 by 2 by 2 MPI processor grid
-  reading atoms ...
-  2500 atoms
-  0 = max # of 1-2 neighbors
-  0 = max # of 1-3 neighbors
-  0 = max # of 1-4 neighbors
-  1 = max # of special neighbors
-  special bonds CPU = 0.00063014 secs
-  read_data CPU = 0.00599909 secs
-velocity        all create  3.0000e+02 12142 rot yes dist gaussian
-
-# Assign potentials
-pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
-WARNING: 93 of 500 force values in table are inconsistent with -dE/dr.
-  Should only be flagged at inflection points (../pair_table.cpp:483)
-WARNING: 254 of 500 distance values in table with relative error
-  over 1e-06 to re-computed values (../pair_table.cpp:492)
-pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
-
-
-
-
-#Recentering during minimization and equilibration
-fix recentering all recenter 0.0 0.0 0.0 units box
-
-#Thermostat & time integration
-timestep        1.0
-thermo          100
-thermo_style    custom etotal ke pe temp evdwl
-
-#minimization
-minimize        1.e-4 0.0 1000 1000
-WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (../min.cpp:168)
-Neighbor list info ...
-  update every 1 steps, delay 0 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 17
-  ghost atom cutoff = 17
-  binsize = 8.5, bins = 8 8 8
-  2 neighbor lists, perpetual/occasional/extra = 2 0 0
-  (1) pair table, perpetual
-      attributes: half, newton on
-      pair build: half/bin/newton
-      stencil: half/bin/3d/newton
-      bin: standard
-  (2) pair local/density, perpetual, copy from (1)
-      attributes: half, newton on
-      pair build: copy
-      stencil: none
-      bin: none
-Per MPI rank memory allocation (min/avg/max) = 7.411 | 7.411 | 7.412 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   1470.3564    2234.7133   -764.35689          300   -764.35689 
-   46.496766    2234.7133   -2188.2165          300   -2188.2165 
-   7.9030246    2234.7133   -2226.8103          300   -2226.8103 
-Loop time of 0.463996 on 8 procs for 121 steps with 2500 atoms
-
-91.4% CPU use with 8 MPI tasks x no OpenMP threads
-
-Minimization stats:
-  Stopping criterion = linesearch alpha is zero
-  Energy initial, next-to-last, final = 
-        -764.356892369     -2227.85589084     -2226.81026984
-  Force two-norm initial, final = 134.911 3.83896
-  Force max component initial, final = 14.1117 1.07422
-  Final line search alpha, max atom move = 5.06747e-10 5.44356e-10
-  Iterations, force evaluations = 121 154
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 0.41442    | 0.41976    | 0.42434    |   0.5 | 90.47
-Bond    | 1.1683e-05 | 2.0713e-05 | 3.5048e-05 |   0.0 |  0.00
-Neigh   | 0.0084722  | 0.0090862  | 0.010038   |   0.5 |  1.96
-Comm    | 0.022712   | 0.028157   | 0.034072   |   1.9 |  6.07
-Output  | 3.1948e-05 | 3.6925e-05 | 6.6996e-05 |   0.0 |  0.01
-Modify  | 0          | 0          | 0          |   0.0 |  0.00
-Other   |            | 0.006937   |            |       |  1.50
-
-Nlocal:    312.5 ave 333 max 299 min
-Histogram: 2 2 0 0 1 0 2 0 0 1
-Nghost:    2546 ave 2580 max 2517 min
-Histogram: 1 1 0 3 0 1 0 0 0 2
-Neighs:    33215.4 ave 37251 max 29183 min
-Histogram: 1 0 0 1 2 2 0 1 0 1
-
-Total # of neighbors = 265723
-Ave neighs/atom = 106.289
-Ave special neighs/atom = 0
-Neighbor list builds = 6
-Dangerous builds = 0
-
-#set up integration parameters
-fix             timeintegration all nve
-fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
-
-#Equilibration (for realistic results, run for 2000000  steps)
-reset_timestep  0
-thermo          200
-thermo_style    custom etotal ke pe temp evdwl
-
-#run equilibration
-run             2000
-WARNING: Fix recenter should come after all other integration fixes (../fix_recenter.cpp:131)
-Per MPI rank memory allocation (min/avg/max) = 6.286 | 6.286 | 6.287 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   177.26822    2234.7133   -2057.4451          300   -2057.4451 
-   736.24287    2151.2608   -1415.0179    288.79688   -1415.0179 
-   963.07617    2090.6433   -1127.5671    280.65926   -1127.5671 
-   1148.9049    2173.1327   -1024.2279    291.73309   -1024.2279 
-   1303.6409    2279.8586   -976.21767    306.06055   -976.21767 
-     1355.42    2281.0383   -925.61826    306.21892   -925.61826 
-   1394.5206    2276.2093   -881.68863    305.57064   -881.68863 
-   1346.9764    2215.2973   -868.32091     297.3935   -868.32091 
-   1381.3654    2248.8061   -867.44063    301.89189   -867.44063 
-   1315.8059    2189.3193   -873.51332    293.90606   -873.51332 
-   1314.4456    2209.7431   -895.29752    296.64787   -895.29752 
-Loop time of 6.38989 on 8 procs for 2000 steps with 2500 atoms
-
-Performance: 27.043 ns/day, 0.887 hours/ns, 312.994 timesteps/s
-80.5% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 5.2693     | 5.3572     | 5.457      |   2.1 | 83.84
-Bond    | 0.00028825 | 0.00033835 | 0.00039148 |   0.0 |  0.01
-Neigh   | 0.0296     | 0.032337   | 0.035071   |   0.9 |  0.51
-Comm    | 0.64679    | 0.73397    | 0.80847    |   5.2 | 11.49
-Output  | 0.00033498 | 0.00051582 | 0.0015228  |   0.0 |  0.01
-Modify  | 0.16395    | 0.18919    | 0.21056    |   3.9 |  2.96
-Other   |            | 0.07636    |            |       |  1.19
-
-Nlocal:    312.5 ave 337 max 295 min
-Histogram: 2 2 0 1 0 0 0 1 1 1
-Nghost:    2551.62 ave 2582 max 2525 min
-Histogram: 2 1 0 0 1 1 1 0 1 1
-Neighs:    33241.8 ave 37659 max 29705 min
-Histogram: 2 0 0 2 2 0 0 0 1 1
-
-Total # of neighbors = 265934
-Ave neighs/atom = 106.374
-Ave special neighs/atom = 0
-Neighbor list builds = 21
-Dangerous builds = 0
-
-#turn off recentering during production run
-unfix recentering
-
-
-#setup trajectory output
-dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
-dump_modify     myDump element M
-dump_modify     myDump sort id
-
-#run production (for realistic results, run for 10000000 steps)
-reset_timestep  0
-thermo          1000
-thermo_style    custom etotal ke pe temp  evdwl
-run             10000
-Per MPI rank memory allocation (min/avg/max) = 7.588 | 7.589 | 7.589 Mbytes
-TotEng KinEng PotEng Temp E_vdwl 
-   1442.5428    2209.7431   -767.20027    296.64787   -767.20027 
-   1391.8624    2262.6889   -870.82656     303.7556   -870.82656 
-    1375.914    2244.6176    -868.7036     301.3296    -868.7036 
-   1345.9064    2227.2324   -881.32599    298.99573   -881.32599 
-   1379.2334    2278.1156   -898.88222    305.82657   -898.88222 
-   1389.7928    2255.8062   -866.01341    302.83163   -866.01341 
-   1380.4549    2258.2108   -877.75582    303.15443   -877.75582 
-   1380.8489    2256.9432   -876.09428    302.98426   -876.09428 
-   1326.5151    2225.7408   -899.22577    298.79549   -899.22577 
-   1376.6025    2253.0128   -876.41028    302.45662   -876.41028 
-   1331.0008    2218.1033   -887.10258    297.77019   -887.10258 
-Loop time of 25.4591 on 8 procs for 10000 steps with 2500 atoms
-
-Performance: 33.937 ns/day, 0.707 hours/ns, 392.787 timesteps/s
-89.3% CPU use with 8 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
----------------------------------------------------------------
-Pair    | 21.635     | 21.916     | 22.237     |   3.9 | 86.08
-Bond    | 0.0011308  | 0.0013149  | 0.0016932  |   0.5 |  0.01
-Neigh   | 0.14593    | 0.15675    | 0.16667    |   1.9 |  0.62
-Comm    | 1.3789     | 1.7502     | 1.9558     |  13.7 |  6.87
-Output  | 0.34664    | 0.82927    | 1.2013     |  32.8 |  3.26
-Modify  | 0.24904    | 0.25842    | 0.26907    |   1.2 |  1.02
-Other   |            | 0.5475     |            |       |  2.15
-
-Nlocal:    312.5 ave 327 max 298 min
-Histogram: 2 0 0 1 1 0 1 1 1 1
-Nghost:    2575 ave 2601 max 2559 min
-Histogram: 2 0 3 1 0 0 0 0 1 1
-Neighs:    33223.2 ave 35920 max 30303 min
-Histogram: 1 1 1 1 0 1 0 0 0 3
-
-Total # of neighbors = 265786
-Ave neighs/atom = 106.314
-Ave special neighs/atom = 0
-Neighbor list builds = 103
-Dangerous builds = 0
-
-
-Total wall time: 0:00:32

examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.1

@@ -0,0 +1,259 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+#
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data
+Reading data file ...
+  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  2500 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.001 seconds
+  read_data CPU = 0.016 seconds
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 254 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 9.535 | 9.535 | 9.535 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1283.8556    2234.7133   -950.85771          300   -950.85771 
+  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
+  -124.79406    2234.7133   -2359.5074          300   -2359.5074 
+   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
+Loop time of 3.74581 on 1 procs for 205 steps with 2500 atoms
+
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+     -950.857712502514  -2361.24417962983  -2361.47519428972
+  Force two-norm initial, final = 135.25170 2.8038329
+  Force max component initial, final = 14.083102 1.1154133
+  Final line search alpha, max atom move = 0.16981022 0.18940857
+  Iterations, force evaluations = 205 223
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.5678     | 3.5678     | 3.5678     |   0.0 | 95.25
+Bond    | 7.5831e-05 | 7.5831e-05 | 7.5831e-05 |   0.0 |  0.00
+Neigh   | 0.12962    | 0.12962    | 0.12962    |   0.0 |  3.46
+Comm    | 0.019204   | 0.019204   | 0.019204   |   0.0 |  0.51
+Output  | 0.00023948 | 0.00023948 | 0.00023948 |   0.0 |  0.01
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.02886    |            |       |  0.77
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6729.00 ave        6729 max        6729 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265637.0 ave      265637 max      265637 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265637
+Ave neighs/atom = 106.25480
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 11
+Dangerous builds = 0
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 8.410 | 8.410 | 8.410 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   -126.7619    2234.7133   -2361.4752          300   -2361.4752 
+   517.05047    2015.8636   -1498.8131    270.62043   -1498.8131 
+   931.78263    2135.4332   -1203.6506     286.6721   -1203.6506 
+   1162.6209    2242.1662   -1079.5453    301.00051   -1079.5453 
+   1164.2129    2211.6204   -1047.4075    296.89989   -1047.4075 
+   1258.0085    2286.5942   -1028.5857    306.96477   -1028.5857 
+   1231.1937     2200.814   -969.62032    295.44917   -969.62032 
+   1251.2144    2245.0533   -993.83885     301.3881   -993.83885 
+   1237.2495    2239.8802   -1002.6307    300.69363   -1002.6307 
+   1232.3342    2224.3415   -992.00722    298.60763   -992.00722 
+   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
+Loop time of 23.6478 on 1 procs for 2000 steps with 2500 atoms
+
+Performance: 7.307 ns/day, 3.284 hours/ns, 84.575 timesteps/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 22.797     | 22.797     | 22.797     |   0.0 | 96.40
+Bond    | 0.00070412 | 0.00070412 | 0.00070412 |   0.0 |  0.00
+Neigh   | 0.2249     | 0.2249     | 0.2249     |   0.0 |  0.95
+Comm    | 0.12259    | 0.12259    | 0.12259    |   0.0 |  0.52
+Output  | 0.00088925 | 0.00088925 | 0.00088925 |   0.0 |  0.00
+Modify  | 0.46447    | 0.46447    | 0.46447    |   0.0 |  1.96
+Other   |            | 0.03711    |            |       |  0.16
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6752.00 ave        6752 max        6752 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265940.0 ave      265940 max      265940 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265940
+Ave neighs/atom = 106.37600
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 20
+Dangerous builds = 0
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 9.918 | 9.918 | 9.918 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1235.3228     2197.191   -961.86817     294.9628   -961.86817 
+   1289.8463    2236.1425   -946.29622    300.19186   -946.29622 
+   1348.0825    2305.0295   -956.94703    309.43963   -956.94703 
+   1279.5478    2241.1582   -961.61041    300.86521   -961.61041 
+   1231.8597    2201.9591   -970.09949    295.60291   -970.09949 
+   1277.3424    2221.3696   -944.02725    298.20867   -944.02725 
+   1296.0116    2222.0998   -926.08818     298.3067   -926.08818 
+   1266.2849    2206.3727   -940.08782     296.1954   -940.08782 
+   1313.2808    2260.5077   -947.22683    303.46278   -947.22683 
+   1309.3076    2234.3895   -925.08198    299.95654   -925.08198 
+   1275.9792    2221.3037   -945.32449    298.19982   -945.32449 
+Loop time of 67.3224 on 1 procs for 10000 steps with 2500 atoms
+
+Performance: 12.834 ns/day, 1.870 hours/ns, 148.539 timesteps/s
+99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 64.476     | 64.476     | 64.476     |   0.0 | 95.77
+Bond    | 0.0014504  | 0.0014504  | 0.0014504  |   0.0 |  0.00
+Neigh   | 0.71333    | 0.71333    | 0.71333    |   0.0 |  1.06
+Comm    | 0.32846    | 0.32846    | 0.32846    |   0.0 |  0.49
+Output  | 0.46997    | 0.46997    | 0.46997    |   0.0 |  0.70
+Modify  | 1.2336     | 1.2336     | 1.2336     |   0.0 |  1.83
+Other   |            | 0.09996    |            |       |  0.15
+
+Nlocal:        2500.00 ave        2500 max        2500 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:        6662.00 ave        6662 max        6662 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:        265774.0 ave      265774 max      265774 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 265774
+Ave neighs/atom = 106.30960
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 104
+Dangerous builds = 0
+
+
+Total wall time: 0:01:34

examples/PACKAGES/local_density/methanol_implicit_water/log.27Oct21.methanol_implicit_water.g++.4

@@ -0,0 +1,259 @@
+LAMMPS (27 Oct 2021)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+# LAMMPS input file for 50.0% methanol mole fraction solution
+# with 2500 methanol molecules in implicit water.
+#
+#
+# Author: David Rosenberger, van der Vegt Group, TU Darmstadt
+#
+# Refer: Rosenberger, Sanyal, Shell, van der Vegt, J. Chem. Theory Comput. 15, 2881-2895 (2019)
+
+
+# Initialize simulation box
+dimension       3
+boundary        p p p
+units           real
+atom_style      molecular
+
+# Set potential styles
+pair_style      hybrid/overlay table spline 500 local/density
+
+# Read molecule data and set initial velocities
+read_data       methanol_implicit_water.data
+Reading data file ...
+  orthogonal box = (-31.123000 -31.123000 -31.123000) to (31.123000 31.123000 31.123000)
+  1 by 2 by 2 MPI processor grid
+  reading atoms ...
+  2500 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.005 seconds
+velocity        all create  3.0000e+02 12142 rot yes dist gaussian
+
+# Assign potentials
+pair_coeff          1     1 table         methanol_implicit_water.pair.table PairMM
+WARNING: 93 of 500 force values in table PairMM are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:465)
+WARNING: 254 of 500 distance values in table 1e-06 with relative error
+WARNING:  over PairMM to re-computed values (src/pair_table.cpp:473)
+pair_coeff          *     * local/density methanol_implicit_water.localdensity.table
+
+
+
+
+#Recentering during minimization and equilibration
+fix recentering all recenter 0.0 0.0 0.0 units box
+
+#Thermostat & time integration
+timestep        1.0
+thermo          100
+thermo_style    custom etotal ke pe temp evdwl
+
+#minimization
+minimize        1.e-4 0.0 1000 1000
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+Your simulation uses code contributions which should be cited:
+
+- pair_style  local/density  command:
+
+@Article{Sanyal16,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation},
+ journal = {J.~Chem.~Phys.},
+ year =    2016,
+ DOI = doi.org/10.1063/1.4958629}
+
+@Article{Sanyal18,
+ author =  {T.Sanyal and M.Scott Shell},
+ title =   {Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy},
+ journal = {J.~Phys.~Chem. B},
+ year =    2018,
+ DOI = doi.org/10.1021/acs.jpcb.7b12446}
+
+CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
+
+WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update every 1 steps, delay 0 steps, check yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 17
+  ghost atom cutoff = 17
+  binsize = 8.5, bins = 8 8 8
+  2 neighbor lists, perpetual/occasional/extra = 2 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+  (2) pair local/density, perpetual, copy from (1)
+      attributes: half, newton on
+      pair build: copy
+      stencil: none
+      bin: none
+Per MPI rank memory allocation (min/avg/max) = 7.855 | 7.855 | 7.855 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1283.8556    2234.7133   -950.85771          300   -950.85771 
+  -10.187232    2234.7133   -2244.9005          300   -2244.9005 
+   -124.3661    2234.7133   -2359.0794          300   -2359.0794 
+   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
+Loop time of 0.528503 on 4 procs for 244 steps with 2500 atoms
+
+99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+Minimization stats:
+  Stopping criterion = energy tolerance
+  Energy initial, next-to-last, final = 
+     -950.857712502527   -2381.2294195605  -2381.42909821383
+  Force two-norm initial, final = 135.25170 2.3117934
+  Force max component initial, final = 14.083102 0.60833889
+  Final line search alpha, max atom move = 0.18347073 0.11161238
+  Iterations, force evaluations = 244 278
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 0.48518    | 0.48843    | 0.49223    |   0.4 | 92.42
+Bond    | 1.0084e-05 | 1.0861e-05 | 1.1483e-05 |   0.0 |  0.00
+Neigh   | 0.018199   | 0.019153   | 0.020036   |   0.5 |  3.62
+Comm    | 0.010229   | 0.014832   | 0.018994   |   2.6 |  2.81
+Output  | 3.7985e-05 | 4.2069e-05 | 5.3874e-05 |   0.0 |  0.01
+Modify  | 0          | 0          | 0          |   0.0 |  0.00
+Other   |            | 0.006032   |            |       |  1.14
+
+Nlocal:        625.000 ave         638 max         618 min
+Histogram: 2 0 0 0 1 0 0 0 0 1
+Nghost:        3613.75 ave        3640 max        3580 min
+Histogram: 1 0 0 0 1 0 0 0 1 1
+Neighs:        66411.2 ave       70713 max       62416 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+
+Total # of neighbors = 265645
+Ave neighs/atom = 106.25800
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 13
+Dangerous builds = 0
+
+#set up integration parameters
+fix             timeintegration all nve
+fix             thermostat all langevin  3.0000e+02  3.0000e+02  1.0000e+02 59915
+
+#Equilibration (for realistic results, run for 2000000  steps)
+reset_timestep  0
+thermo          200
+thermo_style    custom etotal ke pe temp evdwl
+
+#run equilibration
+run             2000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+WARNING: Fix recenter should come after all other integration fixes (src/fix_recenter.cpp:133)
+Per MPI rank memory allocation (min/avg/max) = 6.730 | 6.730 | 6.731 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   -146.7158    2234.7133   -2381.4291          300   -2381.4291 
+   540.68168      2041.44   -1500.7584    274.05395   -1500.7584 
+    945.4949    2163.7509    -1218.256    290.47363    -1218.256 
+   1118.7729    2195.7579    -1076.985    294.77042    -1076.985 
+   1215.0058    2233.2445   -1018.2387    299.80282   -1018.2387 
+   1251.8045    2240.8439   -989.03944      300.823   -989.03944 
+    1206.649    2149.5807   -942.93169    288.57134   -942.93169 
+   1290.6111    2248.3623   -957.75117    301.83231   -957.75117 
+   1312.8944     2219.147   -906.25264     297.9103   -906.25264 
+    1260.002    2211.4176   -951.41561    296.87266   -951.41561 
+   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
+Loop time of 3.56721 on 4 procs for 2000 steps with 2500 atoms
+
+Performance: 48.441 ns/day, 0.495 hours/ns, 560.663 timesteps/s
+99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.3122     | 3.3399     | 3.3633     |   1.0 | 93.63
+Bond    | 7.5941e-05 | 8.062e-05  | 8.7627e-05 |   0.0 |  0.00
+Neigh   | 0.03524    | 0.036666   | 0.037864   |   0.6 |  1.03
+Comm    | 0.080116   | 0.10444    | 0.13373    |   6.1 |  2.93
+Output  | 0.00019977 | 0.00022502 | 0.00029007 |   0.0 |  0.01
+Modify  | 0.077781   | 0.078206   | 0.078752   |   0.1 |  2.19
+Other   |            | 0.007641   |            |       |  0.21
+
+Nlocal:        625.000 ave         637 max         616 min
+Histogram: 1 0 1 0 1 0 0 0 0 1
+Nghost:        3597.25 ave        3610 max        3586 min
+Histogram: 1 0 1 0 0 0 1 0 0 1
+Neighs:        66468.2 ave       69230 max       62721 min
+Histogram: 1 0 0 1 0 0 0 0 0 2
+
+Total # of neighbors = 265873
+Ave neighs/atom = 106.34920
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 20
+Dangerous builds = 0
+
+#turn off recentering during production run
+unfix recentering
+
+
+#setup trajectory output
+dump            myDump all custom 100 methanol_implicit_water.lammpstrj.gz id type x y z element
+dump_modify     myDump element M
+dump_modify     myDump sort id
+
+#run production (for realistic results, run for 10000000 steps)
+reset_timestep  0
+thermo          1000
+thermo_style    custom etotal ke pe temp  evdwl
+run             10000
+  generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Per MPI rank memory allocation (min/avg/max) = 8.071 | 8.071 | 8.071 Mbytes
+TotEng KinEng PotEng Temp E_vdwl 
+   1335.0956    2270.1367   -935.04108    304.75543   -935.04108 
+   1266.2305    2227.2123   -960.98186    298.99303   -960.98186 
+   1304.2289    2238.1343   -933.90544    300.45925   -933.90544 
+   1311.3201    2232.0862    -920.7661    299.64733    -920.7661 
+   1289.9028    2241.3533   -951.45049    300.89139   -951.45049 
+   1314.2234    2244.8514   -930.62797      301.361   -930.62797 
+   1282.2744    2240.6716   -958.39719    300.79987   -958.39719 
+    1239.302    2181.5711    -942.2691    292.86591    -942.2691 
+   1327.0954    2242.6441   -915.54875    301.06468   -915.54875 
+   1334.9799    2239.6841   -904.70423    300.66731   -904.70423 
+   1320.6105    2263.4912   -942.88066     303.8633   -942.88066 
+Loop time of 23.3399 on 4 procs for 10000 steps with 2500 atoms
+
+Performance: 37.018 ns/day, 0.648 hours/ns, 428.451 timesteps/s
+99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 21.343     | 21.606     | 21.766     |   3.7 | 92.57
+Bond    | 0.00045963 | 0.0004817  | 0.0005083  |   0.0 |  0.00
+Neigh   | 0.20708    | 0.22081    | 0.22733    |   1.7 |  0.95
+Comm    | 0.63014    | 0.80326    | 1.0801     |  19.8 |  3.44
+Output  | 0.11791    | 0.14443    | 0.22211    |  11.8 |  0.62
+Modify  | 0.37291    | 0.389      | 0.41719    |   2.7 |  1.67
+Other   |            | 0.1761     |            |       |  0.75
+
+Nlocal:        625.000 ave         636 max         613 min
+Histogram: 1 0 0 0 0 2 0 0 0 1
+Nghost:        3597.00 ave        3613 max        3580 min
+Histogram: 1 0 0 1 0 0 0 1 0 1
+Neighs:        66408.5 ave       69186 max       61728 min
+Histogram: 1 0 0 0 0 0 1 0 1 1
+
+Total # of neighbors = 265634
+Ave neighs/atom = 106.25360
+Ave special neighs/atom = 0.0000000
+Neighbor list builds = 102
+Dangerous builds = 0
+
+
+Total wall time: 0:00:27

examples/README

@@ -75,6 +75,7 @@ eim:      NaCl using the EIM potential
 ellipse:  ellipsoidal particles in spherical solvent, 2d system
 flow:     Couette and Poiseuille flow in a 2d channel
 friction: frictional contact of spherical asperities between 2d surfaces
+gcmc:     Grand Canonical MC with fix gcmc, Widom insertion with fix widom
 gjf:      use of fix langevin Gronbech-Jensen/Farago option
 granregion: use of fix wall/region/gran as boundary on granular particles
 hugoniostat: Hugoniostat shock dynamics
@@ -82,7 +83,6 @@ hyper:    global and local hyperdynamics of diffusion on Pt surface
 indent:   spherical indenter into a 2d solid
 kim:      use of potentials in Knowledge Base for Interatomic Models (KIM)
 latte:    use of LATTE density-functional tight-binding quantum code
-mc:       MC package models: GCMC, Widom, fix mol/swap
 meam:     MEAM test for SiC and shear (same as shear examples)
 melt:     rapid melt of 3d LJ system
 message:  client/server coupling of 2 codes
@@ -167,7 +167,7 @@ The KAPPA directory has example scripts for computing the thermal
 conductivity (kappa) of a LJ liquid using 5 different methods.  See
 the KAPPA/README file for more info.
 
-The MC-LOOP directory has an example script for using LAMMPS as an
+The MC directory has an example script for using LAMMPS as an
 energy-evaluation engine in a iterative Monte Carlo energy-relaxation
 loop.